Items where Year is 2023

Paper

Abou-Alfa, Ghassan K, Norton, Larry, Global Oncology Medical Diplomacy Working Group (2023) Global Oncology Medical Diplomacy Working Group Inaugural Meeting: Defining Worldwide Barriers to Germline Genomics in Cancer Prevention and Management. Annals of Global Health, 89 (1). p. 16. ISSN 2214-9996

Abrams, Benjamin, Pengo, Thomas, Wee, Tse-Luen, Deagle, Rebecca C, Vuillemin, Nelly, Callahan, Linda M, Smith, Megan A, Kubow, Kristopher E, Girard, Anne-Marie, Rappoport, Joshua Z, Bayles, Carol J, Cameron, Lisa A, Cole, Richard, Brown, Claire M (April 2023) Tissue-Like 3D Standard and Protocols for Microscope Quality Management. Microscopy and Microanalysis, 29 (2). pp. 616-634. ISSN 1431-9276

Acerbi, L, Aguillon-Rodriguez, V, Ahmadi, M, Amjad, J, Angelaki, D, Arlandis, J, Ashwood, ZC, Banga, K, Barrell, H, Bayer, HM, Benson, J, Benson, B, Bhagat, J, Birman, D, Bougrova, K, Boussard, J, Bruijns, SA, Carandini, M, Catarino, J, Cazettes, F, Dan, Y, Davatolagh, F, Dayan, P, Denève, S, Dong, LL, Engel, T, Fabbri, M, Fiete, I, Findling, C, Freitas-Silva, L, Ganguli, S, Gercek, B, Ghani, N, Gordeliy, I, Haetzel, LM, Hausser, M, Hiratani, N, Hofer, S, Hu, F, Huber, F, Hurwitz, C, Khanal, A, Krasniak, CS, Krishnagopal, S, Krumin, M, Langdon, C, Latham, P, Lau, P, Lee, H, Liu, A, Mainen, ZF, Vergara, HM, Mcgrory, C, McMannon, B, Meijer, GT, Melin, M, Meshulam, L, Miska, NJ, Mitelut, C, Mohammadi, Z, Mrsic-Flogel, T, Murakami, M, Noel, JP, Nylund, K, Vazquez, AP, Paninski, L, Pezzotta, A, Picard, S, Pillow, JW, Pouget, A, Roth, N, Roy, NA, Saniee, K, Schaeffer, R, Shi, Y, Socha, KZ, Soitu, C, Svoboda, K, Taheri, M, Tessereau, C, Urai, AE, Varol, E, Wells, MJ, Whiteway, MR, Windolf, C, Witten, I, Wool, LE, Zador, AM, Bonacchi, N, Chapuis, GA, Churchland, AK, DeWitt, EEJ, Faulkner, M, Harris, KD, Huntenburg, JM, Hunter, M, Laranjeira, IC, Rossant, C, Sasaki, M, Schartner, MM (January 2023) A modular architecture for organizing, processing and sharing neurophysiology data. Nature Methods, 20 (3). pp. 403-407. ISSN 1548-7091 (Public Dataset)

Adrover, Jose M, McDowell, Sheri AC, He, Xue-Yan, Quail, Daniela F, Egeblad, Mikala (February 2023) NETworking with cancer: The bidirectional interplay between cancer and neutrophil extracellular traps. Cancer Cell. ISSN 1535-6108

Aggarwal, Disha, Russo, Suzanne, Naik, Payal, Bhatia, Sonam, Spector, David L (February 2023) Establishment and Culture of Patient-Derived Breast Organoids. Journal of Visualized Experiments (192). ISSN 1940-087X

Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel F, McCandlish, David M, Lippman, Zachary B (October 2023) Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382 (6668). pp. 315-320. ISSN 0036-8075

Akagi, Keiko, Symer, David E, Mahmoud, Medhat, Jiang, Bo, Goodwin, Sara, Wangsa, Darawalee, Li, Zhengke, Xiao, Weihong, Dunn, Joe Dan, Ried, Thomas, Coombes, Kevin R, Sedlazeck, Fritz J, Gillison, Maura L (January 2023) Intratumoral heterogeneity and clonal evolution induced by HPV integration. Cancer Discovery. ISSN 2159-8274 (Public Dataset)

Alexander, Katherine A, Yu, Ruofan, Skuli, Nicolas, Coffey, Nathan J, Nguyen, Son, Faunce, Christine, Huang, Hua, Dardani, Ian P, Good, Austin L, Lim, Joan, Li, Catherine, Biddle, Nicholas, Joyce, Eric F, Raj, Arjun, Lee, Daniel, Keith, Brian, Simon, M Celeste, Berger, Shelley L (September 2023) Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer. bioRxiv. (Submitted)

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M, Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G, Johnson, Rory, Murphy, Terence D, Pertea, Mihaela, Pruitt, Kim D, Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A, Yandell, Mark, Carninci, Piero, Salzberg, Steven L (March 2023) The status of the human gene catalogue. (Submitted)

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M, Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G, Johnson, Rory, Murphy, Terence D, Pertea, Mihaela, Pruitt, Kim D, Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A, Yandell, Mark, Carninci, Piero, Salzberg, Steven L (October 2023) The status of the human gene catalogue. Nature, 622 (7981). pp. 41-47. ISSN 0028-0836

