 | Up a level |
Abbatemarco, Simona, Bondaz, Alexandra, Schwager, Francoise, Wang, Jing, Hammell, Christopher, Gotta, Monica (April 2021) The UBAP2L ortholog PQN-59 contributes to stress granule assembly and development in C. elegans. BioRxiv. (Unpublished)
Abbatemarco, Simona, Bondaz, Alexandra, Schwager, Francoise, Wang, Jing, Hammell, Christopher M, Gotta, Monica (October 2021) PQN-59 and GTBP-1 contribute to stress granule formation but are not essential for their assembly in C. elegans embryos. Journal of Cell Science. ISSN 0021-9533
Abou-el-Enein, M, Angelis, A, Appelbaum, FR, Andrews, NC, Bates, SE, Bierman, AS, Brenner, MK, Cavazzana, M, Caligiuri, MA, Clevers, H, Cooke, E, Daley, GQ, Dzau, VJ, Ellis, LM, Fineberg, HV, Goldstein, LSB, Gottschalk, S, Hamburg, MA, Ingber, DE, Kohn, DB, Krainer, AR, Maus, MV, Marks, P, Mummery, CL, Pettigrew, RI, Rutter, JL, Teichmann, SA, Terzic, A, Urnov, FD, Williams, DA, Wolchok, JD, Lawler, M, Turtle, CJ, Bauer, G, Ioannidis, JPA (September 2021) Evidence generation and reproducibility in cell and gene therapy research: A call to action. Molecular Therapy - Methods and Clinical Development, 22. pp. 11-14. ISSN 2329-0501 (In Press)
Ackermann, Maximilian, Anders, Hans-Joachim, Bilyy, Rostyslav, Bowlin, Gary L, Daniel, Christoph, De Lorenzo, Rebecca, Egeblad, Mikala, Henneck, Timo, Hidalgo, Andrés, Hoffmann, Markus, Hohberger, Bettina, Kanthi, Yogendra, Kaplan, Mariana J, Knight, Jason S, Knopf, Jasmin, Kolaczkowska, Elzbieta, Kubes, Paul, Leppkes, Moritz, Mahajan, Aparna, Manfredi, Angelo A, Maueröder, Christian, Maugeri, Norma, Mitroulis, Ioannis, Muñoz, Luis E, Narasaraju, Teluguakula, Naschberger, Elisabeth, Neeli, Indira, Ng, Lai Guan, Radic, Marko Z, Ritis, Konstantinos, Rovere-Querini, Patrizia, Schapher, Mirco, Schauer, Christine, Simon, Hans-Uwe, Singh, Jeeshan, Skendros, Panagiotis, Stark, Konstantin, Stürzl, Michael, van der Vlag, Johan, Vandenabeele, Peter, Vitkov, Ljubomir, von Köckritz-Blickwede, Maren, Yanginlar, Cansu, Yousefi, Shida, Zarbock, Alexander, Schett, Georg, Herrmann, Martin (May 2021) Patients with COVID-19: in the dark-NETs of neutrophils. Cell Death and Differentiation. ISSN 1350-9047
Ahmed, Jahed, Alaba, Oluwafemi, Ameen, Gazala, Arora, Vaishali, Arteaga-Vazquez, Mario A, Arun, Alok, Bailey-Serres, Julia, Bartley, Laura E, Bassel, George W, Bergmann, Dominique C, Bertolini, Edoardo, Bhati, Kaushal Kumar, Blanco-Touriñán, Noel, Briggs, Steven P, Brumos, Javier, Buer, Benjamin, Burlaocot, Adrien, Cervantes-Pérez, Sergio Alan, Chen, Sixue, Contreras-Moreira, Bruno, CORPAS, Francisco J, Cruz-Ramirez, Alfredo, Cuevas-Velazquez, Cesar L, Cuperus, Josh T, David, Lisa I, de Folter, Stefan, Denolf, Peter H, Ding, Pingtao, Dwyer, William P, Evans, Matthew MS, George, Nancy, Handakumbura, Pubudu P, Harrison, Maria J, Haswell, Elizabeth S, Herath, Venura, Jiao, Yuling, Jinkerson, Robert E, John, Uwe, Joshi, Sanjay, Joshi, Abhishek, Joubert, Lydia-Marie, Katam, Ramesh, Kaur, Harmanpreet, Kazachkova, Yana, Raju, Sunil K Kenchanmane, Khan, Mather A, Khangura, Rajdeep, Kumar, Ajay, Kumar, Arun, Kumar, Pankaj, Kumar, Pradeep, Lavania, Dhruv, Lew, Tedrick Thomas Salim, Lewsey, Mathew G, Lin, Chien-Yuan, Liu, Dianyi, Liu, Le, Liu, Tie, Lokdarshi, Ansul, My Luong, Ai, Macaulay, Iain C, Mahmud, Sakil, Mähönen, Ari Pekka, Malukani, Kamal Kumar, Marand, Alexandre P, Martin, Carly A, McWhite, Claire D, Mehta, Devang, Martín, Miguel Miñambres, Mortimer, Jenny C, Nikolov, Lachezar A, Nobori, Tatsuya, Nolan, Trevor M, Ogden, Aaron J, Otegui, Marisa S, Ott, Mark-Christoph, Palma, José M, Paul, Puneet, Rehman, Atique U, Romera-Branchat, Maida, Romero, Luis C, Roth, Ronelle, Sah, Saroj K, Shahan, Rachel, Solanki, Shyam, Song, Bao-Hua, Sozzani, Rosangela, Stacey, Gary, Stepanova, Anna N, Taylor, Nicolas L, Tello-Ruiz, Marcela K, Tran, Tuan M, Tripathi, Rajiv Kumar, Vadde, Batthula Vijaya Lakshmi Vadde, Varga, Tamas, Vidovic, Marija, Walley, Justin W, Wang, Zhiyong, Weizbauer, Renate A, Whelan, James, Wijeratne, Asela J, Xiang, Tingting, Xu, Shouling, Yadegari, Ramin, Yu, Houlin, Yuan, Hai Ying, Zanini, Fabio, Zhao, Feng, Zhu, Jie, Zhuang, Xiaohong, Jha, Suryatapa Ghosh, Borowsky, Alexander T, Cole, Benjamin J, Fahlgren, Noah, Farmer, Andrew, Huang, Shao-shan Carol, Karia, Purva, Libault, Marc, Provart, Nicholas J, Rice, Selena L, Saura-Sanchez, Maite, Agarwal, Pinky, Ahkami, Amir H, Anderton, Christopher R, Briggs, Steven P, Brophy, Jennifer AN, Denolf, Peter, Di Costanzo, Luigi F, Exposito-Alonso, Moises, Giacomello, Stefania, Gomez-Cano, Fabio, Kaufmann, Kerstin, Ko, Dae Kwan, Kumar, Sagar, Malkovskiy, Andrey V, Nakayama, Naomi, Obata, Toshihiro, Otegui, Marisa S, Palfalvi, Gergo, Quezada-Rodríguez, Elsa H, Singh, Rajveer, Uhrig, R Glen, Waese, Jamie, Van Wijk, Klaas, Wright, R Clay, Ehrhardt, David W, Birnbaum, Kenneth D, Rhee, Seung Y (September 2021) Vision, challenges and opportunities for a Plant Cell Atlas. eLife, 10. ISSN 2050-084X
Ahmed, Omar, Rossi, Massimiliano, Kovaka, Sam, Schatz, Michael C, Gagie, Travis, Boucher, Christina, Langmead, Ben (June 2021) Pan-genomic Matching Statistics for Targeted Nanopore Sequencing. iScience. p. 102696. ISSN 2589-0042
Ajiro, Masahiko, Awaya, Tomonari, Kim, Young Jin, Iida, Kei, Denawa, Masatsugu, Tanaka, Nobuo, Kurosawa, Ryo, Matsushima, Shingo, Shibata, Saiko, Sakamoto, Tetsunori, Studer, Rolenz, Krainer, Adrian R, Hagiwara, Masatoshi (July 2021) Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia. Nature Communications, 12 (1). p. 4507. ISSN 2041-1723
Almeida, Ana S, Fein, Miriam R, Egeblad, Mikala (June 2021) Multi-color Flow Cytometry for Comprehensive Analysis of the Tumor Immune Infiltrate in a Murine Model of Breast Cancer. Bio-protocol, 11 (11). e4012. ISSN 2331-8325
Almeqdadi, Mohammad, Yueh, Brian, Paredes, Jenny, Akadri, Mubarak, Spagnardi, Marzia, Chung, Charlie, Martello-Rooney, Laura, Beyaz, Semir (May 2021) EXPLORING THE RACIAL DISPARITIES OF COLON CANCER OUTCOMES IN THE SETTING OF OBESITY. In: Digestive Disease Week 2021.
Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary, Schatz, Michael, Soyk, Sebastian (November 2021) Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing. BioRxiv. (Unpublished)
Anderson, Kristin R, Harris, Julie A, Ng, Lydia, Prins, Pjotr, Memar, Sara, Ljungquist, Bengt, Fürth, Daniel, Williams, Robert W, Ascoli, Giorgio A, Dumitriu, Dani (February 2021) Highlights from the Era of Open Source Web-Based Tools. The Journal of Neuroscience, 41 (5). pp. 927-936. ISSN 0270-6474
Ango, Fabrice, Gallo, Nicholas Biron, Van Aelst, Linda (April 2021) Molecular mechanisms of axo-axonic innervation. Current Opinion in Neurobiology, 69. pp. 105-112. ISSN 0959-4388
Auguste, YSS, Isko, E, Cheadle, LM (July 2021) Sensory experience shapes non-neuronal transcriptomic plasticity and cell:cell interactions in primary visual cortex. In: European Meeting on Glial Cells in Health and Disease.
BRAIN Initiative Cell Census Network (BICCN), (October 2021) A multimodal cell census and atlas of the mammalian primary motor cortex. Nature, 598 (7879). pp. 86-102. ISSN 0028-0836
Bakken, Trygve E, Jorstad, Nikolas L, Hu, Qiwen, Lake, Blue B, Tian, Wei, Kalmbach, Brian E, Crow, Megan, Hodge, Rebecca D, Krienen, Fenna M, Sorensen, Staci A, Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian D, Aldridge, Andrew I, Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa G, Crichton, Kirsten, Daigle, Tanya L, Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas T, Herb, Brian R, Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang Eric, Liu, Christine S, Liu, Hanqing, Lucero, Jacinta D, Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy A, Moussa, Marmar, Nery, Joseph R, Nicovich, Philip R, Niu, Sheng-Yong, Orvis, Joshua, Osteen, Julia K, Owen, Scott, Palmer, Carter R, Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora M, Rimorin, Christine, Rivkin, Angeline, Romanow, William J, Sedeño-Cortés, Adriana E, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna Marie, Zhang, Renee, Ament, Seth A, Behrens, M Margarita, Bravo, Hector Corrada, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick R, Höllt, Thomas, Horwitz, Gregory D, Keene, C Dirk, Kharchenko, Peter V, Ko, Andrew L, Lelieveldt, Boudewijn P, Luo, Chongyuan, Mukamel, Eran A, Pinto-Duarte, António, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard H, Smith, Kimberly, Spain, William J, White, Owen R, Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan Z, McCarroll, Steven A, Ting, Jonathan T, Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph R, Linnarsson, Sten, Lein, Ed S (October 2021) Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature, 598 (7879). pp. 111-119. ISSN 0028-0836
Banerjee, Arkarup, Egger, Robert, Long, Michael A (June 2021) Using focal cooling to link neural dynamics and behavior. Neuron. ISSN 0896-6273
Barth, Nicole, Mendive-Tapia, Lorena, Subiros-Funosas, Ramon, Ghashghaie, Ouldouz, Lavilla, Rodolfo, Maiorino, Laura, He, Xue-Yan, Dransfield, Ian, Egeblad, Mikala, Vendrell, Marc (November 2021) A Bivalent Activatable Fluorescent Probe for Screening and Intravital Imaging of Chemotherapy-induced Cancer Cell Death. Angewandte Chemie International Edition. ISSN 1433-7851
Baslan, Timour, Kovaka, Sam, Sedlazeck, Fritz J, Zhang, Yanming, Wappel, Robert, Tian, Sha, Lowe, Scott W, Goodwin, Sara, Schatz, Michael C (September 2021) High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Research. ISSN 0305-1048
Belkhatir, Zehor, Pavon, Michele, Mathews, James C, Pouryahya, Maryam, Deasy, Joseph O, Norton, Larry, Tannenbaum, Allen R (March 2021) Stochastic Norton-Simon-Massague Tumor Growth Modeling: Controlled and Mixed-Effect Uncontrolled Analysis. IEEE Transactions on Control Systems Technology, 29 (2). pp. 704-717. ISSN 1063-6536
Bennett, Richard L, Monagle, Darby C, Sobh, Amin, Vakoc, Christopher, Smalley, Keiran S, Harbour, J William, Licht, Jonathan D (July 2021) Abstract 82: Identification of essential proliferation and trametinib resistance mechanisms in GNAQ-mutant uveal melanoma. In: AACR Annual Meeting 2021.
Benoit, Matthias (August 2021) From Non-self to Self: Stepwise Mutations in Transcription Factors Promote the Transition to Self-Pollination in Tomato. The Plant Cell. ISSN 1532-298X
Benoit, Matthias (May 2021) The right dose: molecular compensation maintains rRNA homeostasis upon reduction of ribosomal gene dosage in Arabidopsis. The Plant Cell, 33 (4). pp. 1089-1090. ISSN 1040-4651
Benoit, Matthias, Drost, Hajk-Georg (April 2021) A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants. Methods in Molecular Biology, 2250. pp. 1-14. ISSN 1064-3745
Beyaz, Semir, Chung, Charlie, Mou, Haiwei, Bauer-Rowe, Khristian E, Xifaras, Michael E, Ergin, Ilgin, Dohnalova, Lenka, Biton, Moshe, Shekhar, Karthik, Eskiocak, Onur, Papciak, Katherine, Ozler, Kadir, Almeqdadi, Mohammad, Yueh, Brian, Fein, Miriam, Annamalai, Damodaran, Valle-Encinas, Eider, Erdemir, Aysegul, Dogum, Karoline, Shah, Vyom, Alici-Garipcan, Aybuke, Meyer, Hannah V, Özata, Deniz M, Elinav, Eran, Kucukural, Alper, Kumar, Pawan, McAleer, Jeremy P, Fox, James G, Thaiss, Christoph A, Regev, Aviv, Roper, Jatin, Orkin, Stuart H, Yilmaz, Ömer H (September 2021) Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell. ISSN 1934-5909
Beyaz, Semir, Mana, Miyeko D, Yilmaz, Ömer H (April 2021) High-fat diet activates a PPAR-δ program to enhance intestinal stem cell function. Cell Stem Cell, 28 (4). pp. 598-599. ISSN 1934-5909
Bhatia, Sonam, Kramer, Melissa, Russo, Suzanne, Naik, Payal, Arun, Gayatri, Brophy, Kyle, Andrews, Peter A, Fan, Cheng, Perou, Charles M, Preall, Jonathan, Ha, Taehoon, Rishi, Arvind, Wilkinson, John Erby, McCombie, William Richard, Kostroff, Karen, Spector, David L (August 2021) Patient-derived triple negative breast cancer organoids provide robust model systems that recapitulate tumor intrinsic characteristics. BioRxiv.
Bibel, Brianna L (October 2021) Regulating the regulator: Phosphorylation-mediated regulation of the RNAi effector protein Argonaute. PhD thesis, Cold Spring Harbor Laboratory.
Bieler, M, Hussain, S, Daaland, ESB, Mirrione, M. M., Henn, F. A., Davanger, S (April 2021) Changes in concentrations of NMDA receptor subunit GluN2B, Arc and syntaxin-1 in dorsal hippocampus Schaffer collateral synapses in a rat learned helplessness model of depression. The Journal of Comparative Neurology, 529 (12). pp. 3194-3205.
Biffi, Giulia, Tuveson, David A (January 2021) Diversity and Biology of Cancer-Associated Fibroblasts. Physiological Reviews, 101 (1). pp. 147-176. ISSN 0031-9333
Blumberg, Amit, Zhao, Yixin, Huang, Yi-Fei, Dukler, Noah, Rice, Edward J, Chivu, Alexandra G, Krumholz, Katie, Danko, Charles G, Siepel, Adam (February 2021) Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biology, 19 (1). p. 30. ISSN 1741-7007
Bodineau, Clément, Tomé, Mercedes, Courtois, Sarah, Costa, Ana SH, Sciacovelli, Marco, Rousseau, Benoit, Richard, Elodie, Vacher, Pierre, Parejo-Pérez, Carlos, Bessede, Emilie, Varon, Christine, Soubeyran, Pierre, Frezza, Christian, Murdoch, Piedad Del Socorro, Villar, Victor H, Durán, Raúl V (August 2021) Two parallel pathways connect glutamine metabolism and mTORC1 activity to regulate glutamoptosis. Nature Communications, 12 (1). p. 4814. ISSN 2041-1723
Bolton, Kelly L, Koh, Youngil, Foote, Michael B, Im, Hogune, Jee, Justin, Sun, Choong Hyun, Safonov, Anton, Ptashkin, Ryan, Moon, Joon Ho, Lee, Ji Yeon, Jung, Jongtak, Kang, Chang Kyung, Song, Kyoung-Ho, Choe, Pyoeng Gyun, Park, Wan Beom, Kim, Hong Bin, Oh, Myoung-Don, Song, Han, Kim, Sugyeong, Patel, Minal, Derkach, Andriy, Gedvilaite, Erika, Tkachuk, Kaitlyn A, Wiley, Brian J, Chan, Ireaneus C, Braunstein, Lior Z, Gao, Teng, Papaemmanuil, Elli, Esther Babady, N, Pessin, Melissa S, Kamboj, Mini, Diaz, Luis A, Ladanyi, Marc, Rauh, Michael J, Natarajan, Pradeep, Machiela, Mitchell J, Awadalla, Philip, Joseph, Vijai, Offit, Kenneth, Norton, Larry, Berger, Michael F, Levine, Ross L, Kim, Eu Suk, Kim, Nam Joong, Zehir, Ahmet (October 2021) Clonal hematopoiesis is associated with risk of severe Covid-19. Nature Communications, 12 (1). p. 5975. ISSN 2041-1723
Bonda, David, Rolle, Cammie, Shivacharan, Rajat, Johnson, Noriah, Barbosa, Daniel, Wulf, Michael, Etkin, Amit, Williams, Nolan, Parvizii, Josef, Kepecs, Adam, Halpern, Casey (August 2021) Causal Manipulation of Anterior Cingulate Neurons in Mice and Human Selectively Affects Approach during Reward-Threat Conflict. In: AMER ASSOC NEUROLOGICAL SURGEONS.