Amor, Corina, Fernández-Maestre, Inés, Chowdhury, Saria, Ho, Yu-Jui, Nadella, Sandeep, Graham, Courtenay, Carrasco, Sebastian E, Nnuji-John, Emmanuella, Feucht, Judith, Hinterleitner, Clemens, Barthet, Valentin JA, Boyer, Jacob A, Mezzadra, Riccardo, Wereski, Matthew G, Tuveson, David A, Levine, Ross L, Jones, Lee W, Sadelain, Michel, Lowe, Scott W (September 2023) Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Research Square. (Submitted)

Arteaga, Carlos L, Cleveland, John L, Foti, Margaret, Mesa, Ruben A, Weiner, Louis M, Willman, Cheryl L, Tuveson, David A (September 2023) AACR Cancer Centers Alliance: Fostering Collaboration and Innovation to Advance Lifesaving Scientific Discoveries for Patients. Molecular Cancer Research. OF1-OF3. ISSN 1541-7786

Artz, Oliver, Ackermann, Amanda, Taylor, Laura, Koo, Peter K, Pedmale, Ullas V (January 2023) Light and temperature regulate m6A-RNA modification to regulate growth in plants. bioRxiv. (Submitted)

Avizemer, Ziv, Martí-Gómez, Carlos, Hoch, Shlomo Yakir, McCandlish, David M, Fleishman, Sarel J (April 2023) Evolutionary paths that link orthogonal pairs of binding proteins. Research Square. (Submitted)

Balasooriya, Gayan I, Spector, David L (April 2023) Allele pairing at Sun1-enriched domains at the nuclear periphery via T1A3 tandem DNA repeats. bioRxiv. (Public Dataset) (Submitted)

Balasooriya, Gayan I, Wee, Tse-Luen, Spector, David L (October 2023) A sub-set of guanine- and cytosine-rich genes are actively transcribed at the nuclear Lamin B1 region. bioRxiv. (Public Dataset) (Submitted)

Ballouz, Sara, Kawaguchi, Risa Karakida, Pena, Maria T, Fischer, Stephan, Crow, Megan, French, Leon, Knight, Frank M, Adams, Linda B, Gillis, Jesse (November 2023) The transcriptional legacy of developmental stochasticity. Nature Communications, 14 (1). p. 7226. ISSN 2041-1723 (Public Dataset)

Banerjee, Arkarup, Chen, Feng, Druckmann, Shaul, Long, Michael A (January 2023) Neural dynamics in the rodent motor cortex enables flexible control of vocal timing. bioRxiv. (Submitted)

Barabási, Dániel L, Bianconi, Ginestra, Bullmore, Ed, Burgess, Mark, Chung, SueYeon, Eliassi-Rad, Tina, George, Dileep, Kovács, István A, Makse, Hernán, Nichols, Thomas E, Papadimitriou, Christos, Sporns, Olaf, Stachenfeld, Kim, Toroczkai, Zoltán, Towlson, Emma K, Zador, Anthony M, Zeng, Hongkui, Barabási, Albert-László, Bernard, Amy, Buzsáki, György (August 2023) Neuroscience Needs Network Science. The Journal of Neuroscience, 43 (34). pp. 5989-5995. ISSN 0270-6474

Beechinor, Ryan J, Abidalhassan, Mustafa F, Small, Deborah F, Hoang, Huong K, Lamba, Ramit, Loehfelm, Thomas W, Foster, Cameron C, Koontz, Michael Z, Kim, Edward Jae-Hoon, Cho, May, Gholami, Sepideh (June 2023) A Case of Heavily Pretreated HER2+ Colorectal Liver Metastases Responsive to Hepatic Arterial Infusion Chemotherapy. Clinical Colorectal Cancer, 22 (2). pp. 245-249. ISSN 1533-0028

Benitz, Simone, Steep, Alexander, Nasser, Malak, Preall, Jonathan, Mahajan, Ujjwal M, McQuithey, Holly, Loveless, Ian, Davis, Erick T, Wen, Hui-Ju, Long, Daniel W, Metzler, Thomas, Zwernik, Samuel, Louw, Michaela, Rempinski, Donald, Salas-Escabillas, Daniel, Brender, Sydney, Song, Linghao, Huang, Ling, Zhang, Zhenyu, Steele, Nina, Regel, Ivonne, Bednar, Filip, Crawford, Howard C (December 2023) ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma. bioRxiv. (Submitted)

Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert A (August 2023) Teosinte Pollen Drive guides maize domestication and evolution by RNAi. bioRxiv. (Public Dataset) (Submitted)

Boato, Francesco, Guan, Xiaofei, Zhu, Yanjie, Ryu, Youngjae, Voutounou, Mariel, Rynne, Christopher, Freschlin, Chase R, Zumbo, Paul, Betel, Doron, Matho, Katie, Makarov, Sergey N, Wu, Zhuhao, Son, Young-Jin, Nummenmaa, Aapo, Huang, Josh Z, Edwards, Dylan J, Zhong, Jian (January 2023) Activation of MAP2K signaling by genetic engineering or HF-rTMS promotes corticospinal axon sprouting and functional regeneration. Science Translational Medicine, 15 (677). eabq6885. ISSN 1946-6234 (Public Dataset)

Bonham, ChristopherA, Mandati, Vinay, Singh, RakeshK, Pappin, DarrylJ, Tonks, NicholasK (March 2023) Coupling substrate-trapping with proximity-labeling to identify protein tyrosine phosphatase PTP1B signaling networks. Journal of Biological Chemistry. p. 104582. ISSN 0021-9258

Brina, Daniela, Ponzoni, Adele, Troiani, Martina, Calì, Bianca, Pasquini, Emiliano, Attanasio, Giuseppe, Mosole, Simone, Mirenda, Michela, D'Ambrosio, Mariantonietta, Colucci, Manuel, Guccini, Ilaria, Revandkar, Ajinkya, Alajati, Abdullah, Tebaldi, Toma, Donzel, Deborah, Lauria, Fabio, Parhizgari, Nahjme, Valdata, Aurora, Maddalena, Martino, Calcinotto, Arianna, Bolis, Marco, Rinaldi, Andrea, Barry, Simon, Rüschoff, Jan Hendrik, Sabbadin, Marianna, Sumanasuriya, Semini, Crespo, Mateus, Sharp, Adam, Yuan, Wei, Grinu, Mathew, Boyle, Alexandra, Miller, Cynthia, Trotman, Lloyd, Delaleu, Nicolas, Fassan, Matteo, Moch, Holger, Viero, Gabriella, de Bono, Johann, Alimonti, Andrea (August 2023) The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. Nature Cancer, 4 (8). pp. 1102-1121. ISSN 2662-1347 (Public Dataset)

Buchanan, JoAnn, da Costa, Nuno Maçarico, Cheadle, Lucas (August 2023) Emerging roles of oligodendrocyte precursor cells in neural circuit development and remodeling. Trends in Neurosciences, 46 (8). pp. 628-639. ISSN 0166-2236

Burr, Ansen HP, Ji, Junyi, Ozler, Kadir, Mentrup, Heather L, Eskiocak, Onur, Yueh, Brian, Cumberland, Rachel, Menk, Ashley V, Rittenhouse, Natalie, Marshall, Chris W, Chiaranunt, Pailin, Zhang, Xiaoyi, Mullinax, Lauren, Overacre-Delgoffe, Abigail, Cooper, Vaughn S, Poholek, Amanda C, Delgoffe, Greg M, Mollen, Kevin P, Beyaz, Semir, Hand, Timothy W (2023) Excess Dietary Sugar Alters Colonocyte Metabolism and Impairs the Proliferative Response to Damage. Cellular and Molecular Gastroenterology and Hepatology, 16 (2). pp. 287-316. ISSN 2352-345X (Public Dataset)

Caballero, Carmela, Irrthum, Alexandre, Goulioti, Theodora, Cameron, David, Norton, Larry, Piccart, Martine (May 2023) International research to address the challenges of metastatic breast cancer: the AURORA Program (BIG 14-01). npj Breast Cancer, 9 (1). p. 42. ISSN 2374-4677

Cable, Jennifer, Rathmell, Jeffrey C, Pearce, Erika L, Ho, Ping-Chih, Haigis, Marcia C, Mamedov, Murad R, Wu, Meng-Ju, Kaech, Susan M, Lynch, Lydia, Febbraio, Mark A, Bapat, Sagar P, Hong, Hanna S, Zou, Weiping, Belkaid, Yasmine, Sullivan, Zuri A, Keller, Andrea, Wculek, Stefanie K, Green, Douglas R, Postic, Catherine, Amit, Ido, Benitah, Salvador Aznar, Jones, Russell G, Reina-Campos, Miguel, Torres, Santiago Valle, Beyaz, Semir, Brennan, Donal, O'Neill, Luke AJ, Perry, Rachel J, Brenner, Dirk (May 2023) Immunometabolism at the crossroads of obesity and cancer-a Keystone Symposia report. Annals of the New York Academy of Sciences, 1523 (1). pp. 38-50. ISSN 0077-8923

Caligiuri, Giuseppina, Tuveson, David A (March 2023) Activated fibroblasts in cancer: Perspectives and challenges. Cancer Cell, 41 (3). pp. 434-449. ISSN 1535-6108

Callaway, Mackenzie K, Dos Santos, Camila O (July 2023) Gestational Breast Cancer - a Review of Outcomes, Pathophysiology, and Model Systems. Journal of Mammary Gland Biology and Neoplasia, 28 (1). p. 16. ISSN 1083-3021

Cano, Alejandro V, Gitschlag, Bryan L, Rozhoňová, Hana, Stoltzfus, Arlin, McCandlish, David M, Payne, Joshua L (May 2023) Mutation bias and the predictability of evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 378 (1877). p. 20220055. ISSN 0962-8436

Chang, Mario C, Staklinski, Stephen J, Malut, Vinay R, Pierre, Geraldine L, Kilberg, Michael S, Merritt, Matthew E (April 2023) Metabolomic Profiling of Asparagine Deprivation in Asparagine Synthetase Deficiency Patient-Derived Cells. Nutrients, 15 (8). p. 1938. ISSN 2072-6643