Borniger, Jeremy C (September 2021) Cancer as a tool for preclinical psychoneuroimmunology. Brain, Behavior, & Immunity - Health. p. 100351. ISSN 2666-3546
Borniger, Jeremy C, de Lecea, Luis (2021) Peripheral Lipopolyssacharide Rapidly Silences REM-Active LHGABA Neurons. Frontiers in Behavioral Neuroscience, 15. p. 649428. ISSN 1662-5153
Bosc, M, Bucchioni, G, Ribot, B, Michelet, T (June 2021) Bypassing use-dependent plasticity in the primary motor cortex to preserve adaptive behavior. Scientific reports, 11 (1). p. 12102. ISSN 2045-2322
Bradley, R, Braybrooke, J, Gray, R, Hills, R, Liu, Z, Peto, R, Davies, L, Dodwell, D, McGale, P, Pan, H, Taylor, C, Anderson, S, Gelber, R, Gianni, L, Jacot, W, Joensuu, H, Moreno-Aspitia, A, Piccart, M, Press, M, Romond, E, Slamon, D, Suman, V, Berry, R, Boddington, C, Clarke, M, Davies, C, Duane, F, Evans, V, Gay, J, Gettins, L, Godwin, J, James, S, Liu, H, MacKinnon, E, Mannu, G, McHugh, T, Morris, P, Read, S, Straiton, E, Wang, Y, Crown, J, de Azambuja, E, Delaloge, S, Fung, H, Geyer, C, Spielmann, M, Valagussa, P, Albain, K, Arriagada, R, Bartlett, J, Bergsten-Nordström, E, Bliss, J, Brain, E, Carey, L, Coleman, R, Cuzick, J, Davidson, N, Del Mastro, L, Di Leo, A, Dignam, J, Dowsett, M, Ejlertsen, B, Francis, P, Gnant, M, Goetz, M, Goodwin, P, Halpin-Murphy, P, Hayes, D, Hill, C, Jagsi, R, Janni, W, Loibl, S, Mamounas, EP, Martín, M, Mukai, H, Nekljudova, V, Norton, L, Ohashi, Y, Pierce, L, Poortmans, P, Raina, V, Rea, D, Regan, M, Robertson, J, Rutgers, E, Spanic, T, Sparano, J, Steger, G, Tang, G, Toi, M, Tutt, A, Viale, G, Wang, X, Whelan, T, Wilcken, N, Wolmark, N, Cameron, D, Bergh, J, Pritchard, KI, Swain, SM (August 2021) Trastuzumab for early-stage, HER2-positive breast cancer: a meta-analysis of 13 864 women in seven randomised trials. The Lancet Oncology, 22 (8). pp. 1139-1150. ISSN 1470-2045
Brownridge, Stephanie R, Beyaz, Semir, Noyes, Nicole, Goldberg, Gary L (September 2021) DEVELOPMENT OF ENDOMETRIAL ORGANOIDS FROM AN ENDOMETRIAL BIOPSY. In: 77th Scientific Congress of the American Society for Reproductive Medicine.
Brägelmann, Johannes, Lorenz, Carina, Borchmann, Sven, Nishii, Kazuya, Wegner, Julia, Meder, Lydia, Ostendorp, Jenny, Ast, David F, Heimsoeth, Alena, Nakasuka, Takamasa, Hirabae, Atsuko, Okawa, Sachi, Dammert, Marcel A, Plenker, Dennis, Klein, Sebastian, Lohneis, Philipp, Gu, Jianing, Godfrey, Laura K, Forster, Jan, Trajkovic-Arsic, Marija, Zillinger, Thomas, Haarmann, Mareike, Quaas, Alexander, Lennartz, Stefanie, Schmiel, Marcel, D'Rozario, Joshua, Thomas, Emily S, Li, Henry, Schmitt, Clemens A, George, Julie, Thomas, Roman K, von Karstedt, Silvia, Hartmann, Gunther, Büttner, Reinhard, Ullrich, Roland T, Siveke, Jens T, Ohashi, Kadoaki, Schlee, Martin, Sos, Martin L (September 2021) MAPK-pathway inhibition mediates inflammatory reprogramming and sensitizes tumors to targeted activation of innate immunity sensor RIG-I. Nature Communications, 12 (1). p. 5505. ISSN 2041-1723
Cable, Jennifer, Heard, Edith, Hirose, Tetsuro, Prasanth, Kannanganattu V, Chen, Ling-Ling, Henninger, Jonathan E, Quinodoz, Sofia A, Spector, David L, Diermeier, Sarah D, Porman, Allison M, Kumar, Dhiraj, Feinberg, Mark W, Shen, Xiaohua, Unfried, Juan Pablo, Johnson, Rory, Chen, Chun-Kan, Wilusz, Jeremy E, Lempradl, Adelheid, McGeary, Sean E, Wahba, Lamia, Pyle, Anna Marie, Hargrove, Amanda E, Simon, Matthew D, Marcia, Marco, Przanowska, Róża K, Chang, Howard Y, Jaffrey, Samie R, Contreras, Lydia M, Chen, Qi, Shi, Junchao, Mendell, Joshua T, He, Lin, Song, Erwei, Rinn, John L, Lalwani, Mukesh Kumar, Kalem, Murat Can, Chuong, Edward B, Maquat, Lynne E, Liu, Xuhang (November 2021) Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals of the New York Academy of Sciences. ISSN 0077-8923
Cable, Jennifer, Pei, Duanqing, Reid, Lola M, Wang, Xin Wei, Bhatia, Sonam, Karras, Panagiotis, Melenhorst, Jan Joseph, Grompe, Markus, Lathia, Justin D, Song, Erwei, Kuo, Calvin J, Zhang, Ning, White, Richard M, Ma, Stephanie Ky, Ma, Lichun, Chin, Y Rebecca, Shen, Michael M, Ng, Irene Oi Lin, Kaestner, Klaus H, Zhou, Lei, Sikandar, Shaheen, Schmitt, Clemens A, Guo, Wei, Wong, Carmen Chak-Lui, Ji, Junfang, Tang, Dean G, Dubrovska, Anna, Yang, Chunzhang, Wiedemeyer, Wolf R, Weissman, Irving L (November 2021) Cancer stem cells: advances in biology and clinical translation-a Keystone Symposia report. Annals of the New York Academy of Sciences. ISSN 0077-8923
Cao, Zhendong, Budinich, Krista A, Huang, Hua, Lu, Bin, Zhang, Zhen, Ren, Diqiu, Zhou, Yeqiao, Huang, Yuhan, Pingul, Bianca, Kingsley, Molly C, Lenard, Alexandra K, Qi, Jun, Carroll, Martin P, Blobel, Gerd A, Faryabi, Robert B, Bernt, Kathrin M, Berger, Shelley L, Shi, Junwei (July 2021) Abstract LB205: The IRF8-MEF2D transcription factor circuit regulated by a druggable multiple post-translational modification (PTM) reader ZMYND8 in acute myeloid leukemia. In: AACR Annual Meeting 2021.
Cao, Zhendong, Budinich, Krista A, Huang, Hua, Ren, Diqiu, Lu, Bin, Zhang, Zhen, Chen, Qingzhou, Zhou, Yeqiao, Huang, Yu-Han, Alikarami, Fatemeh, Kingsley, Molly C, Lenard, Alexandra K, Wakabayashi, Aoi, Khandros, Eugene, Bailis, Will, Qi, Jun, Carroll, Martin P, Blobel, Gerd A, Faryabi, Robert B, Bernt, Kathrin M, Berger, Shelley L, Shi, Junwei (August 2021) ZMYND8-regulated IRF8 transcription axis is an acute myeloid leukemia dependency. Molecular Cell. ISSN 1097-2765
Carlston, Colleen, Weinmann, Robin, Stec, Natalia, Abbatemarco, Simona, Schwager, Francoise, Wang, Jing, Ouyang, Huiwu, Ewald, Collin Y, Gotta, Monica, Hammell, Christopher M (November 2021) PQN-59 antagonizes microRNA-mediated repression during post-embryonic temporal patterning and modulates translation and stress granule formation in C. elegans. PLoS Genetics, 17 (11). e1009599. ISSN 1553-7390
Chandrasekhar, Arjun, Marshall, James AR, Austin, Cortnea, Navlakha, Saket, Gordon, Deborah M (October 2021) Better tired than lost: Turtle ant trail networks favor coherence over short edges. PLoS Computational Biology, 17 (10). e1009523. ISSN 1553-7358
Chang, KC, Spector, DL (January 2021) MaTAR25: a long non-coding RNA involved in breast cancer progression. Molecular and Cellular Oncology, 8 (2). p. 1882286. ISSN 2372-3556
Chen, Shuonan, Loper, Jackson, Chen, Xiaoyin, Vaughan, Alex, Zador, Anthony M, Paninski, Liam (March 2021) BARcode DEmixing through Non-negative Spatial Regression (BarDensr). PLoS Computational Biology, 17 (3). e1008256. ISSN 1553-734X
Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason M, Kinney, Justin B, McCandlish, David M (October 2021) Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer. Proceedings of the National Academy of Sciences of USA, 118 (40). ISSN 1091-6490
Cheng, Derek K, Oni, Tobiloba E, Thalappillil, Jennifer S, Park, Youngkyu, Ting, Hsiu-Chi, Alagesan, Brinda, Prasad, Nadia V, Addison, Kenneth, Rivera, Keith D, Pappin, Darryl J, Van Aelst, Linda, Tuveson, David A (May 2021) Oncogenic KRAS engages an RSK1/NF1 pathway to inhibit wild-type RAS signaling in pancreatic cancer. Proceedings of the National Academy of Sciences of USA, 118 (21). e2016904118-e2016904118. ISSN 0027-8424
Choi, Charlotte P, Tay, Rebecca J, Starostik, Margaret R, Feng, Suhua, Moresco, James J, Montgomery, Brooke E, Xu, Emily, Hammonds, Maya A, Schatz, Michael C, Montgomery, Taiowa A, Yates, John R, Jacobsen, Steven E, Kim, John K (February 2021) SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. eLife, 10. pp. 1-35. ISSN 2050-084X
Chou, Hsiang-Chen, Bhalla, Kuhulika, Demerdesh, Osama El, Klingbeil, Olaf, Hanington, Kaarina, Aganezov, Sergey, Andrews, Peter, Alsudani, Habeeb, Chang, Kenneth, Vakoc, Christopher R, Schatz, Michael C, McCombie, W Richard, Stillman, Bruce (February 2021) The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure. eLife, 10. ISSN 2050-084X
Chou, Tsung-Han, Tajima, Nami, Romero-Hernandez, Annabel, Furukawa, Hiro (February 2021) Structural Basis of Functional Transitions in Mammalian NMDA Receptors. In: Biophysical Society Annual Meeting.
Chu, Timothy H, Khairallah, Camille, Shieh, Jason, Cho, Rhea, Qiu, Zhijuan, Zhang, Yue, Eskiocak, Onur, Thanassi, David G, Kaplan, Mark H, Beyaz, Semir, Yang, Vincent W, Bliska, James B, Sheridan, Brian S (December 2021) γδ T cell IFNγ production is directly subverted by Yersinia pseudotuberculosis outer protein YopJ in mice and humans. PLoS Pathogens, 17 (12). e1010103. ISSN 1553-7374
Cifani, Paolo, Li, Zhi, Luo, Danmeng, Grivainis, Mark, Intlekofer, Andrew M, Fenyö, David, Kentsis, Alex (April 2021) Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. Journal of Proteome Research, 20 (4). pp. 1835-1848. ISSN 1535-3893
Connelly, Carla J, Vidal-Cardenas, Sofia, Goldsmith, Stephanie, Greider, Carol W (November 2021) The Bur1 cyclin-dependent kinase regulates telomere length in Saccharomyces cerevisiae. Yeast. ISSN 0749-503X
Copin, Richard, Baum, Alina, Wloga, Elzbieta, Pascal, Kristen E, Giordano, Stephanie, Fulton, Benjamin O, Zhou, Anbo, Negron, Nicole, Lanza, Kathryn, Chan, Newton, Coppola, Angel, Chiu, Joyce, Ni, Min, Wei, Yi, Atwal, Gurinder S, Hernandez, Annabel Romero, Saotome, Kei, Zhou, Yi, Franklin, Matthew C, Hooper, Andrea T, McCarthy, Shane, Hamon, Sara, Hamilton, Jennifer D, Staples, Hilary M, Alfson, Kendra, Carrion, Ricardo, Ali, Shazia, Norton, Thomas, Somersan-Karakaya, Selin, Sivapalasingam, Sumathi, Herman, Gary A, Weinreich, David M, Lipsich, Leah, Stahl, Neil, Murphy, Andrew J, Yancopoulos, George D, Kyratsous, Christos A (June 2021) The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies. Cell. ISSN 0092-8674
Costa, Iris Munhoz, Moura, Debora Custodio, Lima, Guilherme Meira, Pessoa, Adalberto, dos Santos, Camila Oresco, de Oliveira, Marcos A, Monteiro, Gisele (October 2021) Engineered asparaginase from Erwinia chrysanthemi enhances asparagine hydrolase activity and diminishes enzyme immunoreactivity - a new promise to treat acute lymphoblastic leukemia. Journal of Chemical Technology and Biotechnology. ISSN 0268-2575
Couto, Joao, Musall, Simon, Sun, Xiaonan R, Khanal, Anup, Gluf, Steven, Saxena, Shreya, Kinsella, Ian, Abe, Taiga, Cunningham, John P, Paninski, Liam, Churchland, Anne K (June 2021) Chronic, cortex-wide imaging of specific cell populations during behavior. Nature Protocols. ISSN 1754-2189
Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami E, Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea C, Buchanan, Alex, van Baren, Marijke J, Spangler, Ryan, Rollins, M Rick, Spellman, Paul T, Rozanov, Dmitri, Zhang, Jin, Maher, Christopher A, Caloian, Cristian, Watson, John D, Uhrig, Sebastian, Haas, Brian J, Jain, Miten, Akeson, Mark, Ahsen, Mehmet Eren, SMC-RNA Challenge Participants, , Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul C, Stuart, Joshua M, Ellrott, Kyle (August 2021) A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Cell Systems, 12 (8). 827-838.e5. ISSN 2405-4712
Czégel, Dániel, Giaffar, Hamza, Csillag, Márton, Futó, Bálint, Szathmáry, Eörs (June 2021) Novelty and imitation within the brain: a Darwinian neurodynamic approach to combinatorial problems. Scientific reports, 11 (1). p. 12513. ISSN 2045-2322
Dachet, Fabien, Brown, James B, Valyi-Nagy, Tibor, Narayan, Kunwar D, Serafini, Anna, Boley, Nathan, Gingeras, Thomas R, Celniker, Susan E, Mohapatra, Gayatry, Loeb, Jeffrey A (March 2021) Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Scientific Reports, 11 (1). p. 6078. ISSN 2045-2322
Das, Arun, Schatz, Michael (November 2021) Sketching and sampling approaches for fast and accurate long read classification. BioRxiv. (Unpublished)
Deng, Hanfei, Xiao, Xiong, Yang, Tao, Ritola, Kimberly, Hantman, Adam, Li, Yulong, Huang, Z Josh, Li, Bo (December 2021) A genetically defined insula-brainstem circuit selectively controls motivational vigor. Cell. ISSN 0092-8674
Deroy, Cyril, Stovall-Kurtz, Nicholas, Nebuloni, Federico, Soitu, Cristian, Cook, Peter R, Walsh, Edmond J (2021) Predicting flows through microfluidic circuits with fluid walls. Microsystems and Nanoengineering, 7 (1). p. 93. ISSN 2055-7434
Dewan, R, Chia, R, Ding, J, Hickman, RA, Stein, TD, Abramzon, Y, Ahmed, S, Sabir, MS, Portley, MK, Tucci, A, Ibáñez, K, Shankaracharya, FNU, Keagle, P, Rossi, G, Caroppo, P, Tagliavini, F, Waldo, ML, Johansson, PM, Nilsson, CF, Adeleye, A, Alba, C, Bacikova, D, Hupalo, DN, Martinez, EMG, Pollard, HB, Sukumar, G, Soltis, AR, Tuck, M, Zhang, X, Wilkerson, MD, Smith, BN, Ticozzi, N, Fallini, C, Gkazi, AS, Topp, SD, Kost, J, Scotter, EL, Kenna, KP, Miller, JW, Tiloca, C, Vance, C, Danielson, EW, Troakes, C, Colombrita, C, Al-Sarraj, S, Lewis, EA, King, A, Calini, D, Pensato, V, Castellotti, B, de Belleroche, J, Baas, F, ten Asbroek, ALMA, Sapp, PC, McKenna-Yasek, D, McLaughlin, RL, Polak, M, Asress, S, Esteban-Pérez, J, Muñoz-Blanco, JL, Stevic, Z, D'Alfonso, S, Mazzini, L, Comi, GP, Del Bo, R, Ceroni, M, Gagliardi, S, Querin, G, Bertolin, C, van Rheenen, W, Diekstra, FP, Rademakers, R, van Blitterswijk, M, Boylan, KB, Lauria, G, Duga, S, Corti, S, Cereda, C, Corrado, L, Sorarù, G, Williams, KL, Nicholson, GA, Blair, IP, Leblond-Manry, C, Rouleau, GA, Hardiman, O, Morrison, KE, Veldink, JH, van den Berg, LH, Al-Chalabi, A, Pall, H, Shaw, PJ, Turner, MR, Talbot, K, Taroni, F, García-Redondo, A, Wu, Z, Gellera, C, Ratti, A, Brown, RH (February 2021) Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis. Neuron, 109 (3). 448-460.e4. ISSN 0896-6273
Domínguez, Soledad, Ma, Liang, Yu, Han, Pouchelon, Gabrielle, Mayer, Christian, Spyropoulos, George D, Cea, Claudia, Buzsáki, György, Fishell, Gordon, Khodagholy, Dion, Gelinas, Jennifer N (July 2021) A transient postnatal quiescent period precedes emergence of mature cortical dynamics. eLife, 10. ISSN 2050-084X
Dong, Ao, He, Kaikai, Dudok, Barna, Farrell, Jordan S, Guan, Wuqiang, Liput, Daniel J, Puhl, Henry L, Cai, Ruyi, Wang, Huan, Duan, Jiali, Albarran, Eddy, Ding, Jun, Lovinger, David M, Li, Bo, Soltesz, Ivan, Li, Yulong (November 2021) A fluorescent sensor for spatiotemporally resolved imaging of endocannabinoid dynamics in vivo. Nature Biotechnology. ISSN 1087-0156