Chang, Mario C, Staklinski, Stephen J, Merritt, Matthew E, Kilberg, Michael S (2023) A method for measurement of human asparagine synthetase (ASNS) activity and application to ASNS protein variants associated with ASNS deficiency. Biology Methods and Protocols, 8 (1). bpad026. ISSN 2396-8923

Chatterjee, Deeptiman, Deng, Wu-Min (2023) Standardization of Single-Cell RNA-Sequencing Analysis Workflow to Study Drosophila Ovary. Methods in Molecular Biology, 2677. pp. 151-171. ISSN 1064-3745

Cheadle, Lucas (May 2023) Neuron-glia communication through bona fide synapses. Nature Reviews Neuroscience. ISSN 1471-003X

Chibaya, Loretah, Murphy, Katherine C, DeMarco, Kelly D, Gopalan, Sneha, Liu, Haibo, Parikh, Chaitanya N, Lopez-Diaz, Yvette, Faulkner, Melissa, Li, Junhui, Morris, John P, Ho, Yu-Jui, Chana, Sachliv K, Simon, Janelle, Luan, Wei, Kulick, Amanda, de Stanchina, Elisa, Simin, Karl, Zhu, Lihua Julie, Fazzio, Thomas G, Lowe, Scott W, Ruscetti, Marcus (June 2023) EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance. Nature Cancer, 4 (6). pp. 872-892. ISSN 2662-1347

Chung, Taemoon, Garcia, Libia, Swamynathan, Manojit M, Froeling, Fieke EM, Trotman, Lloyd C, Tuveson, David A, Lyons, Scott K (April 2023) Internally Controlled and Dynamic Optical Measures of Functional Tumor Biology. Analytical Chemistry, 95 (13). pp. 5661-5670. ISSN 0003-2700

Ciren, Danielle, Zebell, Sophia, Lippman, Zachary B (December 2023) Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. bioRxiv. (Submitted)

Clarke, Jennifer L, Cooper, Laurel D, Poelchau, Monica F, Berardini, Tanya Z, Elser, Justin, Farmer, Andrew D, Ficklin, Stephen, Kumari, Sunita, Laporte, Marie-Angélique, Nelson, Rex T, Sadohara, Rie, Selby, Peter, Thessen, Anne E, Whitehead, Brandon, Sen, Taner Z (November 2023) Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. Database : the journal of biological databases and curation, 2023. baad076. ISSN 1758-0463

Collins, Sierra M, Alexander, Katherine A, Lundh, Stefan, Dimitri, Alexander J, Zhang, Zhen, Good, Charly R, Fraietta, Joseph A, Berger, Shelley L (July 2023) TOX2 coordinates with TET2 to positively regulate central memory differentiation in human CAR T cells. Science Advances, 9 (29). ISSN 2375-2548

Corona, Alberto, Choe, Jane, Muñoz-Castañeda, Rodrigo, Osten, Pavel, Shea, Stephen D (July 2023) A circuit from the locus coeruleus to the anterior cingulate cortex modulates offspring interactions in mice. Cell Reports, 42 (7). p. 112771. ISSN 2211-1247

Costa, Iris Munhoz, Effer, Brian, Costa-Silva, Tales Alexandre, Chen, Chen, Ciccone, Michael F, Pessoa, Adalberto, Dos Santos, Camila O, Monteiro, Gisele (July 2023) Cathepsin B Is Not an Intrinsic Factor Related to Asparaginase Resistance of the Acute Lymphoblastic Leukemia REH Cell Line. International Journal of Molecular Sciences, 24 (13). p. 11215. ISSN 1661-6596

Cowley, Benjamin R, Calhoun, Adam J, Rangarajan, Nivedita, Turner, Maxwell H, Pillow, Jonathan W, Murthy, Mala (October 2023) One-to-one mapping between deep network units and real neurons uncovers a visual population code for social behavior. bioRxiv. (Public Dataset) (Submitted)

Cowley, Benjamin R, Stan, Patricia L, Pillow, Jonathan W, Smith, Matthew A (November 2023) Compact deep neural network models of visual cortex. bioRxiv. (Submitted)

D'Angelica, Michael I, Ellis, Ryan J, Liu, Jason B, Brajcich, Brian C, Gönen, Mithat, Thompson, Vanessa M, Cohen, Mark E, Seo, Susan K, Zabor, Emily C, Babicky, Michele L, Bentrem, David J, Behrman, Stephen W, Bertens, Kimberly A, Celinski, Scott A, Chan, Carlos HF, Dillhoff, Mary, Dixon, Matthew EB, Fernandez-Del Castillo, Carlos, Gholami, Sepideh, House, Michael G, Karanicolas, Paul J, Lavu, Harish, Maithel, Shishir K, McAuliffe, John C, Ott, Mark J, Reames, Bradley N, Sanford, Dominic E, Sarpel, Umut, Scaife, Courtney L, Serrano, Pablo E, Smith, Travis, Snyder, Rebecca A, Talamonti, Mark S, Weber, Sharon M, Yopp, Adam C, Pitt, Henry A, Ko, Clifford Y (May 2023) Piperacillin-Tazobactam Compared With Cefoxitin as Antimicrobial Prophylaxis for Pancreatoduodenectomy: A Randomized Clinical Trial. JAMA: Journal of the American Medical Association, 329 (18). pp. 1579-1588. ISSN 0098-7484

Dalla, Christina, Jaric, Ivana, Pavlidi, Pavlina, Hodes, Georgia E, Kokras, Nikolaos, Bespalov, Anton, Kas, Martien J, Steckler, Thomas, Kabbaj, Mohamed, Würbel, Hanno, Marroco, Jordan, Tollkuhn, Jessica, Shansky, Rebecca, Bangasser, Debra, Becker, Jill B, McCarthy, Margaret, Ferland-Beckham, Chantelle (October 2023) Practical solutions for including Sex As a Biological Variable (SABV) in preclinical neuropsychopharmacological research. Journal of Neuroscience Methods. p. 110003. ISSN 0165-0270

Dantas, Ezequiel, Murthy, Anirudh, Ahmed, Tanvir, Ahmed, Mujmmail, Ramsamooj, Shakti, Hurd, Maurice A, Lam, Tiffany, Malbari, Murtaza, Agrusa, Christopher, Elemento, Olivier, Zhang, Chen, Pappin, Darryl J, McGraw, Timothy E, Stiles, Brendon M, Altorki, Nasser K, Goncalves, Marcus D (October 2023) TIMP1 is an early biomarker for detection and prognosis of lung cancer. Clinical and Translational Medicine, 13 (10). e1391. ISSN 2001-1326 (Public Dataset)

Daye, Dania, Panagides, John, Norton, Larry, Ahmed, Muneeb, Fukuma, Eisuke, Ward, Robert C, Gomez, Daniel, Kokabi, Nima, Vogl, Thomas, Abi-Jaoudeh, Nadine, Deipolyi, Amy (July 2023) New Frontiers in the Role of Locoregional Therapies in Breast Cancer: Proceedings from the Society of Interventional Radiology Foundation Research Consensus Panel. Journal of Vascular and Interventional Radiology. S1051-0443(23)00497. ISSN 1051-0443

Degroat, Thomas J, Wiersielis, Kimberly, Denney, Katherine, Kodali, Sowmya, Daisey, Sierra, Tollkuhn, Jessica, Samuels, Benjamin A, Roepke, Troy A (December 2023) Chronic stress and its effects on behavior, RNA expression of the bed nucleus of the stria terminalis, and the M-current of NPY neurons. Psychoneuroendocrinology, 161. p. 106920. ISSN 0306-4530

Deng, Cecilia H, Naithani, Sushma, Kumari, Sunita, Cobo-Simón, Irene, Quezada-Rodríguez, Elsa H, Skrabisova, Maria, Gladman, Nick, Correll, Melanie J, Sikiru, Akeem Babatunde, Afuwape, Olusola O, Marrano, Annarita, Rebollo, Ines, Zhang, Wentao, Jung, Sook (December 2023) Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database : the journal of biological databases and curation, 2023. ISSN 1758-0463

Denney, Katherine, Wu, Melody, Sun, Simón E, Moon, Soyoun, Tollkuhn, Jessica (2023) Comparative analysis of gonadal hormone receptor expression in the house mouse, meadow vole, and prairie vole brain. (Submitted)

Denney, Katherine A, Wu, Melody V, Sun, Simón ED, Moon, Soyoun, Tollkuhn, Jessica (November 2023) Comparative analysis of gonadal hormone receptor expression in the postnatal house mouse, meadow vole, and prairie vole brain. Hormones and Behavior, 158. p. 105463. ISSN 0018-506X

Deshmukh, Meghshree, Subhash, Santhilal, Hu, Zhicheng, Mohammad, Majd, Jarneborn, Anders, Pullerits, Rille, Jin, Tao, Kopparapu, Pradeep Kumar (2023) Gene expression of S100a8/a9 predicts Staphylococcus aureus-induced septic arthritis in mice. Frontiers in Microbiology, 14. p. 1146694. ISSN 1664-302X (Public Dataset)

Devaraj, Anantharam, Singh, Manvendra, Narayanavari, Suneel A, Yong, Guo, Chen, Jiaxuan, Wang, Jichang, Becker, Mareike, Walisko, Oliver, Schorn, Andrea, Cseresznyés, Zoltán, Raskó, Tamás, Radscheit, Kathrin, Selbach, Matthias, Ivics, Zoltán, Izsvák, Zsuzsanna (April 2023) HMGXB4 Targets Sleeping Beauty Transposition to Germinal Stem Cells. International Journal of Molecular Sciences, 24 (8). p. 7283. ISSN 1661-6596

Devos, Katrien M, Qi, Peng, Bahri, Bochra A, Gimode, Davis M, Jenike, Katharine, Manthi, Samuel J, Lule, Dagnachew, Lux, Thomas, Martinez-Bello, Liliam, Pendergast, Thomas H, Plott, Chris, Saha, Dipnarayan, Sidhu, Gurjot S, Sreedasyam, Avinash, Wang, Xuewen, Wang, Hao, Wright, Hallie, Zhao, Jianxin, Deshpande, Santosh, de Villiers, Santie, Dida, Mathews M, Grimwood, Jane, Jenkins, Jerry, Lovell, John, Mayer, Klaus FX, Mneney, Emmarold E, Ojulong, Henry F, Schatz, Michael C, Schmutz, Jeremy, Song, Bo, Tesfaye, Kassahun, Odeny, Damaris A (June 2023) Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nature Communications, 14 (1). p. 3694. ISSN 2041-1723