Dreyer, Stephan B, Upstill-Goddard, Rosie, Paulus-Hock, Viola, Paris, Clara, Lampraki, Eirini-Maria, Dray, Eloise, Serrels, Bryan, Caligiuri, Giuseppina, Rebus, Selma, Plenker, Dennis, Galluzzo, Zachary, Brunton, Holly, Cunningham, Richard, Tesson, Mathias, Nourse, Craig, Bailey, Ulla-Maja, Jones, Marc, Moran-Jones, Kim, Wright, Derek W, Duthie, Fraser, Oien, Karin, Evers, Lisa, McKay, Colin J, McGregor, Grant A, Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephan, Dziubinski, Michele L, Candido, Juliana, Balkwill, Frances, Barry, Simon T, Grützmann, Robert, Rahib, Lola, Glasgow Precision Oncology Laboratory,, , Australian Pancreatic Cancer Genome Initiative, , Johns, Amber, Pajic, Marina, Froeling, Fieke EM, Beer, Phillip, Musgrove, Elizabeth A, Petersen, Gloria M, Ashworth, Alan, Frame, Margaret C, Crawford, Howard C, Simeone, Diane M, Lord, Chris, Mukhopadhyay, Debabrata, Pilarsky, Christian, Tuveson, David A, Cooke, Susanna L, Jamieson, Nigel B, Morton, Jennifer P, Sansom, Owen J, Bailey, Peter J, Biankin, Andrew V, Chang, David K (January 2021) Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer. Gastroenterology, 160 (1). 362-377.e13. ISSN 0016-5085
Du, Yanfang, Lunde, China, Li, Yunfu, Jackson, David, Hake, Sarah, Zhang, Zuxin (February 2021) Gene duplication at the Fascicled ear1 locus controls the fate of inflorescence meristem cells in maize. Proceedings of the National Academy of Sciences of USA, 118 (7). e2019218118-e2019218118. ISSN 0027-8424
Dudok, Barna, Szoboszlay, Miklos, Paul, Anirban, Klein, Peter M, Liao, Zhenrui, Hwaun, Ernie, Szabo, Gergely G, Geiller, Tristan, Vancura, Bert, Wang, Bor-Shuen, McKenzie, Sam, Homidan, Jesslyn, Klaver, Lianne MF, English, Daniel F, Huang, Z Josh, Buzsáki, György, Losonczy, Attila, Soltesz, Ivan (October 2021) Recruitment and inhibitory action of hippocampal axo-axonic cells during behavior. Neuron. ISSN 0896-6273
Dugourd, Aurelien, Kuppe, Christoph, Sciacovelli, Marco, Gjerga, Enio, Gabor, Attila, Emdal, Kristina B, Vieira, Vitor, Bekker-Jensen, Dorte B, Kranz, Jennifer, Bindels, Eric MJ, Costa, Ana SH, Sousa, Abel, Beltrao, Pedro, Rocha, Miguel, Olsen, Jesper V, Frezza, Christian, Kramann, Rafael, Saez-Rodriguez, Julio (January 2021) Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses. Molecular Systems Biology, 17 (1). e9730. ISSN 1744-4292
Dukler, Noah, Mughal, Mehreen, Ramani, Ritika, Huang, Yi-Fei, Siepel, Adam (September 2021) Extreme purifying selection against point mutations in the human genome. BioRxiv. (Unpublished)
Dvorkin, Roman, Shea, Stephen D (April 2021) Precise and pervasive phasic bursting in locus coeruleus during maternal behavior. bioRxiv. (Unpublished)
da Silva, Edaise M, Selenica, Pier, Vahdatinia, Mahsa, Pareja, Fresia, Da Cruz Paula, Arnaud, Ferrando, Lorenzo, Gazzo, Andrea M, Dopeso, Higinio, Ross, Dara S, Bakhteri, Ariya, Riaz, Nadeem, Chandarlapaty, Sarat, Razavi, Pedram, Norton, Larry, Wen, Hannah Y, Brogi, Edi, Weigelt, Britta, Zhang, Hong, Reis-Filho, Jorge S (April 2021) TERT promoter hotspot mutations and gene amplification in metaplastic breast cancer. npj Breast Cancer, 7 (1). p. 43. ISSN 2374-4677
Elgin, Sarah CR, Hays, Shan, Mingo, Vida, Shaffer, Christopher D, Williams, Jason (June 2021) Building Back More Equitable STEM Education: Teach Science by Engaging Students in Doing Science. BioRxiv. (Unpublished)
Elkin, Rena, Oh, Jung Hun, Liu, Ying L, Selenica, Pier, Weigelt, Britta, Reis-Filho, Jorge S, Zamarin, Dmitriy, Deasy, Joseph O, Norton, Larry, Levine, Arnold J, Tannenbaum, Allen R (November 2021) Geometric network analysis provides prognostic information in patients with high grade serous carcinoma of the ovary treated with immune checkpoint inhibitors. npj Genomic Medicine, 6 (1). p. 99. ISSN 2056-7944
Engel, Tatiana A, Schölvinck, Marieke L, Lewis, Christopher M (October 2021) The diversity and specificity of functional connectivity across spatial and temporal scales. NeuroImage, 245. p. 118692. ISSN 1053-8119
Fearon, Douglas T, Janowitz, Tobias (March 2021) AMD3100/Plerixafor overcomes immune inhibition by the CXCL12-KRT19 coating on pancreatic and colorectal cancer cells. British Journal of Cancer. ISSN 0007-0920
Feng, Xiang, Noguchi, Yasunori, Barbon, Marta, Stillman, Bruce, Speck, Christian, Li, Huilin (June 2021) The structure of ORC–Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Nature Communications, 12 (1). ISSN 2041-1723
Ferraro, Emanuela, Razavi, Pedram, Chandarlapaty, Sarat, Modi, Shanu, Wen, Hannah Yong, Brogi, Edi, Norton, Larry, Robson, Mark E, Dang, Chau T (May 2021) Change in HER2 status after neoadjuvant chemotherapy (NAC) with trastuzumab and pertuzumab (HP) in patients with HER2-positive early-stage breast cancer. In: American Society of Clinical Oncology.
Ferro, Austin, Auguste, Yohan SS, Cheadle, Lucas (2021) Microglia, Cytokines, and Neural Activity: Unexpected Interactions in Brain Development and Function. Frontiers in Immunology, 12. p. 703527. ISSN 1664-3224
Fischer, Stephan, Crow, Megan, Harris, Benjamin D, Gillis, Jesse (July 2021) Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. Nature Protocols. ISSN 1754-2189
Fischer, Stephan, Gillis, Jesse (September 2021) Defining the extent of gene function using ROC curvature. BioRxiv. (Unpublished)
Fischer, Stephan, Gillis, Jesse (November 2021) How many markers are needed to robustly determine a cell's type? iScience, 24 (11). p. 103292. ISSN 2589-0042
Fischer, Stephan, Gillis, Jesse (June 2021) How many markers are needed to robustly determine a cell’s type? BioRxiv. (Unpublished)
Fisher, Matthew L, Balinth, Seamus, Hwangbo, Yon, Wu, Caizhi, Ballon, Carlos, Wilkinson, John E, Goldberg, Gary L, Mills, Alea A (October 2021) BRD4 REGULATES TRANSCRIPTION FACTOR ∆Np63αTO DRIVE A CANCER STEM CELL PHENOTYPE IN SQUAMOUS CELL CARCINOMAS. Cancer Research. canres.0707.2021-canres.0707.2021. ISSN 0008-5472
Fiskus, Warren, Mill, Christopher P, Nabet, Behnam, Perera, Dimuthu, Birdwell, Christine, Manshouri, Taghi, Lara, Bernardo, Kadia, Tapan M, DiNardo, Courtney, Takahashi, Koichi, Daver, Naval, Bose, Prithviraj, Masarova, Lucia, Pemmaraju, Naveen, Kornblau, Steven, Borthakur, Gautam, Montalban-Bravo, Guillermo, Manero, Guillermo Garcia, Sharma, Sunil, Stubbs, Matthew, Su, Xiaoping, Green, Michael R, Coarfa, Cristian, Verstovsek, Srdan, Khoury, Joseph D, Vakoc, Christopher R, Bhalla, Kapil N (May 2021) Superior efficacy of co-targeting GFI1/KDM1A and BRD4 against AML and post-MPN secondary AML cells. Blood Cancer Journal, 11 (5). p. 98. ISSN 2044-5385
Fouks, Bertrand, Brand, Philipp, Nguyen, Hung N, Herman, Jacob, Camara, Francisco, Ence, Daniel, Hagen, Darren E, Hoff, Katharina J, Nachweide, Stefanie, Romoth, Lars, Walden, Kimberly KO, Guigo, Roderic, Stanke, Mario, Narzisi, Giuseppe, Yandell, Mark, Robertson, Hugh M, Koeniger, Nikolaus, Chantawannakul, Panuwan, Schatz, Michael C, Worley, Kim C, Robinson, Gene E, Elsik, Christine G, Rueppell, Olav (May 2021) The genomic basis of evolutionary differentiation among honey bees. Genome Research, 31 (7). pp. 1203-1215. ISSN 1088-9051
Francis, Nikita, Borniger, Jeremy C (September 2021) Cancer as a homeostatic challenge: the role of the hypothalamus. Trends in Neurosciences. ISSN 0166-2236
Frederiksen, Sabrina B, Holm, Lise L, Larsen, Martin R, Doktor, Thomas K, Andersen, Henriette S, Hastings, Michelle L, Hua, Yimin, Krainer, Adrian R, Andresen, Brage S (March 2021) Identification of SRSF10 as a regulator of SMN2 ISS-N1. Human Mutation, 42 (3). pp. 246-260. ISSN 1059-7794
Fujii, T, Rehman, H, Chung, SY, Shen, J, Newman, J, Wu, V, Hines, A, Azimi-Nekoo, E, Fayyaz, F, Lee, M, Raptis, G, Egeblad, M, Zhu, X (July 2021) Treatment with granulocyte-colony stimulating factor (G-CSF) is not associated with increased risk of brain metastasis in patients with de novo stage IV breast cancer. Journal of Cancer, 12 (18). pp. 5687-5692. ISSN 1837-9664
Furlan, Alessandro, Corona, Alberto, Boyle, Sara, Sharma, Radhashree, Rubino, Rachel, Habel, Jill, Gablenz, Eva Carlotta, Giovanniello, Jacqueline, Beyaz, Semir, Janowitz, Tobias, Shea, Stephen D, Li, Bo (August 2021) Neurotensin neurons in the central extended amygdala control energy balance. BioRxiv. (Unpublished)
Furukawa, H, Simorowski, N, Michalski, K (January 2021) Effective production of oligomeric membrane proteins by EarlyBac-insect cell system. In: Methods in Enzymology. Elsevier.
Gao, ChongFeng, Wisniewski, Luke, Liu, Ying, Staal, Ben, Beddows, Ian, Plenker, Dennis, Aldakkak, Mohammed, Hall, Johnathan, Barnett, Daniel, Gouda, Mirna Kheir, Allen, Peter, Drake, Richard, Zureikat, Amer, Huang, Ying, Evans, Douglas, Singhi, Aatur, Brand, Randall E, Tuveson, David A, Tsai, Susan, Haab, Brian B (January 2021) Detection of Chemotherapy-resistant Pancreatic Cancer Using a Glycan Biomarker, sTRA. Clinical Cancer Research, 27 (1). pp. 226-236. ISSN 1078-0432
Garg, Ankur, Roske, Yvette, Yamada, Shinnosuke, Uehata, Takuya, Takeuchi, Osamu, Heinemann, Udo (May 2021) PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases. Nucleic Acids Research, 49 (9). pp. 5369-5381. ISSN 0305-1048
Ge, Eva J, Bush, Ashley I, Casini, Angela, Cobine, Paul A, Cross, Justin R, DeNicola, Gina M, Dou, Q Ping, Franz, Katherine J, Gohil, Vishal M, Gupta, Sanjeev, Kaler, Stephen G, Lutsenko, Svetlana, Mittal, Vivek, Petris, Michael J, Polishchuk, Roman, Ralle, Martina, Schilsky, Michael L, Tonks, Nicholas K, Vahdat, Linda T, Van Aelst, Linda, Xi, Dan, Yuan, Peng, Brady, Donita C, Chang, Christopher J (November 2021) Connecting copper and cancer: from transition metal signalling to metalloplasia. Nature Reviews Cancer. ISSN 1474-175X
Gearty, Sofia V, Dündar, Friederike, Zumbo, Paul, Espinosa-Carrasco, Gabriel, Shakiba, Mojdeh, Sanchez-Rivera, Francisco J, Socci, Nicholas D, Trivedi, Prerak, Lowe, Scott W, Lauer, Peter, Mohibullah, Neeman, Viale, Agnes, DiLorenzo, Teresa P, Betel, Doron, Schietinger, Andrea (November 2021) An autoimmune stem-like CD8 T cell population drives type 1 diabetes. Nature. ISSN 0028-0836
Genkin, Mikhail, Hughes, Owen, Engel, Tatiana A (October 2021) Learning non-stationary Langevin dynamics from stochastic observations of latent trajectories. Nature Communications, 12 (1). p. 5986. ISSN 2041-1723
Ghosh, Arunava, Girish, Vishruth, Yuan, Monet Lou, Coakley, Raymond D, Wrennall, Joe A, Alexis, Neil E, Sausville, Erin L, Vasudevan, Anand, Chait, Alexander R, Sheltzer, Jason M, Tarran, Robert (November 2021) Combustible and Electronic Cigarette Exposures Increase ACE2 Activity and SARS-CoV-2 Spike Binding. American Journal of Respiratory and Critical Care Medicine. ISSN 1073-449X
Ghosh, Sanchari, Zador, Anthony M (March 2021) Corticostriatal Plasticity Established by Initial Learning Persists after Behavioral Reversal. eNeuro, 8 (2). pp. 1-10. ISSN 2373-2822
Giel, Marie-Claire, Barrow, Andrew S, Smedley, Christopher J, Lewis, William, Moses, John E (June 2021) Aminium cation-radical catalysed selective hydration of (E)-aryl enynes. Chemical Communications. ISSN 1359-7345
Giovanniello, Jacqueline, Ahrens, Sandra, Yu, Kai, Li, Bo (June 2021) Sex-Specific Stress-Related Behavioral Phenotypes and Central Amygdala Dysfunction in a Mouse Model of 16p11.2 Microdeletion. Biological Psychiatry Global Open Science, 1 (1). pp. 59-69. ISSN 2667-1743
Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, JA, Severin, J, Hayashizaki, Y, Itoh, M, Tagami, M, Murata, M, Kojima-Ishiyama, M, Noma, S, Noguchi, S, Kasukawa, T, Hasegawa, A, Suzuki, H, Nishiyori-Sueki, H, Frith, MC, Abugessaisa, I, Aitken, S, Aken, BL, Alam, I, Alam, T, Alasiri, R, Alhendi, AMN, Alinejad-Rokny, H, Alvarez, MJ, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Archer, J, Archibald, AL, Arner, E, Arner, P, Asai, K, Ashoor, H, Astrom, G, Babina, M, Baillie, JK, Bajic, VB, Bajpai, A, Baker, S, Baldarelli, RM, Balic, A, Bansal, M, Batagov, AO, Batzoglou, S, Beckhouse, AG, Beltrami, AP, Beltrami, CA, Bertin, N, Bhattacharya, S, Bickel, PJ, Blake, JA, Blanchette, M, Bodega, B, Bonetti, A, Bono, H, Bornholdt, J, Bttcher, M, Bougouffa, S, Boyd, M, Breda, J, Brombacher, F, Brown, JB, Bult, CJ, Burroughs, AM, Burt, DW, Busch, A, Caglio, G, Califano, A, Cameron, CJ, Cannistraci, CV, Carbone, A, Carlisle, AJ, Carninci, P, Carter, KW, Cesselli, D, Chang, JC, Chen, JC, Chen, Y, Chierici, M, Christodoulou, J, Ciani, Y, Clark, EL, Coskun, M, Dalby, M, Dalla, E, Daub, CO, Davis, CA, de Hoon, MJL, de Rie, D, Denisenko, E, Deplancke, B, Detmar, M, Deviatiiarov, R, Di Bernardo, D, Diehl, AD, Dieterich, LC (June 2021) Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1). ISSN 2041-1723 (In Press)
Guerler, Aysam, Baker, Dannon, van den Beek, Marius, Gruening, Bjoern, Bouvier, Dave, Coraor, Nate, Shank, Stephen, Zehr, Jordan, Schatz, Michael, Nekrutenko, Anton (March 2021) Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. BioRxiv. (Unpublished)
Hanasoge Somasundara, Amritha Varshini, Moss, Matthew A, Feigman, Mary J, Chen, Chen, Cyrill, Samantha L, Ciccone, Michael F, Trousdell, Marygrace C, Vollbrecht, Macy, Li, Siran, Kendall, Jude, Beyaz, Semir, Wilkinson, John E, Dos Santos, Camila O (December 2021) Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis. Cell Reports, 37 (10). p. 110099. ISSN 2211-1247
Hansen, Kasper B, Wollmuth, Lonnie P, Bowie, Derek, Furukawa, Hiro, Menniti, Frank S, Sobolevsky, Alexander I, Swanson, Geoffrey T, Swanger, Sharon A, Greger, Ingo H, Nakagawa, Terunaga, McBain, Chris J, Jayaraman, Vasanthi, Low, Chian-Ming, Dell'Acqua, Mark L, Diamond, Jeffrey S, Camp, Chad R, Perszyk, Riley E, Yuan, Hongjie, Traynelis, Stephen F (October 2021) Structure, Function, and Pharmacology of Glutamate Receptor Ion Channels. Pharmacological Reviews, 73 (4). pp. 298-487. ISSN 0031-6997
Harris, Benjamin, Lee, John, Gillis, Jesse (August 2021) A Meta-Analytic Single-Cell Atlas of Mouse Bone Marrow Hematopoietic Development. BioRxiv. (Unpublished)
Harris, Benjamin D (October 2021) Atlas level scRNAseq analysis reveals the functional landscape of cell types. PhD thesis, Cold Spring Harbor Laboratory.