Drew, J, Morgan, W, Galindo, S, Kleinschmit, AJ, McWilliams, M, Pauley, M, Triplett, EW, Williams, J, Murdoch, B, Rosenwald, A (January 2023) Revisiting barriers to implementation of bioinformatics into life sciences education. Frontiers in Education, 8. ISSN 2504-284X

Dzien, Piotr, Mackintosh, Agata, Malviya, Gaurav, Johnson, Emma, Soloviev, Dmitry, Brown, Gavin, Uribe, Alejandro Huerta, Nixon, Colin, Lyons, Scott K, Maddocks, Oliver, Blyth, Karen, Lewis, David Y (2023) Positron emission tomography imaging of the sodium iodide symporter senses real-time energy stress in vivo. Cancer & Metabolism, 11 (1). ISSN 2049-3002

Early Breast Cancer Trialists’ Collaborative Group (EBCTCG). Ele, Early Breast Cancer Trialists’ Collaborative Group (EBCTCG) (April 2023) Anthracycline-containing and taxane-containing chemotherapy for early-stage operable breast cancer: a patient-level meta-analysis of 100 000 women from 86 randomised trials. The Lancet, 401 (10384). pp. 1277-1292. ISSN 0140-6736

Einson, Jonah, Glinos, Dafni, Boerwinkle, Eric, Castaldi, Peter, Darbar, Dawood, de Andrade, Mariza, Ellinor, Patrick, Fornage, Myriam, Gabriel, Stacey, Germer, Soren, Gibbs, Richard, Hersh, Craig P, Johnsen, Jill, Kaplan, Robert, Konkle, Barbara A, Kooperberg, Charles, Nassir, Rami, Loos, Ruth JF, Meyers, Deborah A, Mitchell, Braxton D, Psaty, Bruce, Vasan, Ramachandran S, Rich, Stephen S, Rienstra, Michael, Rotter, Jerome I, Saferali, Aabida, Shoemaker, M Benjamin, Silverman, Edwin, Smith, Albert Vernon, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mohammadi, Pejman, Castel, Stephane E, Iossifov, Ivan, Lappalainen, Tuuli (January 2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. bioRxiv. (Submitted)

Einson, Jonah, Glinos, Dafni, Boerwinkle, Eric, Castaldi, Peter, Darbar, Dawood, de Andrade, Mariza, Ellinor, Patrick, Fornage, Myriam, Gabriel, Stacey, Germer, Soren, Gibbs, Richard, Hersh, Craig P, Johnsen, Jill, Kaplan, Robert, Konkle, Barbara A, Kooperberg, Charles, Nassir, Rami, Loos, Ruth JF, Meyers, Deborah A, Mitchell, Braxton D, Psaty, Bruce, Vasan, Ramachandran S, Rich, Stephen S, Rienstra, Michael, Rotter, Jerome I, Saferali, Aabida, Shoemaker, Moore Benjamin, Silverman, Edwin, Smith, Albert Vernon, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mohammadi, Pejman, Castel, Stephane E, Iossifov, Ivan, Lappalainen, Tuuli (August 2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. Genetics, 224 (4). iyad115. ISSN 0016-6731

Ely, Zackery A, Mathey-Andrews, Nicolas, Naranjo, Santiago, Gould, Samuel I, Mercer, Kim L, Newby, Gregory A, Cabana, Christina M, Rideout, William M, Jaramillo, Grissel Cervantes, Khirallah, Jennifer M, Holland, Katie, Randolph, Peyton B, Freed-Pastor, William A, Davis, Jessie R, Kulstad, Zachary, Westcott, Peter MK, Lin, Lin, Anzalone, Andrew V, Horton, Brendan L, Pattada, Nimisha B, Shanahan, Sean-Luc, Ye, Zhongfeng, Spranger, Stefani, Xu, Qiaobing, Sánchez-Rivera, Francisco J, Liu, David R, Jacks, Tyler (May 2023) A prime editor mouse to model a broad spectrum of somatic mutations in vivo. Nature Biotechnology. ISSN 1087-0156 (Public Dataset)

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Hazra, Rasmani, Utama, Raditya, Naik, Payal, Dobin, Alexander, Spector, David L (January 2023) Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA-sequencing datasets. bioRxiv. (Submitted)

Heberle, Bernardo Aguzzoli, Brandon, J Anthony, Page, Madeline L, Nations, Kayla A, Dikobe, Ketsile I, White, Brendan J, Gordon, Lacey A, Fox, Grant A, Wadsworth, Mark E, Doyle, Patricia H, Williams, Brittney A, Fox, Edward J, Shantaraman, Anantharaman, Ryten, Mina, Goodwin, Sara, Ghiban, Elena, Wappel, Robert, Mavruk-Eskipehlivan, Senem, Miller, Justin B, Seyfried, Nicholas T, Nelson, Peter T, Fryer, John D, Ebbert, Mark TW (December 2023) Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity. bioRxiv. (Submitted)

Hegelmeyer, Nuri K, Parkin, Lia A, Previti, Mary L, Andrade, Joshua, Utama, Raditya, Sejour, Richard J, Gardin, Justin, Muller, Stephanie, Ketchum, Steven, Yurovsky, Alisa, Futcher, Bruce, Goodwin, Sara, Ueberheide, Beatrix, Seeliger, Jessica C (October 2023) Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. mBio. e0084123. ISSN 2150-7511

Hegelmeyer, Nuri K, Previti, Mary L, Andrade, Joshua, Utama, Raditya, Sejour, Richard J, Gardin, Justin, Muller, Stephanie, Ketchum, Steven, Yurovsky, Alisa, Futcher, Bruce, Goodwin, Sara, Ueberheide, Beatrix, Seeliger, Jessica C (March 2023) Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. bioRxiv. (Submitted)

Heidegger, Simon, Stritzke, Florian, Dahl, Sarah, Daßler-Plenker, Juliane, Joachim, Laura, Buschmann, Dominik, Fan, Kaiji, Sauer, Carolin M, Ludwig, Nils, Winter, Christof, Enssle, Stefan, Li, Suqi, Perl, Markus, Görgens, André, Haas, Tobias, Orberg, Erik Thiele, Göttert, Sascha, Wölfel, Catherine, Engleitner, Thomas, Cortés-Ciriano, Isidro, Rad, Roland, Herr, Wolfgang, Giebel, Bernd, Ruland, Jürgen, Bassermann, Florian, Coch, Christoph, Hartmann, Gunther, Poeck, Hendrik (September 2023) Targeting nucleic acid sensors in tumor cells to reprogram biogenesis and RNA cargo of extracellular vesicles for T cell-mediated cancer immunotherapy. Cell Reports Medicine, 4 (9). p. 101171. ISSN 2666-3791

Herrejon Chavez, Florisela, Luo, Hanzhi, Cifani, Paolo, Pine, Alli, Chu, Karen L, Joshi, Suhasini, Barin, Ersilia, Schurer, Alexandra, Chan, Mandy, Chang, Kathryn, Han, Grace YQ, Pierson, Aspen J, Xiao, Michael, Yang, Xuejing, Kuehm, Lindsey M, Hong, Yuning, Nguyen, Diu TT, Chiosis, Gabriela, Kentsis, Alex, Leslie, Christina, Vu, Ly P, Kharas, Michael G (April 2023) RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nature Communications, 14 (1). p. 2290. ISSN 2041-1723 (Public Dataset)

Herridge, Rowan P, Dolata, Jakub, Migliori, Valentina, de Santis Alves, Cristiane, Borges, Filipe, Van Ex, Frédéric, Lin, Ann, Bajczyk, Mateusz, Leonardi, Tommaso, Hendrick, Alan, Schorn, Andrea J, Kouzarides, Tony, Martienssen, Robert A (August 2023) Pseudouridine guides germline small RNA transport and epigenetic inheritance. bioRxiv. (Public Dataset)

Hillowe, Andrew, Gordon, Chris, Wang, Liqun, Rizzo, Robert C, Trotman, Lloyd C, Ojima, Iwao, Bialkowska, Agnieszka, Kaczocha, Martin (2023) Fatty acid binding protein 5 regulates docetaxel sensitivity in taxane-resistant prostate cancer cells. PLoS One, 18 (10). e0292483. ISSN 1932-6203 (Public Dataset)

Hirschhorn, Daniel, Budhu, Sadna, Kraehenbuehl, Lukas, Gigoux, Mathieu, Schröder, David, Chow, Andrew, Ricca, Jacob M, Gasmi, Billel, De Henau, Olivier, Mangarin, Levi Mark B, Li, Yanyun, Hamadene, Linda, Flamar, Anne-Laure, Choi, Hyejin, Cortez, Czrina A, Liu, Cailian, Holland, Aliya, Schad, Sara, Schulze, Isabell, Betof Warner, Allison, Hollmann, Travis J, Arora, Arshi, Panageas, Katherine S, Rizzuto, Gabrielle A, Duhen, Rebekka, Weinberg, Andrew D, Spencer, Christine N, Ng, David, He, Xue-Yan, Albrengues, Jean, Redmond, David, Egeblad, Mikala, Wolchok, Jedd D, Merghoub, Taha (March 2023) T cell immunotherapies engage neutrophils to eliminate tumor antigen escape variants. Cell, 186 (7). 1432-1447.e17. ISSN 0092-8674 (Public Dataset)

Hitchcock, Kathryn E, Miller, Eric D, Shi, Qian, Dixon, Jesse G, Gholami, Sepideh, White, Sarah B, Wu, Christina, Goulet, Christopher C, George, Manju, Jee, Kyung-Wook, Wright, Chadwick L, Yaeger, Rona, Shergill, Ardaman, Hong, Theodore S, George, Thomas J, O'Reilly, Eileen M, Meyerhardt, Jeffrey A, Romesser, Paul B (December 2023) Alliance for Clinical Trials in Oncology (Alliance) trial A022101/NRG-GI009: A pragmatic randomized phase III trial evaluating total ablative therapy for patients with limited metastatic colorectal cancer: evaluating radiation, ablation, and surgery (ERASur). Research Square. (Submitted)