Harris, Benjamin D, Crow, Megan, Fischer, Stephan, Gillis, Jesse (May 2021) Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. Cell Systems. ISSN 2405-4712
Harris, Nomi L, Cock, Peter JA, Fields, Christopher J, Hokamp, Karsten, Maia, Jessica, Munoz-Torres, Monica, Sharan, Malvika, Williams, Jason (October 2021) BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference. F1000Research, 10. p. 1054. ISSN 2046-1402
He, C., Bozler, J., Janssen, K. A., Wilusz, J. E., Garcia, B. A., Schorn, A. J., Bonasio, R. (January 2021) TET2 chemically modifies tRNAs and regulates tRNA fragment levels. Nature Structural and Molecular Biology, 28 (1). pp. 62-70. ISSN 1545-9993
Hejase, Hussein, Mo, Ziyi, Campagna, Leonardo, Siepel, Adam (June 2021) SIA: Selection Inference Using the Ancestral Recombination Graph. BioRxiv. (Unpublished)
Hejase, Hussein A, Mo, Ziyi, Campagna, Leonardo, Siepel, Adam (November 2021) A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph. Molecular Biology and Evolution. ISSN 0737-4038
Hendelman, Anat, Zebell, Sophia, Rodriguez-Leal, Daniel, Dukler, Noah, Robitaille, Gina, Wu, Xuelin, Kostyun, Jamie, Tal, Lior, Wang, Peipei, Bartlett, Madelaine E, Eshed, Yuval, Efroni, Idan, Lippman, Zachary B (April 2021) Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell, 184 (7). 1724-1739.e16. ISSN 0092-8674
Henry, Samantha, Trousdell, Marygrace C, Cyrill, Samantha L, Zhao, Yixin, Feigman, Mary J, Bouhuis, Julia M, Aylard, Dominik A, Siepel, Adam, Dos Santos, Camila O (May 2021) Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland. Journal of Mammary Gland Biology and Neoplasia. ISSN 1083-3021
Hills-Muckey, Kelly, Martinez, Michael AQ, Stec, Natalia, Hebbar, Shilpa, Saldanha, Joanne, Medwig-Kinney, Taylor N, Moore, Frances EQ, Ivanova, Maria, Morao, Ana, Ward, JD, Moss, Eric G, Ercan, Sevinc, Zinovyeva, Anna Y, Matus, David Q, Hammell, Christopher M (October 2021) An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans. Genetics: a periodical record of investigations bearing on heredity and variation. ISSN 1943-2631
Hirschhorn, Daniel, Budhu, Sadna, Schroder, David, Kraehenbuehl, Lukas, Flammar, Anne-Laurent, Chow, Andrew, Schulze, Isabell, Schad, Sara, Ricca, Jacob, Gasmi, Billel, De Henau, Olivier, Mangarin, Levi, Redmond, David, Cortez, Czrina, Liu, Cailian, Holland, Aliya, Gigoux, Mathieu, Arora, Asrhi, Panageas, Katherine, Rizzuto, Gabrielle, Albrengues, Jean, Egeblad, Mikala, Wolchok, Jedd, Merghoub, Taha (November 2021) T CELL IMMUNOTHERAPIES TRIGGER NEUTROPHIL ACTIVATION TO ELIMINATE TUMOR ANTIGEN ESCAPE VARIANTS. In: SITC 36th Anniversary Annual Meeting (SITC 2021).
Hoffmann, Markus, Hofmann-Winkler, Heike, Smith, Joan C, Krüger, Nadine, Arora, Prerna, Sørensen, Lambert K, Søgaard, Ole S, Hasselstrøm, Jørgen Bo, Winkler, Michael, Hempel, Tim, Raich, Lluís, Olsson, Simon, Danov, Olga, Jonigk, Danny, Yamazoe, Takashi, Yamatsuta, Katsura, Mizuno, Hirotaka, Ludwig, Stephan, Noé, Frank, Kjolby, Mads, Braun, Armin, Sheltzer, Jason M, Pöhlmann, Stefan (March 2021) Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity. EBioMedicine, 65. p. 103255. ISSN 2352-3964
Hossain, Manzar, Bhalla, Kuhulika, Stillman, Bruce (March 2021) Multiple, short protein binding motifs in ORC1 and CDC6 control the initiation of DNA replication. Molecular Cell. ISSN 1097-2765
How, Javier J, Navlakha, Saket, Chalasani, Sreekanth H (November 2021) Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans. PLoS Computational Biology, 17 (11). e1009591. ISSN 1553-7358
Hu, Haifei, Scheben, Armin, Verpaalen, Brent, Tirnaz, Soodeh, Bayer, Philipp E, Hodel, Richard GJ, Batley, Jacqueline, Soltis, Douglas E, Soltis, Pamela S, Edwards, David (July 2021) Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. New Phytologist. ISSN 0028-646X
Hu, Tuo, Shukla, Surendra K, Vernucci, Enza, He, Chunbo, Wang, Dezhen, King, Ryan J, Jha, Kanupriya, Siddhanta, Kasturi, Mullen, Nicholas J, Attri, Kuldeep S, Murthy, Divya, Chaika, Nina V, Thakur, Ravi, Mulder, Scott E, Pacheco, Camila G, Fu, Xiao, High, Robin R, Yu, Fang, Lazenby, Audrey, Steegborn, Clemens, Lan, Ping, Mehla, Kamiya, Rotili, Dante, Chaudhary, Sarika, Valente, Sergio, Tafani, Marco, Mai, Antonello, Auwerx, Johan, Verdin, Eric, Tuveson, David, Singh, Pankaj K (July 2021) Metabolic Rewiring by Loss of Sirt5 Promotes Kras-induced Pancreatic Cancer Progression. Gastroenterology. ISSN 0016-5085
Hu, Ying, Colantonio, Vincent, Müller, Bárbara SF, Leach, Kristen A, Nanni, Adalena, Finegan, Christina, Wang, Bo, Baseggio, Matheus, Newton, Carter J, Juhl, Emily M, Hislop, Lillian, Gonzalez, Juan M, Rios, Esteban F, Hannah, L Curtis, Swarts, Kelly, Gore, Michael A, Hennen-Bierwagen, Tracie A, Myers, Alan M, Settles, A Mark, Tracy, William F, Resende, Marcio FR (February 2021) Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nature Communications, 12 (1). p. 1227. ISSN 2041-1723
Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, Dawe, R Kelly (August 2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373 (6555). pp. 655-662. ISSN 0036-8075
Hulse-Kemp, Amanda M, Bostan, Hamed, Chen, Shiyu, Ashrafi, Hamid, Stoffel, Kevin, Sanseverino, Walter, Li, Linzhou, Cheng, Shifeng, Schatz, Michael C, Garvin, Tyler, du Toit, Lindsey J, Tseng, Elizabeth, Chin, Jason, Iorizzo, Massimo, Van Deynze, Allen (June 2021) An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids. The Plant Genome. e20101. ISSN 1940-3372
Hutton, Elizabeth R, Vakoc, Christopher R, Siepel, Adam (September 2021) ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens. Genome Biology, 22 (1). p. 278. ISSN 1474-760X
Hyun, Minsuk, Taranda, Julian, Radeljic, Gianna, Miner, Lauren, Wang, Wengang, Ochandarena, Nicole, Huang, Kee Wui, Osten, Pavel, Sabatini, Bernardo L (January 2021) Social isolation uncovers a circuit underlying context-dependent territory-covering micturition. Proceedings of the National Academy of Sciences of USA, 118 (1). e2018078118-e2018078118. ISSN 0027-8424
Ibrahim, Leena Ali, Huang, Shuhan, Fernandez-Otero, Marian, Sherer, Mia, Qiu, Yanjie, Vemuri, Spurti, Xu, Qing, Machold, Robert, Pouchelon, Gabrielle, Rudy, Bernardo, Fishell, Gord (November 2021) Bottom-up inputs are required for establishment of top-down connectivity onto cortical layer 1 neurogliaform cells. Neuron, 109 (21). 3473-3485.e5. ISSN 0896-6273
Inam, H, Sokirniy, I, Rao, Y, Shah, A, Naeemikia, F, O'Brien, E, Dong, C, McCandlish, DM, Pritchard, JR (November 2021) Genomic and experimental evidence that ALK<sup>ATI</sup> does not predict single agent sensitivity to ALK inhibitors. iScience, 24 (11). p. 103343. ISSN 2589-0042
International Brain Laboratory, , Aguillon-Rodriguez, Valeria, Angelaki, Dora, Bayer, Hannah, Bonacchi, Niccolo, Carandini, Matteo, Cazettes, Fanny, Chapuis, Gaelle, Churchland, Anne K, Dan, Yang, Dewitt, Eric, Faulkner, Mayo, Forrest, Hamish, Haetzel, Laura, Häusser, Michael, Hofer, Sonja B, Hu, Fei, Khanal, Anup, Krasniak, Christopher, Laranjeira, Ines, Mainen, Zachary F, Meijer, Guido, Miska, Nathaniel J, Mrsic-Flogel, Thomas D, Murakami, Masayoshi, Noel, Jean-Paul, Pan-Vazquez, Alejandro, Rossant, Cyrille, Sanders, Joshua, Socha, Karolina, Terry, Rebecca, Urai, Anne E, Vergara, Hernando, Wells, Miles, Wilson, Christian J, Witten, Ilana B, Wool, Lauren E, Zador, Anthony M (May 2021) Standardized and reproducible measurement of decision-making in mice. eLife, 10. ISSN 2050-084X
Ipsaro, Jonathan J, O'Brien, Paul A, Bhattacharya, Shibani, Palmer, Arthur G, Joshua-Tor, Leemor (March 2021) Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons. Cell Reports, 34 (13). p. 108914. ISSN 2211-1247
Iyer, Shruti V, Kramer, Melissa, Goodwin, Sara, McCombie, W Richard (July 2021) Understanding genetic variation in cancer using nanopore targeted sequencing. In: AACR Annual Meeting 2021.
Janowitz, Tobias, Kleeman, Sam, Vonderheide, Robert H (April 2021) Reconsidering Dexamethasone for Antiemesis when Combining Chemotherapy and Immunotherapy. The Oncologist, 26 (4). pp. 269-273. ISSN 1083-7159
Jia, Xiaoming, Goes, Fernando S, Locke, Adam E, Palmer, Duncan, Wang, Weiqing, Cohen-Woods, Sarah, Genovese, Giulio, Jackson, Anne U, Jiang, Chen, Kvale, Mark, Mullins, Niamh, Nguyen, Hoang, Pirooznia, Mehdi, Rivera, Margarita, Ruderfer, Douglas M, Shen, Ling, Thai, Khanh, Zawistowski, Matthew, Zhuang, Yongwen, Abecasis, Gonçalo, Akil, Huda, Bergen, Sarah, Burmeister, Margit, Chapman, Sinéad, DelaBastide, Melissa, Juréus, Anders, Kang, Hyun Min, Kwok, Pui-Yan, Li, Jun Z, Levy, Shawn E, Monson, Eric T, Moran, Jennifer, Sobell, Janet, Watson, Stanley, Willour, Virginia, Zöllner, Sebastian, Adolfsson, Rolf, Blackwood, Douglas, Boehnke, Michael, Breen, Gerome, Corvin, Aiden, Craddock, Nick, DiFlorio, Arianna, Hultman, Christina M, Landen, Mikael, Lewis, Cathryn, McCarroll, Steven A, Richard McCombie, W, McGuffin, Peter, McIntosh, Andrew, McQuillin, Andrew, Morris, Derek, Myers, Richard M, O'Donovan, Michael, Ophoff, Roel, Boks, Marco, Kahn, Rene, Ouwehand, Willem, Owen, Michael, Pato, Carlos, Pato, Michele, Posthuma, Danielle, Potash, James B, Reif, Andreas, Sklar, Pamela, Smoller, Jordan, Sullivan, Patrick F, Vincent, John, Walters, James, Neale, Benjamin, Purcell, Shaun, Risch, Neil, Schaefer, Catherine, Stahl, Eli A, Zandi, Peter P, Scott, Laura J (January 2021) Investigating rare pathogenic/likely pathogenic exonic variation in bipolar disorder. Molecular Psychiatry. ISSN 1359-4184
Joo, Hannah R, Liang, Hexin, Chung, Jason E, Geaghan-Breiner, Charlotte, Fan, Jiang Lan, Nachman, Benjamin P, Kepecs, Adam, Frank, Loren M (August 2021) Rats use memory confidence to guide decisions. Current Biology. ISSN 0960-9822
Kawaguchi, Risa K., Takahashi, Masamichi, Miyake, Mototaka, Kinoshita, Manabu, Takahashi, Satoshi, Ichimura, Koichi, Hamamoto, Ryuji, Narita, Yoshitaka, Sese, Jun (July 2021) Assessing Versatile Machine Learning Models for Glioma Radiogenomic Studies across Hospitals. Cancers, 13 (14). p. 3611. ISSN 2072-6694
Kawaguchi, Risa Karakida, Tang, Ziqi, Fischer, Stephan, Tripathy, Rohit, Koo, Peter, Gillis, Jesse (April 2021) Exploiting marker genes for robust classification and characterization of single-cell chromatin accessibility. BioRxiv. (Unpublished)
Khouider, Souraya, Borges, Filipe, LeBlanc, Chantal, Ungru, Alexander, Schnittger, Arp, Martienssen, Robert, Colot, Vincent, Bouyer, Daniel (January 2021) Male fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function. Nature Communications, 12 (1). p. 410. ISSN 2041-1723
Kim, Young Jin, Nomakuchi, Tomoki, Papaleonidopoulou, Foteini, Krainer, Adrian (July 2021) Gene-Specific Nonsense-Mediated mRNA Decay Targeting for Cystic Fibrosis Therapy. BioRxiv. (Unpublished)
Kim, Young Jin, Sivetz, Nicole, Layne, Jessica, Voss, Dillon, Yang, Lucia, Zhang, Qian, Krainer, Adrian (August 2021) Exon-Skipping Antisense Oligonucleotides for Cystic Fibrosis Therapy. BioRxiv. (Unpublished)
Kirsche, Melanie, Das, Arun, Schatz, Michael C (May 2021) Sapling: accelerating suffix array queries with learned data models. Bioinformatics, 37 (6). pp. 744-749. ISSN 1367-4803
Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Aganezov, Sergey, Schatz, Michael (May 2021) Jasmine: Population-scale structural variant comparison and analysis. BioRxiv. (Unpublished)
Kirsche, Melanie, Schatz, Michael C (October 2021) Democratizing long-read genome assembly. Cell Systems, 12 (10). pp. 945-947. ISSN 2405-4712
Kolamunnage-Dona, Ruwanthi, Berhane, Sarah, Potts, Harry, Williams, Edward H, Tanner, James, Janowitz, Tobias, Hoare, Matthew, Johnson, Philip (May 2021) Sorafenib is associated with a reduced rate of tumour growth and liver function deterioration in HCV-induced hepatocellular carcinoma. Journal of Hepatology. ISSN 0168-8278
Koo, Peter K, Majdandzic, Antonio, Ploenzke, Matthew, Anand, Praveen, Paul, Steffan B (May 2021) Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks. PLoS Computational Biology, 17 (5). e1008925. ISSN 1553-7358
Koo, Peter K, Ploenzke, Matt (March 2021) Improving representations of genomic sequence motifs in convolutional networks with exponential activations. Nature Machine Intelligence, 3 (3). pp. 258-266. ISSN 2522-5839
Kovaka, Sam, Fan, Yunfan, Ni, Bohan, Timp, Winston, Schatz, Michael C (April 2021) Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Nature Biotechnology, 39 (4). pp. 431-441. ISSN 1087-0156
Krause, William C, Rodriguez, Ruben, Gegenhuber, Bruno, Matharu, Navneet, Rodriguez, Andreas N, Padilla-Roger, Adriana M, Toma, Kenichi, Herber, Candice B, Correa, Stephanie M, Duan, Xin, Ahituv, Nadav, Tollkuhn, Jessica, Ingraham, Holly A (October 2021) Oestrogen engages brain MC4R signalling to drive physical activity in female mice. Nature. ISSN 0028-0836
Kumar, Rakesh, Hortobagy, Gabriel N, Albanell, Joan, Arribas, Joaquín, Norton, Larry (June 2021) In Memoriam: José Baselga's Journey in Cancer Medicine. Clinical Cancer Research, 27 (12). pp. 3499-3502. ISSN 1078-0432
Kumari, Sunita, Kumar, Vivek, Beilsmith, Kathleen, Seaver, Samuel MD, Canon, Shane, Dehal, Paramvir, Gu, Tian, Joachimiak, Marcin, Lerma-Ortiz, Claudia, Liu, Filipe, Lu, Zhenyuan, Pearson, Eric, Ranjan, Priya, Riel, William, Henry, Christopher S, Arkin, Adam P, Ware, Doreen (November 2021) A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in response to Drought Stress in Sorghum. Current Plant Biology. p. 100229. ISSN 2214-6628
Kweon, Hyae Yon, Lee, Mi-Ni, Dorfel, Max, Seo, Seungwoon, Gottlieb, Leah, PaPazyan, Thomas, McTiernan, Nina, Ree, Rasmus, Bolton, David, Garcia, Andrew, Flory, Michael, Crain, Jonathan, Sebold, Alison, Lyons, Scott, Ismail, Ahmed, Marchi, Elaine, Sonn, Seong-Keun, Jeong, Se-Jin, Jeon, Sejin, Ju, Shinyeong, Conway, Simon J, Kim, Taesoo, Kim, Hyun-Seok, Lee, Cheolju, Roh, Tae-Young, Arnesen, Thomas, Marmorstein, Ronen, Oh, Gootaeg, Lyon, Gholson J (August 2021) Naa12 compensates for Naa10 in mice in the amino-terminal acetylation pathway. eLife, 10. ISSN 2050-084X
La Manno, Gioele, Siletti, Kimberly, Furlan, Alessandro, Gyllborg, Daniel, Vinsland, Elin, Mossi Albiach, Alejandro, Mattsson Langseth, Christoffer, Khven, Irina, Lederer, Alex R, Dratva, Lisa M, Johnsson, Anna, Nilsson, Mats, Lönnerberg, Peter, Linnarsson, Sten (July 2021) Molecular architecture of the developing mouse brain. Nature. ISSN 0028-0836
Laubscher, Dominik, Gryder, Berkley E, Sunkel, Benjamin D, Andresson, Thorkell, Wachtel, Marco, Das, Sudipto, Roschitzki, Bernd, Wolski, Witold, Wu, Xiaoli S, Chou, Hsien-Chao, Song, Young K, Wang, Chaoyu, Wei, Jun S, Wang, Meng, Wen, Xinyu, Ngo, Quy Ai, Marques, Joana G, Vakoc, Christopher R, Schäfer, Beat W, Stanton, Benjamin Z, Khan, Javed (November 2021) BAF complexes drive proliferation and block myogenic differentiation in fusion-positive rhabdomyosarcoma. Nature Communications, 12 (1). p. 6924. ISSN 2041-1723
Lawrence, R, Ranade, N, Sullivan, D (June 2021) Quantitative towers in finite difference calculus approximating the continuum. Quarterly Journal of Mathematics, 72 (1-2). pp. 515-545. ISSN 0033-5606
Lee, Seung Cho, Martienssen, Robert A (January 2021) Phase separation in plant miRNA processing. Nature Cell Biology, 23 (1). pp. 5-6. ISSN 1465-7392
Lee, Seung Cho, Martienssen, Robert A (September 2021) Regulation of retrotransposition in Arabidopsis. Biochemical Society Transactions. ISSN 0300-5127
Lee, Yu-Chen, Lin, Song-Chang, Yu, Guoyu, Zhu, Ming, Song, Jian, Rivera, Keith, Pappin, Darryl, Logothetis, Christopher, Panaretakis, Theocharis, Wang, Guocan, Yu-Lee, Li-Yuan, Lin, Sue-Hwa (November 2021) Prostate tumor-induced stromal reprogramming generates Tenascin C that promotes prostate cancer metastasis through YAP/TAZ inhibition. BioRxiv. (Unpublished)
Lee, Yu-Chen, Lin, Song-Chang, Yu, Guoyu, Zhu, Ming, Song, Jian H, Rivera, Keith, Pappin, Darryl J, Logothetis, Christopher J, Panaretakis, Theocharis, Wang, Guocan, Yu-Lee, Li-Yuan, Lin, Sue-Hwa (November 2021) Prostate tumor-induced stromal reprogramming generates Tenascin C that promotes prostate cancer metastasis through YAP/TAZ inhibition. Oncogene. ISSN 0950-9232
Li, Suhua, Li, Gencheng, Gao, Bing, Pujari, Sidharam P, Chen, Xiaoyan, Kim, Hyunseok, Zhou, Feng, Klivansky, Liana M, Liu, Yi, Driss, Hafedh, Liang, Dong-Dong, Lu, Jianmei, Wu, Peng, Zuilhof, Han, Moses, John, Sharpless, K Barry (August 2021) SuFExable polymers with helical structures derived from thionyl tetrafluoride. Nature Chemistry. ISSN 1755-4330
Li, Xinran, Zhou, Jiaqi, Zhao, Wenjuan, Wen, Qing, Wang, Weijie, Peng, Huipai, Gao, Yuan, Bouchonville, Kelly J, Offer, Steven M, Chan, Kuiming, Wang, Zhiquan, Li, Nan, Gan, Haiyun (September 2021) Defining Proximity Proteomics of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling. Genomics Proteomics and Bioinformatics. ISSN 1672-0229
Lin, Guifang, He, Cheng, Zheng, Jun, Koo, Dal-Hoe, Le, Ha, Zheng, Huakun, Tamang, Tej Man, Lin, Jinguang, Liu, Yan, Zhao, Mingxia, Hao, Yangfan, McFraland, Frank, Wang, Bo, Qin, Yang, Tang, Haibao, McCarty, Donald R, Wei, Hairong, Cho, Myeong-Je, Park, Sunghun, Kaeppler, Heidi, Kaeppler, Shawn M, Liu, Yunjun, Springer, Nathan, Schnable, Patrick S, Wang, Guoying, White, Frank F, Liu, Sanzhen (June 2021) Chromosome-level genome assembly of a regenerable maize inbred line A188. Genome biology, 22 (1). p. 175. ISSN 1474-760X
Liu, L, Lindsay, PL, Jackson, D (May 2021) Next generation cereal crop yield enhancement: From knowledge of inflorescence development to practical engineering by genome editing. International Journal of Molecular Sciences, 22 (10). p. 5167. ISSN 1661-6596
Liu, Lei, Chen, Richelle, Fugina, Christopher John, Siegel, Ben, Jackson, David (April 2021) High-Throughput and Low-Cost Genotyping Method for Plant Genome Editing. Curr Protoc, 1 (4). e100. ISSN 2691-1299
Liu, Lei, Gallagher, Joseph, Arevalo, Edgar Demesa, Chen, Richelle, Skopelitis, Tara, Wu, Qingyu, Bartlett, Madelaine, Jackson, David (March 2021) Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes. Nature Plants, 7 (3). pp. 287-294. ISSN 2055-026X
Liu, Songlei, Punthambaker, Sukanya, Iyer, Eswar PR, Ferrante, Thomas, Goodwin, Daniel, Fürth, Daniel, Pawlowski, Andrew C, Jindal, Kunal, Tam, Jenny M, Mifflin, Lauren, Alon, Shahar, Sinha, Anubhav, Wassie, Asmamaw T, Chen, Fei, Cheng, Anne, Willocq, Valerie, Meyer, Katharina, Ling, King-Hwa, Camplisson, Conor K, Kohman, Richie E, Aach, John, Lee, Je Hyuk, Yankner, Bruce A, Boyden, Edward S, Church, George M (March 2021) Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses. Nucleic Acids Research. ISSN 0305-1048
Lohia, Ruchi, Hansen, Matthew, Brannigan, Grace H (February 2021) Hydrophobicity Based Sequence Blobulation Approach Captures Functional Modularity: Disease-Associated Mutations are Enriched in Hydrophobic Blobs. In: Biophysical Society Annual Meeting.
Lu, Shaina, Fürth, Daniel, Gillis, Jesse (October 2021) Integrative analysis methods for spatial transcriptomics. Nature Methods. ISSN 1548-7091
Lu, Shaina, Ortiz, Cantin, Fürth, Daniel, Fischer, Stephan, Meletis, Konstantinos, Zador, Anthony, Gillis, Jesse (July 2021) Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain. PLoS Biology, 19 (7). e3001341. ISSN 1545-7885
Luckett, Kathleen A, Cracchiolo, Jennifer R, Krishnamoorthy, Gnana P, Leandro-Garcia, Luis Javier, Nagarajah, James, Saqcena, Mahesh, Lester, Rona, Im, Soo Y, Zhao, Zhen, Lowe, Scott W, de Stanchina, Elisa, Sherman, Eric J, Ho, Alan L, Leach, Steven D, Knauf, Jeffrey A, Fagin, James A (May 2021) Co-inhibition of SMAD and MAPK signaling enhances 124I uptake in BRAF-mutant thyroid cancers. Endocrine-Related Cancer, 28 (6). pp. 391-402. ISSN 1351-0088
Lukow, Devon A, Sausville, Erin L, Suri, Pavit, Chunduri, Narendra Kumar, Wieland, Angela, Leu, Justin, Smith, Joan C, Girish, Vishruth, Kumar, Ankith A, Kendall, Jude, Wang, Zihua, Storchova, Zuzana, Sheltzer, Jason M (August 2021) Chromosomal instability accelerates the evolution of resistance to anti-cancer therapies. Developmental Cell. ISSN 1534-5807
Lukow, Devon A, Sheltzer, Jason M (September 2021) Chromosomal instability and aneuploidy as causes of cancer drug resistance. Trends in Cancer. ISSN 2405-8033
Lyons, S. K., Francis, K. P., Contag, C. H. (August 2021) Functional Imaging Using Bioluminescent Reporter Genes in Living Subjects. In: Molecular Imaging (Second Edition). Academic Press, pp. 113-141. ISBN 9780128163870
Lyons, Scott K, Plenker, Dennis, Trotman, Lloyd C (July 2021) Advances in preclinical evaluation of experimental antibody-drug conjugates. Cancer Drug Resistance, 4. pp. 745-754. ISSN 2578-532X
Ma, Wai Kit, Voss, Dillon M, Scharner, Juergen, Costa, Ana SH, Lin, Kuang-Ting, Jeon, Hyun Yong, Wilkinson, John E, Jackson, Michaela, Rigo, Frank, Bennett, C Frank, Krainer, Adrian R (December 2021) ASO-based PKM splice-switching therapy inhibits hepatocellular carcinoma growth. Cancer Research. canres.0948.2020-canres.0948.2020. ISSN 0008-5472
Macpherson, Tom, Churchland, Anne, Sejnowski, Terry, DiCarlo, James, Kamitani, Yukiyasu, Takahashi, Hidehiko, Hikida, Takatoshi (September 2021) Natural and Artificial Intelligence: A brief introduction to the interplay between AI and neuroscience research. Neural Networks. ISSN 0893-6080
Maiorino, Laura, Daßler-Plenker, Juliane, Sun, Lijuan, Egeblad, Mikala (November 2021) Innate Immunity and Cancer Pathophysiology. Annual Review of Pathology: Mechanisms of Disease, 17 (1). ISSN 1553-4006
Malik, Sarah A, Zhu, Chencan, Li, Jinyu, LaComb, Joseph F, Denoya, Paula I, Kravets, Igor, Miller, Joshua D, Yang, Jie, Kramer, Melissa, McCombie, W Richard, Robertson, Charles E, Frank, Daniel N, Li, Ellen (April 2021) Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections. World Journal of Gastroenterology, 27 (14). pp. 1465-1482. ISSN 1007-9327
Matho, Katherine S, Huilgol, Dhananjay, Galbavy, William, He, Miao, Kim, Gukhan, An, Xu, Lu, Jiangteng, Wu, Priscilla, Di Bella, Daniela J, Shetty, Ashwin S, Palaniswamy, Ramesh, Hatfield, Joshua, Raudales, Ricardo, Narasimhan, Arun, Gamache, Eric, Levine, Jesse M, Tucciarone, Jason, Szelenyi, Eric, Harris, Julie A, Mitra, Partha P, Osten, Pavel, Arlotta, Paola, Huang, Z Josh (October 2021) Genetic dissection of the glutamatergic neuron system in cerebral cortex. Nature, 598 (7879). pp. 182-187. ISSN 0028-0836
Maturana, Carola J, Verpeut, Jessica L, Kooshkbaghi, Mahdi, Engel, Esteban A (June 2021) Novel tool to quantify with single-cell resolution the number of incoming AAV genomes co-expressed in the mouse nervous system. Gene Therapy (Basingstoke). ISSN 0969-7128
Maurice, C, Dalvai, M, Lambrot, R, Deschênes, A, Scott-Boyer, MP, McGraw, S, Chan, D, Côté, N, Ziv-Gal, A, Flaws, JA, Droit, A, Trasler, J, Kimmins, S, Bailey, JL (June 2021) Early-life exposure to environmental contaminants perturbs the sperm epigenome and induces negative pregnancy outcomes for three generations via the paternal lineage. Epigenomes, 5 (2). p. 10. ISSN 2075-4655
McCandlish, DM (September 2021) System-specificity of genotype-phenotype map structure: Comment on “From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics” by Susanna Manrubia et al. Physics of Life Reviews. ISSN 1571-0645
Meze, Katarina, Axhemi, Armend, Thomas, Dennis, Joshua-Tor, Leemor (October 2021) The 3 '-5 ' Exonuclease Dis3L2 Undergoes Conformational Dynamics During Structured RNA Degradation. In: Protein Science 35th Anniversary Symposium.
Mikhailik, Anatoly, Michurina, Tatyana V, Dikranian, Krikor, Hearn, Stephen, Maxakov, Vladimir I, Siller, Saul S, Takemaru, Ken-Ichi, Enikolopov, Grigori, Peunova, Natalia (May 2021) nNOS regulates ciliated cell polarity, ciliary beat frequency, and directional flow in mouse trachea. Life science alliance, 4 (5). ISSN 2575-1077
Mitra, PP (May 2021) Fitting elephants in modern machine learning by statistically consistent interpolation. Nature Machine Intelligence, 3 (5). pp. 378-386. ISSN 2522-5839
Miyagi, Miriam, Guthman, Eartha Mae, Sun, Simón E Dow-Kuang (December 2021) Transgender rights rely on inclusive language. Science, 374 (6575). pp. 1568-1569. ISSN 0036-8075
Mo, Ziyi, Scheben, Armin, Steinberg, Joshua, Siepel, Adam, Martienssen, Robert (March 2021) Circadian immunity, sunrise time and the seasonality of respiratory infections. medRxiv. (Unpublished)
Molik, David C, Tomlinson, DeAndre, Davitt, Shane, Morgan, Eric L, Sisk, Matthew, Roche, Benjamin, Meyers, Natalie, Pfrender, Michael E (April 2021) Combining natural language processing and metabarcoding to reveal pathogen-environment associations. PLoS Neglected Tropical Diseases, 15 (4). e0008755. ISSN 1935-2735
Moore, Keith J. M., Cahill, Jeremy, Aidelberg, Guy, Aronoff, Rachel, Bektaş, Ali, Bezdan, Daniela, Butler, Daniel J., Chittur, Sridar V., Codyre, Martin, Federici, Fernan, Tanner, Nathan A., Tighe, Scott W., True, Randy, Ware, Sarah B., Wyllie, Anne L., Afshin, Evan E., Bendesky, Andres, Chang, Connie B., Dela Rosa, Richard, Elhaik, Eran, Erickson, David, Goldsborough, Andrew S., Grills, George, Hadasch, Kathrin, Hayden, Andrew, Her, Seong-Young, Karl, Julie A., Kim, Chang Hee, Kriegel, Alison J., Kunstman, Thomas, Landau, Zeph, Land, Kevin, Langhorst, Bradley W., Lindner, Ariel B., Mayer, Benjamin E., McLaughlin, Lee A., McLaughlin, Matthew T., Molloy, Jenny, Mozsary, Christopher, Nadler, Jerry L., D'Silva, Melinee, Ng, David, O'Connor, David H., Ongerth, Jerry E., Osuolale, Olayinka, Pinharanda, Ana, Plenker, Dennis, Ranjan, Ravi, Rosbash, Michael, Rotem, Assaf, Segarra, Jacob, Schürer, Stephan, Sherrill-Mix, Scott, Solo-Gabriele, Helena, To, Shaina, Vogt, Merly C., Yu, Albert D., Mason, Christopher E. (September 2021) Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. Journal of Biomolecular Techniques : JBT, 32 (3). pp. 228-275. ISSN 1524-0215
Moreno, Pablo, Fexova, Silvie, George, Nancy, Manning, Jonathan R, Miao, Zhichiao, Mohammed, Suhaib, Muñoz-Pomer, Alfonso, Fullgrabe, Anja, Bi, Yalan, Bush, Natassja, Iqbal, Haider, Kumbham, Upendra, Solovyev, Andrey, Zhao, Lingyun, Prakash, Ananth, García-Seisdedos, David, Kundu, Deepti J, Wang, Shengbo, Walzer, Mathias, Clarke, Laura, Osumi-Sutherland, David, Tello-Ruiz, Marcela Karey, Kumari, Sunita, Ware, Doreen, Eliasova, Jana, Arends, Mark J, Nawijn, Martijn C, Meyer, Kerstin, Burdett, Tony, Marioni, John, Teichmann, Sarah, Vizcaíno, Juan Antonio, Brazma, Alvis, Papatheodorou, Irene (November 2021) Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Research. ISSN 0305-1048
Moukarzel, Lea A, Ferrando, Lorenzo, Da Cruz Paula, Arnaud, Brown, David N, Geyer, Felipe C, Pareja, Fresia, Piscuoglio, Salvatore, Papanastasiou, Anastasios D, Fusco, Nicola, Marchiò, Caterina, Abu-Rustum, Nadeem R, Murali, Rajmohan, Brogi, Edi, Wen, Hannah Y, Norton, Larry, Soslow, Robert A, Vincent-Salomon, Anne, Reis-Filho, Jorge S, Weigelt, Britta (April 2021) The genetic landscape of metaplastic breast cancers and uterine carcinosarcomas. Molecular Oncology, 15 (4). pp. 1024-1039. ISSN 1574-7891
Munir, Hafsa, Jones, James O, Janowitz, Tobias, Hoffmann, Markus, Euler, Maximilien, Martins, Carla P, Welsh, Sarah J, Shields, Jacqueline D (January 2021) Stromal-driven and Amyloid β-dependent induction of neutrophil extracellular traps modulates tumor growth. Nature Communications, 12 (1). p. 683. ISSN 2041-1723
Muñoz-Castañeda, Rodrigo, Zingg, Brian, Matho, Katherine S, Chen, Xiaoyin, Wang, Quanxin, Foster, Nicholas N, Li, Anan, Narasimhan, Arun, Hirokawa, Karla E, Huo, Bingxing, Bannerjee, Samik, Korobkova, Laura, Park, Chris Sin, Park, Young-Gyun, Bienkowski, Michael S, Chon, Uree, Wheeler, Diek W, Li, Xiangning, Wang, Yun, Naeemi, Maitham, Xie, Peng, Liu, Lijuan, Kelly, Kathleen, An, Xu, Attili, Sarojini M, Bowman, Ian, Bludova, Anastasiia, Cetin, Ali, Ding, Liya, Drewes, Rhonda, D'Orazi, Florence, Elowsky, Corey, Fischer, Stephan, Galbavy, William, Gao, Lei, Gillis, Jesse, Groblewski, Peter A, Gou, Lin, Hahn, Joel D, Hatfield, Joshua T, Hintiryan, Houri, Huang, Junxiang Jason, Kondo, Hideki, Kuang, Xiuli, Lesnar, Philip, Li, Xu, Li, Yaoyao, Lin, Mengkuan, Lo, Darrick, Mizrachi, Judith, Mok, Stephanie, Nicovich, Philip R, Palaniswamy, Ramesh, Palmer, Jason, Qi, Xiaoli, Shen, Elise, Sun, Yu-Chi, Tao, Huizhong W, Wakemen, Wayne, Wang, Yimin, Yao, Shenqin, Yuan, Jing, Zhan, Huiqing, Zhu, Muye, Ng, Lydia, Zhang, Li I, Lim, Byung Kook, Hawrylycz, Michael, Gong, Hui, Gee, James C, Kim, Yongsoo, Chung, Kwanghun, Yang, X William, Peng, Hanchuan, Luo, Qingming, Mitra, Partha P, Zador, Anthony M, Zeng, Hongkui, Ascoli, Giorgio A, Josh Huang, Z, Osten, Pavel, Harris, Julie A, Dong, Hong-Wei (October 2021) Cellular anatomy of the mouse primary motor cortex. Nature, 598 (7879). pp. 159-166. ISSN 0028-0836
Naish, Matthew, Alonge, Michael, Wlodzimierz, Piotr, Tock, Andrew J, Abramson, Bradley W, Schmücker, Anna, Mandáková, Terezie, Jamge, Bhagyshree, Lambing, Christophe, Kuo, Pallas, Yelina, Natasha, Hartwick, Nolan, Colt, Kelly, Smith, Lisa M, Ton, Jurriaan, Kakutani, Tetsuji, Martienssen, Robert A, Schneeberger, Korbinian, Lysak, Martin A, Berger, Frédéric, Bousios, Alexandros, Michael, Todd P, Schatz, Michael C, Henderson, Ian R (November 2021) The genetic and epigenetic landscape of the Arabidopsis centromeres. Science, 374 (6569). eabi7489. ISSN 0036-8075
Navlakha, Saket, Morjaria, Sejal, Perez-Johnston, Rocio, Zhang, Allen, Taur, Ying (May 2021) Projecting COVID-19 disease severity in cancer patients using purposefully-designed machine learning. BMC Infectious Diseases, 21 (1). p. 391. ISSN 1471-2334
Nie, Shujun, Wang, Bo, Ding, Haiping, Lin, Haijian, Zhang, Li, Li, Qigui, Wang, Yujiao, Zhang, Bin, Liang, Anping, Zheng, Qi, Wang, Hui, Lv, Huayang, Zhu, Kun, Jia, Minghui, Wang, Xiaotong, Du, Jiyuan, Zhao, Runtai, Jiang, Zhenzhen, Xia, Caina, Qiao, Zhenghao, Li, Xiaohu, Liu, Boyan, Zhu, Hongbo, An, Rong, Li, Yucui, Jiang, Qian, Chen, Benfang, Zhang, Hongkai, Wang, Dening, Tang, Changxiao, Yuan, Yang, Dai, Jie, Zhan, Jing, He, Weiqiang, Wang, Xuebo, Shi, Jian, Wang, Bin, Gong, Min, He, Xiujing, Li, Peng, Huang, Li, Li, Hui, Pan, Chao, Huang, Hong, Yuan, Guangsheng, Lan, Hai, Nie, Yongxin, Li, Xinzheng, Zhao, Xiangyu, Zhang, Xiansheng, Pan, Guangtang, Wu, Qingyu, Xu, Fang, Zhang, Zhiming (July 2021) Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement. The Plant journal : for cell and molecular biology. ISSN 1365-313X
Nielsen, Sebastian R, Strøbech, Jan E, Horton, Edward R, Jackstadt, Rene, Laitala, Anu, Bravo, Marina C, Maltese, Giorgia, Jensen, Adina RD, Reuten, Raphael, Rafaeva, Maria, Karim, Saadia A, Hwang, Chang-Il, Arnes, Luis, Tuveson, David A, Sansom, Owen J, Morton, Jennifer P, Erler, Janine T (June 2021) Suppression of tumor-associated neutrophils by lorlatinib attenuates pancreatic cancer growth and improves treatment with immune checkpoint blockade. Nature Communications, 12 (1). p. 3414. ISSN 2041-1723
Ning, Qiang, Jian, Yinan, Du, Yanfang, Li, Yunfu, Shen, Xiaomeng, Jia, Haitao, Zhao, Ran, Zhan, Jimin, Yang, Fang, Jackson, David, Liu, Lei, Zhang, Zuxin (October 2021) An ethylene biosynthesis enzyme controls quantitative variation in maize ear length and kernel yield. Nature Communications, 12 (1). p. 5832. ISSN 2041-1723
Nizam, Aaron, Chung, Charlie, Goldberg, Gary L, Beyaz, Semir (July 2021) Abstract LB236: Utilizing endometrial tumor organoids to model cancer immunomodulation. In: AACR Annual Meeting 2021.
Nizam, Aaron, Chung, Charlie, Goldberg, Gary L, Beyaz, Semir (July 2021) Utilizing endometrial tumor organoids to model cancer immunomodulation. In: AACR Annual Meeting 2021.
Norton, Larry (October 2021) IS THE MAXIMUM TOLERATED DOSE (MDT) STILL THE OPTIMAL GOAL FOR CANCER DRUGS? In: UNSPECIFIED.
Nowlan, Alexandra C (April 2021) An amygdalo-cortical circuit for multisensory processing in maternal behavior. PhD thesis, Cold Spring Harbor Laboratory.
Olson, Andrew J, Ware, Doreen (July 2021) Ranked Choice Voting for Representative Transcripts with TRaCE. Bioinformatics. ISSN 1367-4803
Ortiz-Ramírez, Carlos, Guillotin, Bruno, Xu, Xiaosa, Rahni, Ramin, Zhang, Sanqiang, Yan, Zhe, Coqueiro Dias Araujo, Poliana, Demesa-Arevalo, Edgar, Lee, Laura, Van Eck, Joyce, Gingeras, Thomas R, Jackson, David, Gallagher, Kimberly L, Birnbaum, Kenneth D (December 2021) Ground tissue circuitry regulates organ complexity in maize and Setaria. Science, 374 (6572). pp. 1247-1252. ISSN 0036-8075
Osterbaan, Larissa J, Hoyle, Victoria, Curtis, Michelle, DeBlasio, Stacy, Rivera, Keith D, Heck, Michelle, Fuchs, Marc (May 2021) Identification of protein interactions of grapevine fanleaf virus RNA-dependent RNA polymerase during infection of by affinity purification and tandem mass spectrometry. The Journal of general virology, 102 (5). ISSN 1465-2099
Osterbaan, Larissa J, Hoyle, Victoria, Curtis, Michelle, DeBlasio, Stacy, Rivera, Keith D, Heck, Michelle, Fuchs, Marc (May 2021) Identification of protein interactions of grapevine fanleaf virus RNA-dependent RNA polymerase during infection of by affinity purification and tandem mass spectrometry. The Journal of general virology, 102 (5). ISSN 1465-2099
Ostrovsky, A, Hillman-Jackson, J, Bouvier, D, Clements, D, Afgan, E, Blankenberg, D, Schatz, MC, Nekrutenko, A, Taylor, J, Team, TG, Lariviere, D (February 2021) Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update. Current Protocols, 1 (2). ISSN 2691-1299
Panea, C, Zhang, R, VanValkenburgh, J, Ni, M, Adler, C, Wei, Y, Ochoa, F, Schmahl, J, Tang, Y, Siao, CJ, Poueymirou, W, Espert, J, Lim, WK, Atwal, GS, Murphy, AJ, Sleeman, MA, Hovhannisyan, Z, Haxhinasto, S (July 2021) Butyrophilin-like 2 regulates site-specific adaptations of intestinal γδ intraepithelial lymphocytes. Communications Biology, 4 (1). ISSN 2399-3642 (In Press)
Papayannakos, Christopher J, DeVoti, James A, Israr, Mohd, Alsudani, Habeeb, Bonagura, Vincent, Steinberg, Bettie M (July 2021) Extracellular vesicles produced by primary human keratinocytes in response to TLR agonists induce stimulus-specific responses in antigen-presenting cells. Cellular Signalling, 83. p. 109994. ISSN 0898-6568
Peng, Hanchuan, Xie, Peng, Liu, Lijuan, Kuang, Xiuli, Wang, Yimin, Qu, Lei, Gong, Hui, Jiang, Shengdian, Li, Anan, Ruan, Zongcai, Ding, Liya, Yao, Zizhen, Chen, Chao, Chen, Mengya, Daigle, Tanya L, Dalley, Rachel, Ding, Zhangcan, Duan, Yanjun, Feiner, Aaron, He, Ping, Hill, Chris, Hirokawa, Karla E, Hong, Guodong, Huang, Lei, Kebede, Sara, Kuo, Hsien-Chi, Larsen, Rachael, Lesnar, Phil, Li, Longfei, Li, Qi, Li, Xiangning, Li, Yaoyao, Li, Yuanyuan, Liu, An, Lu, Donghuan, Mok, Stephanie, Ng, Lydia, Nguyen, Thuc Nghi, Ouyang, Qiang, Pan, Jintao, Shen, Elise, Song, Yuanyuan, Sunkin, Susan M, Tasic, Bosiljka, Veldman, Matthew B, Wakeman, Wayne, Wan, Wan, Wang, Peng, Wang, Quanxin, Wang, Tao, Wang, Yaping, Xiong, Feng, Xiong, Wei, Xu, Wenjie, Ye, Min, Yin, Lulu, Yu, Yang, Yuan, Jia, Yuan, Jing, Yun, Zhixi, Zeng, Shaoqun, Zhang, Shichen, Zhao, Sujun, Zhao, Zijun, Zhou, Zhi, Huang, Z Josh, Esposito, Luke, Hawrylycz, Michael J, Sorensen, Staci A, Yang, X William, Zheng, Yefeng, Gu, Zhongze, Xie, Wei, Koch, Christof, Luo, Qingming, Harris, Julie A, Wang, Yun, Zeng, Hongkui (October 2021) Morphological diversity of single neurons in molecularly defined cell types. Nature, 598 (7879). pp. 174-181. ISSN 0028-0836
Pereira, L, Sapkota, M, Alonge, M, Zheng, Y, Zhang, Y, Razifard, H, Taitano, NK, Schatz, MC, Fernie, AR, Wang, Y, Fei, Z, Caicedo, AL, Tieman, DM, van der Knaap, E (June 2021) Natural Genetic Diversity in Tomato Flavor Genes. Frontiers in Plant Science, 12. ISSN 1664-462X
Petti, Samantha, Bhattacharya, Nicholas, Rao, Roshan, Dauparas, Justas, Thomas, Neil, Zhou, Juannan, Rush, Alexander M, Koo, Peter K, Ovchinnikov, Sergey (October 2021) End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. BioRxiv. (Unpublished)
Phatnani, H, Kwan, J, Sareen, D, Broach, JR, Simmons, Z, Arcila-Londono, X, Lee, EB, Van Deerlin, VM, Shneider, NA, Fraenkel, E, Ostrow, LW, Baas, F, Zaitlen, N, Berry, JD, Malaspina, A, Fratta, P, Cox, GA, Thompson, LM, Finkbeiner, S, Dardiotis, E, Miller, TM, Chandran, S, Pal, S, Hornstein, E, MacGowan, DJ, Heiman-Patterson, T, Hammell, MG, Patsopoulos, NA, Butovsky, O, Dubnau, J, Nath, A, Bowser, R, Harms, M, Poss, M, Phillips-Cremins, J, Crary, J, Atassi, N, Lange, DJ, Adams, DJ, Stefanis, L, Gotkine, M, Baloh, RH, Babu, S, Raj, T, Paganoni, S, Shalem, O, Smith, C, Zhang, B, Harris, B, Broce, I, Drory, V, Ravits, J, McMillan, C, Menon, V, Wu, L, Altschuler, S, Li, J, Lim, RG, Kaye, JA, Dardov, V, Coyne, AN, Wu, J, Milani, P, Cheng, A, Thompson, TG, Ornelas, L, Frank, A, Adam, M, Banuelos, MG, Casale, M, Cox, V, Escalante-Chong, R, Daigle, JG, Gomez, E, Hayes, L, Holewenski, R, Lei, S, Lenail, A, Lima, L, Mandefro, B, Matlock, A, Panther, L, Patel-Murray, NL, Pham, J, Ramamoorthy, D, Sachs, K, Shelley, B, Stocksdale, J, Trost, H, Wilhelm, M, Venkatraman, V, Wassie, BT, Wyman, S, Yang, S, Van Eyk, JE, Lloyd, TE, Finkbeiner, S, Rothstein, JD, Svendsen, CN (November 2021) An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients. iScience, 24 (11). p. 103221. ISSN 2589-0042
Pisano, Thomas J, Dhanerawala, Zahra M, Kislin, Mikhail, Bakshinskaya, Dariya, Engel, Esteban A, Hansen, Ethan J, Hoag, Austin T, Lee, Junuk, de Oude, Nina L, Venkataraju, Kannan Umadevi, Verpeut, Jessica L, Hoebeek, Freek E, Richardson, Ben D, Boele, Henk-Jan, Wang, Samuel S-H (September 2021) Homologous organization of cerebellar pathways to sensory, motor, and associative forebrain. Cell reports, 36 (12). p. 109721. ISSN 2211-1247
Pisupati, Sashank, Chartarifsky-Lynn, Lital, Khanal, Anup, Churchland, Anne K (January 2021) Lapses in perceptual decisions reflect exploration. eLife, 10. pp. 1-27. ISSN 2050-084X
Pouchelon, Gabrielle, Dwivedi, Deepanjali, Bollmann, Yannick, Agba, Chimuanya K, Xu, Qing, Mirow, Andrea MC, Kim, Sehyun, Qiu, Yanjie, Sevier, Elaine, Ritola, Kimberly D, Cossart, Rosa, Fishell, Gord (November 2021) The organization and development of cortical interneuron presynaptic circuits are area specific. Cell Reports, 37 (6). p. 109993. ISSN 2211-1247
Rallis, KS, Kleeman, SO, Grant, M, Ordidge, KL, Sahdev, A, Powles, T (January 2021) Radiomics for Renal Cell Carcinoma: Predicting Outcomes from Immunotherapy and Targeted Therapies—A Narrative Review. European Urology Focus. ISSN 2405-4569
Ranallo-Benavidez, T Rhyker, Lemmon, Zachary, Soyk, Sebastian, Aganezov, Sergey, Salerno, William J, McCoy, Rajiv C, Lippman, Zachary B, Schatz, Michael C, Sedlazeck, Fritz J (May 2021) Optimized sample selection for cost-efficient long-read population sequencing. Genome Research, 31 (5). pp. 910-918. ISSN 1088-9051
Ricardo-Lax, Inna, Luna, Joseph M, Thao, Tran Thi Nhu, Le Pen, Jérémie, Yu, Yingpu, Hoffmann, H-Heinrich, Schneider, William M, Razooky, Brandon S, Fernandez-Martinez, Javier, Schmidt, Fabian, Weisblum, Yiska, Trüeb, Bettina Salome, Berenguer Veiga, Inês, Schmied, Kimberly, Ebert, Nadine, Michailidis, Eleftherios, Peace, Avery, Sánchez-Rivera, Francisco J, Lowe, Scott W, Rout, Michael P, Hatziioannou, Theodora, Bieniasz, Paul D, Poirier, John T, MacDonald, Margaret R, Thiel, Volker, Rice, Charles M (October 2021) Replication and single-cycle delivery of SARS-CoV-2 replicons. Science. ISSN 0036-8075
Rosado, Daniele, Ackermann, Amanda, Spassibojko, Olya, Rossi, Magdalena, Pedmale, Ullas V (October 2021) WRKY transcription factors and ethylene signaling modify root growth during the shade avoidance response. Plant Physiology. ISSN 1532-2548
Rozowsky, Joel, Drenkow, Jorg, Yang, Yucheng, Gursoy, Gamze, Galeev, Timur, Borsari, Beatrice, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Gao, Jiahao, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Liu, Jason, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Adrian, Jessika, Aganezov, Sergey, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Tianxiao, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, Seth, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Cherry, Michael, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Snyder, Michael, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Guigo, Roderic, Bernstein, Bradley, Gingeras, Thomas, Gerstein, Mark (April 2021) Multi-tissue integrative analysis of personal epigenomes. BioRxiv. (Unpublished)
Ruiz-Ortiz, Jenelys, Tollkuhn, Jessica (January 2021) Specificity in sociogenomics: Identifying causal relationships between genes and behavior. Hormones and Behaviour, 127. p. 104882. ISSN 0018-506X
Rupert, Deborah D, Alvarez, George V, Burdge, Eric J, Nahvi, Roxanna J, Schell, Spencer M, Faustino, Francis L (November 2021) Student-Run Free Clinics Stand at a Critical Junction Between Undergraduate Medical Education, Clinical Care, and Advocacy. Academic Medicine, Publis. ISSN 1040-2446
Safaric Tepes, Polona, Pal, Debjani, Lindsted, Trine, Ibarra, Ingrid, Lujambio, Amaia, Jimenez Sabinina, Vilma, Senturk, Serif, Miller, Madison, Korimerla, Navya, Huang, Jiahao, Glassman, Lawrence, Lee, Paul, Zeltsman, David, Hyman, Kevin, Esposito, Michael, Hannon, Greg, Sordella, Raffaella (July 2021) An epigenetic switch regulates the ontogeny of AXL positive/EGFR-TKI resistant cells by modulating miR-335 expression. eLife, 10. ISSN 2050-084X
Safaric Tepes, Polona, Segovia, Danilo, Jevtic, Sania, Ramirez, Daniel, Lyons, Scott K, Sordella, Raffaella (November 2021) Patient-derived xenografts and in vitro model show rationale for imatinib mesylate repurposing in HEY1-NCoA2-driven mesenchymal chondrosarcoma. Laboratory Investigation. ISSN 0023-6837
Schmack, K, Bosc, M, Ott, T, Sturgill, JF, Kepecs, A (April 2021) Striatal dopamine mediates hallucination-like perception in mice. Science, 372 (6537). eabf4740-eabf4740. ISSN 0036-8075
Schmack, Katharina, Bosc, Marion, Sturgill, James, Ott, Torben, Kepecs, Adam (May 2021) Hallucination-Like Perception in Mice Provides Neural-Circuit Insights Into Dopamine Hypothesis of Psychosis. In: Society of Biological Psychiatry Annual Meeting.
Schmack, Katharina, Ott, Torben, Kepecs, Adam (November 2021) Computational Psychiatry Across Species to Study the Biology of Hallucinations. JAMA Psychiatry. ISSN 2168-622X
Schwartz, Christopher J, Brogi, Edi, Marra, Antonio, Da Cruz Paula, Arnaud F, Nanjangud, Gouri J, da Silva, Edaise M, Patil, Sujata, Shah, Shreena, Ventura, Katia, Razavi, Pedram, Norton, Larry, D'alfonso, Timothy, Weigelt, Britta, Pareja, Fresia, Reis-Filho, Jorge S, Wen, Hannah Y (October 2021) The clinical behavior and genomic features of the so-called adenoid cystic carcinomas of the solid variant with basaloid features. Modern Pathology. ISSN 0893-3952
Seidman, Andrew D, de Stanchina, Elisa, Norton, Larry, Morikawa, Aki (January 2021) Comparative Effectiveness Research Needs to Consider Optimal Dosing and Scheduling. Journal of Clinical Oncology, 39 (3). pp. 253-254. ISSN 0732-183X
Sharma, A, Jayakumar, J, Sankaran, N, Mitra, PP, Chakraborti, S, Sreenivasa Kumar, P (January 2021) ConnExt-BioBERT: Leveraging Transfer Learning for Brain-Connectivity Extraction from Neuroscience Articles. In: International Conference on Brain Informatics.
Sharma, Ashika, Jayakumar, Jaikishan, Mitra, Partha P, Chakraborti, Sutanu, Kumar, P Sreenivasa (June 2021) Application of Supervised Machine Learning to Extract Brain Connectivity Information from Neuroscience Research Articles. Interdisciplinary Sciences: Computational Life Sciences. ISSN 1913-2751
Shen, Yang, Wang, Julia, Navlakha, Saket (August 2021) A Correspondence between Normalization Strategies in Artificial and Biological Neural Networks. Neural Computation. pp. 1-25. ISSN 0899-7667
Sheu, Yi-Jun, Kawaguchi, Risa Karakida, Gillis, Jesse, Stillman, Bruce (May 2021) Prevalent and Dynamic Binding of the Cell Cycle Checkpoint Kinase Rad53 to Gene Promoters. BioRxiv. (Unpublished)
Shuvaev, Sergey A, Tran, Ngoc B, Stephenson-Jones, Marcus, Li, Bo, Koulakov, Alexei A (January 2021) Neural Networks With Motivation. Frontiers in Systems Neuroscience, 14. p. 609316. ISSN 1662-5137
Siepel, Adam (January 2021) A Unified Probabilistic Modeling Framework for Eukaryotic Transcription Based on Nascent RNA Sequencing Data. BioRxiv. (Unpublished)
Silva, Talita M, Borniger, Jeremy C, Alves, Michele Joana, Alzate Correa, Diego, Zhao, Jing, Fadda, Paolo, Toland, Amanda Ewart, Takakura, Ana C, Moreira, Thiago S, Czeisler, Catherine M, Otero, José Javier (April 2021) Machine learning approaches reveal subtle differences in breathing and sleep fragmentation in Phox2b-derived astrocytes ablated mice. Journal of Neurophysiology, 125 (4). pp. 1164-1179. ISSN 0022-3077
Skalenko, Kyle, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina, Winkelman, Jared, Cope, Alexander, Taylor, Deanne, Shah, Premal, Ebright, Richard, Kinney, Justin, Zhang, Yu, Nickels, Bryce (April 2021) Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. BioRxiv. (Unpublished)
Skalenko, Kyle S, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina O, Winkelman, Jared T, Cope, Alexander L, Taylor, Deanne M, Shah, Premal, Ebright, Richard H, Kinney, Justin B, Zhang, Yu, Nickels, Bryce E (July 2021) Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. Proceedings of the National Academy of Sciences of USA, 118 (27). e2106388118-e2106388118. ISSN 0027-8424
Smedley, Christopher J, Homer, Joshua A, Gialelis, Timothy L, Barrow, Andrew S, Koelln, Rebecca A, Moses, John Edward (November 2021) Accelerated SuFEx Click Chemistry For Modular Synthesis. Angewandte Chemie International Edition. ISSN 1433-7851
Sroka, Martyna W, Vakoc, Christopher R (February 2021) An epigenetic tipping point in cancer comes under the microscope. Nature, 590 (7846). pp. 399-400. ISSN 0028-0836
Steele, Nina G, Biffi, Giulia, Kemp, Samantha, Zhang, Yaqing, Drouillard, Donovan, Syu, LiJyun, Hao, Yuan, Oni, Tobiloba, Brosnan, Erin, Elyada, Ela, Doshi, Abhishek, Hansma, Christa, Espinoza, Carlos, Abbas, Ahmed, The, Stephanie, Irizarry-Negron, Valerie, Halbrook, Christopher, Franks, Nicole, Hoffman, Megan, Carpenter, Eileen, Nwosu, Zeribe, Park, Youngkyu, Crawford, Howard, Lyssiotis, Costas, Frankel, Timothy, Rao, Arvind, Bednar, Filip, Dlugosz, Andrzej, Preall, Jonathan, Tuveson, David, Allen, Benjamin, Di Magliano, Marina Pasca (July 2021) Inhibition of Hedgehog signaling alters fibroblast composition in pancreatic cancer. In: AACR Annual Meeting 2021.
Steele, Nina G, Biffi, Giulia, Kemp, Samantha B, Zhang, Yaqing, Drouillard, Donovan, Syu, LiJyun, Hao, Yuan, Oni, Tobiloba E, Brosnan, Erin, Elyada, Ela, Doshi, Abhishek, Hansma, Christa, Espinoza, Carlos, Abbas, Ahmed, The, Stephanie, Irizarry-Negron, Valerie, Halbrook, Christopher J, Franks, Nicole E, Hoffman, Megan T, Brown, Kristee, Carpenter, Eileen S, Nwosu, Zeribe C, Johnson, Craig, Lima, Fatima, Anderson, Michelle A, Park, Youngkyu, Crawford, Howard C, Lyssiotis, Costas A, Frankel, Timothy L, Rao, Arvind, Bednar, Filip, Dlugosz, Andrzej A, Preall, Jonathan B, Tuveson, David A, Allen, Benjamin L, Pasca di Magliano, Marina (April 2021) Inhibition of Hedgehog Signaling Alters Fibroblast Composition in Pancreatic Cancer. Clinical Cancer Research, 27 (7). pp. 2023-2037. ISSN 1078-0432
Su, Q, Kim, SY, Adewale, F, Zhou, Y, Aldler, C, Ni, M, Wei, Y, Burczynski, ME, Atwal, GS, Sleeman, MW, Murphy, AJ, Xin, Y, Cheng, X (November 2021) Single-cell RNA transcriptome landscape of hepatocytes and non-parenchymal cells in healthy and NAFLD mouse liver. iScience, 24 (11). p. 103233. ISSN 2589-0042
Sun, Lijuan, Kees, Tim, Almeida, Ana Santos, Liu, Bodu, He, Xue-Yan, Ng, David, Han, Xiao, Spector, David L, McNeish, Iain A, Gimotty, Phyllis, Adams, Sylvia, Egeblad, Mikala (September 2021) Activating a collaborative innate-adaptive immune response to control metastasis. Cancer Cell. ISSN 1535-6108
Sun, Yu-Chi, Chen, Xiaoyin, Fischer, Stephan, Lu, Shaina, Zhan, Huiqing, Gillis, Jesse, Zador, Anthony M (May 2021) Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. Nature Neuroscience. ISSN 1097-6256
Sutton, Elizabeth J, Braunstein, Lior Z, El-Tamer, Mahmoud B, Brogi, Edi, Hughes, Mary, Bryce, Yolanda, Gluskin, Jill S, Powell, Simon, Woosley, Alyssa, Tadros, Audree, Sevilimedu, Varadan, Martinez, Danny F, Toni, Larowin, Smelianskaia, Olga, Nyman, C Gregory, Razavi, Pedram, Norton, Larry, Fung, Maggie M, Sedorovich, James D, Sacchini, Virgilio, Morris, Elizabeth A (January 2021) Accuracy of Magnetic Resonance Imaging-Guided Biopsy to Verify Breast Cancer Pathologic Complete Response After Neoadjuvant Chemotherapy: A Nonrandomized Controlled Trial. Jama Network Open, 4 (1). e2034045. ISSN 2574-3805
Syrjanen, Johanna, Michalski, Kevin, Kawate, Toshimitsu, Furukawa, Hiro (April 2021) On the molecular nature of large-pore channels. Journal of Molecular Biology. p. 166994. ISSN 0022-2836
Syrjanen, Johanna L, Michalski, Kevin, Chou, Tsung-Han, Rao, Shanlin, Henze, Eric, Kumpf, Julia M, Simorowski, Noriko, Grant, Tim, Grigorieff, Nikolaus, Tucker, Stephen J, Kawate, Toshimitsu, Furukawa, Hiro (February 2021) Exploring the Three-Dimensional Architectures of Two Families of Large Pore Channels (CALHM1,2 and Pannexin1). In: Biophysical Society Annual Meeting.
Takao, Sumiko, Forbes, Lauren, Uni, Masahiro, Cheng, Shuyuan, Pineda, Jose Mario Bello, Tarumoto, Yusuke, Cifani, Paolo, Minuesa, Gerard, Chen, Celine, Kharas, Michael G, Bradley, Robert K, Vakoc, Christopher R, Koche, Richard P, Kentsis, Alex (February 2021) Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. eLife, 10. pp. 1-46. ISSN 2050-084X
Taranda, Julian, Mathew, Grinu, Watrud, Kaitlin, El-Amine, Nour, Lee, Matthew F, Elowsky, Corey, Bludova, Anastasiia, Escobar Avelar, Sintia, Nowak, Dawid G, Wee, Tse-Luen, Wilkinson, John E, Trotman, Lloyd C, Osten, Pavel (November 2021) Combined whole-organ imaging at single-cell resolution and immunohistochemical analysis of prostate cancer and its liver and brain metastases. Cell Reports, 37 (7). p. 110027. ISSN 2211-1247
Tello-Ruiz, M. K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D., D'Eustachio, P., Stein, L. D., Gupta, A., Xu, W., Regala, J., Papatheodorou, I., Kersey, P. J., Flicek, P., Taylor, C., Jaiswal, P., Ware, D. (January 2021) Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res, 49 (D1). D1452-d1463. ISSN 0305-1048 (Print)0305-1048
Tello-Ruiz, Marcela Karey, Wei, Sharon, Olson, Andrew, Gupta, Parul, Naithani, Sushma, Chougule, Kapeel, Kumari, Sunita, Kumar, Vivek, D'Eustachio, Peter, Papatheodorou, Irene, Contreras-Moreira, Bruno, Jaiswal, Pankaj, Ware, Doreen (September 2021) Gramene's Reference Genomes and Comparative Resources for Horticultural Species. In: Abstracts of Presentations from American Society of Horticultural Science 2021 Annual Conference.
Thielen, Peter M, Wohl, Shirlee, Mehoke, Thomas, Ramakrishnan, Srividya, Kirsche, Melanie, Falade-Nwulia, Oluwaseun, Trovão, Nídia S, Ernlund, Amanda, Howser, Craig, Sadowski, Norah, Morris, C Paul, Hopkins, Mark, Schwartz, Matthew, Fan, Yunfan, Gniazdowski, Victoria, Lessler, Justin, Sauer, Lauren, Schatz, Michael C, Evans, Jared D, Ray, Stuart C, Timp, Winston, Mostafa, Heba H (March 2021) Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area. JCI Insight, 6 (6). ISSN 2379-3708
Tollkuhn, Jessica (October 2021) NEURAL TARGET GENES OF ESTROGEN RECEPTOR ALPHA SPECIFY SEX DIFFERENCES IN THE BRAIN. In: 68th Annual Meeting of the American Academy of Child & Adolescent Psychiatry.
Tracey, KJ (July 2021) From human to mouse and back offers hope for patients with fibromyalgia. Journal of Clinical Investigation, 131 (13). ISSN 0021-9738
Tran, Thu M, Demesa-Arevalo, Edgar, Kitagawa, Munenori, Garcia-Aguilar, Marcelina, Grimanelli, Daniel, Jackson, David (April 2021) An Optimized Whole-Mount Immunofluorescence Method for Shoot Apices. Curr Protoc, 1 (4). e101. ISSN 2691-1299
Trivedi, Gaurang, Inoue, Daichi, Zhang, Lingbo (July 2021) Targeting low-risk myelodysplastic syndrome with novel therapeutic strategies. Trends in Molecular Medicine. ISSN 1471-4914
Truong, Thu H, Benner, Elizabeth A, Hagen, Kyla M, Temiz, Nuri A, Kerkvliet, Carlos Perez, Wang, Ying, Cortes-Sanchez, Emilio, Yang, Chieh-Hsiang, Trousdell, Marygrace C, Pengo, Thomas, Guillen, Katrin P, Welm, Bryan E, Dos Santos, Camila O, Telang, Sucheta, Lange, Carol A, Ostrander, Julie H (June 2021) PELP1/SRC-3-dependent regulation of metabolic PFKFB kinases drives therapy resistant ER+ breast cancer. Oncogene. ISSN 0950-9232
Tuveson, David A (April 2021) Fighting the Sixth Decade of the Cancer War with Better Cancer Models. Cancer Discovery, 11 (4). pp. 801-804. ISSN 2159-8274
Urai, Anne E, Aguillon-Rodriguez, Valeria, Laranjeira, Inês C, Cazettes, Fanny, International Brain Laboratory, , Mainen, Zachary F, Churchland, Anne K (January 2021) Citric Acid Water as an Alternative to Water Restriction for High-Yield Mouse Behavior. eNeuro, 8 (1). pp. 1-8. ISSN 2373-2822
Vasudevan, Anand, Schukken, Klaske M, Sausville, Erin L, Girish, Vishruth, Adebambo, Oluwadamilare A, Sheltzer, Jason M (February 2021) Aneuploidy as a promoter and suppressor of malignant growth. Nature Reviews Cancer, 21 (2). pp. 89-103. ISSN 1474-175X
Vaughn, Justin N, Korani, Walid, Stein, Joshua C, Edwards, Jeremy D, Peterson, Daniel G, Simpson, Sheron A, Youngblood, Ramey C, Grimwood, Jane, Chougule, Kapeel, Ware, Doreen H, McClung, Anna M, Scheffler, Brian E (March 2021) Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genetics, 17 (3). e1009389. ISSN 1553-7404
Vornhagen, Jay, Bassis, Christine M, Ramakrishnan, Srividya, Hein, Robert, Mason, Sophia, Bergman, Yehudit, Sunshine, Nicole, Fan, Yunfan, Holmes, Caitlyn L, Timp, Winston, Schatz, Michael C, Young, Vincent B, Simner, Patricia J, Bachman, Michael A (April 2021) A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor. PLoS Pathogens, 17 (4). e1009537. ISSN 1553-7366
Vranken, Sofie, Wernberg, Thomas, Scheben, Armin, Severn-Ellis, Anita, Batley, Jacqueline, Philipp, Bayer Emanuel, Edwards, David, Wheeler, David, Coleman, Melinda Ann (May 2021) Genotype-environment mismatch of kelp forests under climate change. Molecular Ecology. ISSN 0962-1083
Wan, Ledong, Lin, Kuan-Ting, Rahman, Mohammad A, Wang, Zhikai, Park, Youngkyu, Tuveson, David A, Krainer, Adrian R (November 2021) Loss of compensatory feedback mechanism involving splicing factor SRSF1 accelerates Kras(G12D)-mediated pancreatic cancer initiation. In: AACR Virtual Special Conference on Pancreatic Cancer.
Wang, Bor-Shuen, Bernardez Sarria, Maria Sol, An, Xu, He, Miao, Alam, Nazia M, Prusky, Glen T, Crair, Michael C, Huang, Z Josh (February 2021) Retinal and Callosal Activity-Dependent Chandelier Cell Elimination Shapes Binocularity in Primary Visual Cortex. Neuron, 109 (3). 502-515.e7. ISSN 0896-6273
Wang, Kejun, Hu, Haifei, Tian, Yadong, Li, Jingyi, Scheben, Armin, Zhang, Chenxi, Li, Yiyi, Wu, Junfeng, Yang, Lan, Fan, Xuewei, Sun, Guirong, Li, Donghua, Zhang, Yanhua, Han, Ruili, Jiang, Ruirui, Huang, Hetian, Yan, Fengbin, Wang, Yanbin, Li, Zhuanjian, Li, Guoxi, Liu, Xiaojun, Li, Wenting, Edwards, David, Kang, Xiangtao (July 2021) The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Molecular Biology and Evolution. ISSN 0737-4038
Wang, Minghui, Gallo, Nicholas B, Tai, Yilin, Li, Bo, Van Aelst, Linda (April 2021) Oligophrenin-1 moderates behavioral responses to stress by regulating parvalbumin interneuron activity in the medial prefrontal cortex. Neuron. ISSN 0896-6273
Wang, Xingang, Aguirre, Lyndsey, Rodríguez-Leal, Daniel, Hendelman, Anat, Benoit, Matthias, Lippman, Zachary B (April 2021) Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nature Plants, 7 (4). pp. 419-427. ISSN 2055-026X
Ward, Zachary J, Atun, Rifat, Hricak, Hedvig, Asante, Kwanele, McGinty, Geraldine, Sutton, Elizabeth J, Norton, Larry, Scott, Andrew M, Shulman, Lawrence N (August 2021) The impact of scaling up access to treatment and imaging modalities on global disparities in breast cancer survival: a simulation-based analysis. The Lancet Oncology. ISSN 1470-2045
Wei, Yiliang, Huang, Yu-Han, Skopelitis, Damianos S, Iyer, Shruti V, Costa, Ana SH, Yang, Zhaolin, Kramer, Melissa, Adelman, Emmalee R, Klingbeil, Olaf, Demerdash, Osama E, Polyanskaya, Sofya A, Chang, Kenneth, Goodwin, Sara, Hodges, Emily, McCombie, W Richard, Figueroa, Maria E, Vakoc, Christopher R (September 2021) SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia. Cancer Discovery. candisc.1849.2020-candisc.1849.2020. ISSN 2159-8274
Werner, Jonathan, Ballouz, Sara, Hover, John, Gillis, Jesse (September 2021) Cross-tissue analysis of allelic X-chromosome inactivation ratios resolves features of human development. BioRxiv. (Unpublished)
Wiede, Florian, Lu, Kun-Hui, Du, Xin, Zeissig, Mara N, Xu, Rachel, Goh, Pei Kee, Xirouchaki, Chrysovalantou E, Hogarth, Samuel J, Greatorex, Spencer, Sek, Kevin, Daly, Roger J, Beavis, Paul A, Darcy, Phillip K, Tonks, Nicholas K, Tiganis, Tony (November 2021) PTP1B is an intracellular checkpoint that limits T cell and CAR T cell anti-tumor immunity. Cancer Discovery. ISSN 2159-8274
Williams, Alexia, Pena, Catherine, Laman-Maharg, Abigail, Ordonez-Sanchez, Evelyn, Xu, Christine, Ramos-Maciel, Stephanie, Hao, Rebecca, Yokoyama, Sae, Labonte, Benoit, Wu, Melody, Tollkuhn, Jessica, Zachariou, Venetia, Nestler, Eric, Trainor, Brian (May 2021) The Effects of Regulator of G-Protein Signaling 2 (RGS2) on Depression-Like Behavior in Female California Mice. In: Society for Biological Psychiatry Annual Meeting.
Williams, Edward H, Flint, Thomas R, Connell, Claire M, Giglio, Daniel, Lee, Hassal, Ha, Taehoon, Gablenz, Eva, Bird, Nicholas J, Weaver, James MJ, Potts, Harry, Whitley, Cameron T, Bookman, Michael A, Lynch, Andy G, Meyer, Hannah V, Tavaré, Simon, Janowitz, Tobias (March 2021) CamGFR v2: A New Model for Estimating the Glomerular Filtration Rate from Standardized or Non-standardized Creatinine in Patients with Cancer. Clinical Cancer Research, 27 (5). pp. 1381-1390. ISSN 1078-0432
Wojnarowicz, Paulina M, Escolano, Marta Garcia, Huang, Yun-Han, Desai, Bina, Chin, Yvette, Shah, Riddhi, Xu, Sijia, Yadav, Saurabh, Yaklichkin, Sergey, Ouerfelli, Ouathek, Soni, Rajesh Kumar, Philip, John, Montrose, David C, Healey, John H, Rajasekhar, Vinagolu K, Garland, William A, Ratiu, Jeremy, Zhuang, Yuan, Norton, Larry, Rosen, Neal, Hendrickson, Ronald C, Zhou, Xi Kathy, Iavarone, Antonio, Massague, Joan, Dannenberg, Andrew J, Lasorella, Anna, Benezra, Robert (May 2021) Anti-tumor effects of an ID antagonist with no observed acquired resistance. npj Breast Cancer, 7 (1). p. 58. ISSN 2374-4677
Wolter, Felix, Schindele, Patrick, Beying, Natalja, Scheben, Armin, Puchta, Holger (August 2021) Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants. The Plant Cell. ISSN 1532-298X
Wong, Willard, Brogi, Edi, Reis-Filho, Jorge S, Plitas, George, Robson, Mark, Norton, Larry, Morrow, Monica, Wen, Hannah Y (July 2021) Poor response to neoadjuvant chemotherapy in metaplastic breast carcinoma. npj Breast Cancer, 7 (1). p. 96. ISSN 2374-4677
Wortman, Juliana C, He, Ting-Fang, Solomon, Shawn, Zhang, Robert Z, Rosario, Anthony, Wang, Roger, Tu, Travis Y, Schmolze, Daniel, Yuan, Yuan, Yost, Susan E, Li, Xuefei, Levine, Herbert, Atwal, Gurinder, Lee, Peter P, Yu, Clare C (July 2021) Spatial distribution of B cells and lymphocyte clusters as a predictor of triple-negative breast cancer outcome. npj Breast Cancer, 7 (1). p. 84. ISSN 2374-4677
Wu, Yaoyao, Johnson, Lynn, Song, Baoxing, Romay, Cinta, Stitzer, Michelle, Siepel, Adam, Buckler, Edward, Scheben, Armin (June 2021) A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants. BioRxiv. (Unpublished)
Xu, Zhuwei, Green, Brian, Benoit, Nicole, Sobel, Jack D, Schatz, Michael C, Wheelan, Sarah, Cormack, Brendan P (March 2021) Cell wall protein variation, break-induced replication, and subtelomere dynamics in Candida glabrata. Molecular Microbiology. ISSN 0950-382X
Xue, Alexander T, Schrider, Daniel R, Kern, Andrew D, Ag1000g Consortium, (March 2021) Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning. Molecular Biology and Evolution, 38 (3). pp. 1168-1183. ISSN 0737-4038
Yan, Stephanie M, Sherman, Rachel M, Taylor, Dylan J, Nair, Divya R, Bortvin, Andrew N, Schatz, Michael C, McCoy, Rajiv C (September 2021) Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife, 10. ISSN 2050-084X
Yang, Huan, Lundbäck, Peter, Ottosson, Lars, Erlandsson-Harris, Helena, Venereau, Emilie, Bianchi, Marco E, Al-Abed, Yousef, Andersson, Ulf, Tracey, Kevin J (June 2021) Redox modifications of cysteine residues regulate the cytokine activity of HMGB1. Molecular Medicine, 27 (1). p. 58. ISSN 1076-1551
Yang, Huan, Zeng, Qiong, Silverman, Harold A, Gunasekaran, Manojkumar, George, Sam J, Devarajan, Alex, Addorisio, Meghan E, Li, Jianhua, Tsaava, Téa, Shah, Vivek, Billiar, Timothy R, Wang, Haichao, Brines, Michael, Andersson, Ulf, Pavlov, Valentin A, Chang, Eric H, Chavan, Sangeeta S, Tracey, Kevin J (August 2021) HMGB1 released from nociceptors mediates inflammation. Proceedings of the National Academy of Sciences of USA, 118 (33). e2102034118-e2102034118. ISSN 0027-8424
Yang, Jung-In, Ha, Taehoon, Zhou, Edward, Tzanavaris, Chris, Devoe, Craig E, Zhu, Xinhua, Boyd, Jeff (May 2021) Association of TP53 mutation status and GATA6 amplification with clinical outcome of pancreatic cancer. In: 2021 ASCO Annual Meeting I.
Yang, RS, Xu, F, Wang, YM, Zhong, WS, Dong, L, Shi, YN, Tang, TJ, Sheng, HJ, Jackson, D, Yang, F (December 2021) Glutaredoxins regulate maize inflorescence meristem development via redox control of TGA transcriptional activity. Nature Plants. ISSN 2055-0278
Yang, T, Alessandri-Haber, N, Fury, W, Schaner, M, Breese, R, LaCroix-Fralish, M, Kim, J, Adler, C, Macdonald, LE, Atwal, GS, Bai, Y (October 2021) AdRoit is an accurate and robust method to infer complex transcriptome composition. Communications Biology, 4 (1). ISSN 2399-3642 (In Press)
Yang, Wen-Hsuan, Qiu, Yijian, Stamatatos, Olivia, Janowitz, Tobias, Lukey, Michael J (May 2021) Enhancing the Efficacy of Glutamine Metabolism Inhibitors in Cancer Therapy. Trends in Cancer. ISSN 2405-8033
Yang, Yang, Paul, Anirban, Bach, Thao Nguyen, Huang, Z Josh, Zhang, Michael Q (July 2021) Single-cell alternative polyadenylation analysis delineates GABAergic neuron types. BMC Biology, 19 (1). p. 144. ISSN 1741-7007
Yang, Zhaolin, Wu, Xiaoli S, Wei, Yiliang, Polyanskaya, Sofya A, Iyer, Shruti V, Jung, Moonjung, Lach, Francis P, Adelman, Emmalee R, Klingbeil, Olaf, Milazzo, Joseph P, Kramer, Melissa, Demerdash, Osama E, Chang, Kenneth, Goodwin, Sara, Hodges, Emily, McCombie, W Richard, Figueroa, Maria E, Smogorzewska, Agata, Vakoc, Christopher R (April 2021) Transcriptional silencing of ALDH2 confers a dependency on Fanconi anemia proteins in acute myeloid leukemia. Cancer Discovery. ISSN 2159-8274
Yao, Zizhen, Liu, Hanqing, Xie, Fangming, Fischer, Stephan, Adkins, Ricky S, Aldridge, Andrew I, Ament, Seth A, Bartlett, Anna, Behrens, M Margarita, Van den Berge, Koen, Bertagnolli, Darren, de Bézieux, Hector Roux, Biancalani, Tommaso, Booeshaghi, A Sina, Bravo, Héctor Corrada, Casper, Tamara, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Crichton, Kirsten, Crow, Megan, Dee, Nick, Dougherty, Elizabeth L, Doyle, Wayne I, Dudoit, Sandrine, Fang, Rongxin, Felix, Victor, Fong, Olivia, Giglio, Michelle, Goldy, Jeff, Hawrylycz, Mike, Herb, Brian R, Hertzano, Ronna, Hou, Xiaomeng, Hu, Qiwen, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, Li, Yang Eric, Lucero, Jacinta D, Luo, Chongyuan, Mahurkar, Anup, McMillen, Delissa, Nadaf, Naeem M, Nery, Joseph R, Nguyen, Thuc Nghi, Niu, Sheng-Yong, Ntranos, Vasilis, Orvis, Joshua, Osteen, Julia K, Pham, Thanh, Pinto-Duarte, Antonio, Poirion, Olivier, Preissl, Sebastian, Purdom, Elizabeth, Rimorin, Christine, Risso, Davide, Rivkin, Angeline C, Smith, Kimberly, Street, Kelly, Sulc, Josef, Svensson, Valentine, Tieu, Michael, Torkelson, Amy, Tung, Herman, Vaishnav, Eeshit Dhaval, Vanderburg, Charles R, van Velthoven, Cindy, Wang, Xinxin, White, Owen R, Huang, Z Josh, Kharchenko, Peter V, Pachter, Lior, Ngai, John, Regev, Aviv, Tasic, Bosiljka, Welch, Joshua D, Gillis, Jesse, Macosko, Evan Z, Ren, Bing, Ecker, Joseph R, Zeng, Hongkui, Mukamel, Eran A (October 2021) A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature, 598 (7879). pp. 103-110. ISSN 0028-0836
Yates, Andrew D, Allen, James, Amode, Ridwan M, Azov, Andrey G, Barba, Matthieu, Becerra, Andrés, Bhai, Jyothish, Campbell, Lahcen I, Carbajo Martinez, Manuel, Chakiachvili, Marc, Chougule, Kapeel, Christensen, Mikkel, Contreras-Moreira, Bruno, Cuzick, Alayne, Da Rin Fioretto, Luca, Davis, Paul, De Silva, Nishadi H, Diamantakis, Stavros, Dyer, Sarah, Elser, Justin, Filippi, Carla V, Gall, Astrid, Grigoriadis, Dionysios, Guijarro-Clarke, Cristina, Gupta, Parul, Hammond-Kosack, Kim E, Howe, Kevin L, Jaiswal, Pankaj, Kaikala, Vinay, Kumar, Vivek, Kumari, Sunita, Langridge, Nick, Le, Tuan, Luypaert, Manuel, Maslen, Gareth L, Maurel, Thomas, Moore, Benjamin, Muffato, Matthieu, Mushtaq, Aleena, Naamati, Guy, Naithani, Sushma, Olson, Andrew, Parker, Anne, Paulini, Michael, Pedro, Helder, Perry, Emily, Preece, Justin, Quinton-Tulloch, Mark, Rodgers, Faye, Rosello, Marc, Ruffier, Magali, Seager, James, Sitnik, Vasily, Szpak, Michal, Tate, John, Tello-Ruiz, Marcela K, Trevanion, Stephen J, Urban, Martin, Ware, Doreen, Wei, Sharon, Williams, Gary, Winterbottom, Andrea, Zarowiecki, Magdalena, Finn, Robert D, Flicek, Paul (November 2021) Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. ISSN 0305-1048
Yoon, Seungtai, Munoz, Adriana, Yamrom, Boris, Lee, Yoon-Ha, Andrews, Peter, Marks, Steven, Wang, Zihua, Reeves, Catherine, Winterkorn, Lara, Krieger, Abba M, Buja, Andreas, Pradhan, Kith, Ronemus, Michael, Baldwin, Kristin K, Levy, Dan, Wigler, Michael, Iossifov, Ivan (September 2021) Rates of contributory de novo mutation in high and low-risk autism families. Communications Biology, 4 (1). p. 1026. ISSN 2399-3642
Yu, Allen T, Berasain, Carmen, Bhatia, Sonam, Rivera, Keith, Liu, Bodu, Rigo, Frank, Pappin, Darryl J, Spector, David L (May 2021) PHAROH lncRNA regulates Myc translation in hepatocellular carcinoma via sequestering TIAR. eLife, 10. ISSN 2050-084X
Yu, Jia-Ray, LeRoy, Gary, Bready, Devin, Frenster, Joshua D., Saldaña-Meyer, Ricardo, Jin, Ying, Descostes, Nicolas, Stafford, James M., Placantonakis, Dimitris G., Reinberg, Danny (July 2021) The H3K36me2 writer-reader dependency in H3K27M-DIPG. Science Advances, 7 (29). ISSN 2375-2548
Yuan, Yuxuan, Scheben, Armin, Edwards, David, Chan, Ting-Fung (November 2021) Towards haplotype studies in polyploid plants to assist breeding. Molecular Plant. ISSN 1674-2052
Zahid, Huda, Buchholz, Caroline R, Singh, Manjulata, Ciccone, Michael F, Chan, Alice, Nithianantham, Stanley, Shi, Ke, Aihara, Hideki, Fischer, Marcus, Schönbrunn, Ernst, Dos Santos, Camila O, Landry, Joseph W, Pomerantz, William CK (September 2021) New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. Journal of Medicinal Chemistry. ISSN 0022-2623
Zebell, S (September 2021) A TALENt for reviving old questions about cytoplasmic male sterility. Plant Physiology, 187 (1). pp. 14-16. ISSN 0032-0889
Zebell, Sophia (March 2021) Gene body silencing parental alleles for vigorous hybrid rice. Plant Physiology, 186 (2). pp. 822-823. ISSN 0032-0889
Zebell, Sophia (October 2021) More is more (DNA and cells) with AELs. Plant Physiology, 187 (2). pp. 676-677. ISSN 1532-2548
Zhang, R, Atwal, GS, Lim, WK (March 2021) Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. Patterns, 2 (3). p. 100211. ISSN 2666-3899
Zhang, Wen, Hawkins, Peter G, He, Jing, Gupta, Namita T, Liu, Jinrui, Choonoo, Gabrielle, Jeong, Se W, Chen, Calvin R, Dhanik, Ankur, Dillon, Myles, Deering, Raquel, Macdonald, Lynn E, Thurston, Gavin, Atwal, Gurinder S (May 2021) A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity. Science Advances, 7 (20). eabf5835-eabf5835. ISSN 2375-2548
Zhang, Xian, Guan, Wuqiang, Yang, Tao, Furlan, Alessandro, Xiao, Xiong, Yu, Kai, An, Xu, Galbavy, William, Ramakrishnan, Charu, Deisseroth, Karl, Ritola, Kimberly, Hantman, Adam, He, Miao, Josh Huang, Z, Li, Bo (October 2021) Genetically identified amygdala-striatal circuits for valence-specific behaviors. Nature Neuroscience, 24. pp. 1586-1600. ISSN 1097-6256
Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles, Siepel, Adam (March 2021) Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells. BioRxiv. (Unpublished)
Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles G, Siepel, Adam (August 2021) Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. ISSN 1367-4803
Zhao, Yixin, Lu, Guang-An, Yang, Hao, Lin, Pei, Liufu, Zhongqi, Tang, Tian, Xu, Jin (April 2021) Run or Die in the Evolution of New MicroRNAs-Testing the Red Queen Hypothesis on De Novo New Genes. Molecular Biology and Evolution, 38 (4). pp. 1544-1553. ISSN 0737-4038
Zhu, Chuanmei, Liu, Lei, Crowell, Olivia, Zhao, Hui, Brutnell, Thomas P, Jackson, David, Kellogg, Elizabeth A (2021) The CLV3 Homolog in Setaria viridis Selectively Controls Inflorescence Meristem Size. Frontiers in Plant Science, 12. p. 636749. ISSN 1664-462X
Ziamtsov, I, Faizi, K, Navlakha, S (September 2021) Branch-pipe: Improving graph skeletonization around branch points in 3D point clouds. Remote Sensing, 13 (19). ISSN 2072-4292
Šafarič Tepeš, Polona, Sordella, Raffaella (September 2021) A New Toolkit for Evaluating Gene Functions using Conditional Cas9 Stabilization. Journal of Visualized Experiments (175). ISSN 1940-087X