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Homer, JA, Xu, L, Kayambu, N, Zheng, Q, Choi, EJ, Kim, BM, Sharpless, KB, Zuilhof, H, Dong, J, Moses, JE (December 2023) Sulfur fluoride exchange. Nature Reviews Methods Primers, 3 (1). ISSN 2662-8449 (In Press)

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Hu, Thomas, Allam, Mayar, Cai, Shuangyi, Henderson, Walter, Yueh, Brian, Garipcan, Aybuke, Ievlev, Anton V, Afkarian, Maryam, Beyaz, Semir, Coskun, Ahmet F (December 2023) Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology. Nature Communications, 14 (1). p. 8260. ISSN 2041-1723

Hu, Yuzhao, Rosado, Daniele, Lindb Ck, Louise N, Micko, Julie, Pedmale, Ullas V (January 2023) Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis. bioRxiv. (Submitted)

Hu, Yixin, Stillman, Bruce (January 2023) Origins of DNA replication in eukaryotes. Molecular Cell. S1097-2765(22)01203. ISSN 1097-2765

Huilgol, Dhananjay, Levine, Jesse M, Galbavy, William, Wang, Bor-Shuen, He, Miao, Suryanarayana, Shreyas M, Huang, Z Josh (August 2023) Direct and indirect neurogenesis generate a mosaic of distinct glutamatergic projection neuron types in cerebral cortex. Neuron, 111 (16). 2557-2569.e4. ISSN 0896-6273

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Husbands, Aman Y, Feller, Antje, Aggarwal, Vasudha, Dresden, Courtney E, Holub, Ashton S, Ha, Taekjip, Timmermans, Marja CP (March 2023) The START domain potentiates HD-ZIPIII transcriptional activity. The Plant Cell. ISSN 1040-4651

Inglis, John R (January 2023) Introduction: 35 years on. Genes and Development, 37 (1-2). p. 1. ISSN 0890-9369

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Jain, Anant, Nakahata, Yoshihisa, Watabe, Tetsuya, Rusina, Polina, South, Kelly, Adachi, Kengo, Yan, Long, Simorowski, Noriko, Furukawa, Hiro, Yasuda, Ryohei (August 2023) Dendritic, delayed, and stochastic CaMKII activation underlies behavioral time scale plasticity in CA1 synapses. (Submitted)

James, Ranjit Immanuel, Verma, Richa, Johnson, Latif Rajesh, Manesh, Abi, Jayakumar, Jaikishan, Sen, Mousumi, Joseph, Jayaraj, Kumarasami, Ramdayalan, Mitra, Partha P, Sivaprakasam, Mohanasankar, Varghese, George M (July 2023) A Standardized Protocol for the Safe Retrieval of Infectious Postmortem Human Brain for Studying Whole-Brain Pathology. American Journal of Forensic Medicine and Pathology. ISSN 0195-7910

Jbara, Amina, Lin, Kuan-Ting, Stossel, Chani, Siegfried, Zahava, Shqerat, Haya, Amar-Schwartz, Adi, Elyada, Ela, Mogilevsky, Maxim, Raitses-Gurevich, Maria, Johnson, Jared L, Yaron, Tomer M, Ovadia, Ofek, Jang, Gun Ho, Danan-Gotthold, Miri, Cantley, Lewis C, Levanon, Erez Y, Gallinger, Steven, Krainer, Adrian R, Golan, Talia, Karni, Rotem (May 2023) RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Nature, 617 (7959). pp. 147-153. ISSN 0028-0836 (Public Dataset)

Jiao, Yinping, Nigam, Deepti, Barry, Kerrie, Daum, Chris, Yoshinaga, Yuko, Lipzen, Anna, Khan, Adil, Parasa, Sai-Praneeth, Wei, Sharon, Lu, Zhenyuan, Tello-Ruiz, Marcela K, Dhiman, Pallavi, Burow, Gloria, Hayes, Chad, Chen, Junping, Brandizzi, Federica, Mortimer, Jenny, Ware, Doreen, Xin, Zhanguo (December 2023) A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes. The Plant Journal. ISSN 0960-7412

Jorstad, Nikolas L, Close, Jennie, Johansen, Nelson, Yanny, Anna Marie, Barkan, Eliza R, Travaglini, Kyle J, Bertagnolli, Darren, Campos, Jazmin, Casper, Tamara, Crichton, Kirsten, Dee, Nick, Ding, Song-Lin, Gelfand, Emily, Goldy, Jeff, Hirschstein, Daniel, Kiick, Katelyn, Kroll, Matthew, Kunst, Michael, Lathia, Kanan, Long, Brian, Martin, Naomi, McMillen, Delissa, Pham, Trangthanh, Rimorin, Christine, Ruiz, Augustin, Shapovalova, Nadiya, Shehata, Soraya, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Callaway, Edward M, Hof, Patrick R, Keene, C Dirk, Levi, Boaz P, Linnarsson, Sten, Mitra, Partha P, Smith, Kimberly, Hodge, Rebecca D, Bakken, Trygve E, Lein, Ed S (October 2023) Transcriptomic cytoarchitecture reveals principles of human neocortex organization. Science, 382 (6667). eadf6812. ISSN 0036-8075

Jorstad, Nikolas L, Song, Janet HT, Exposito-Alonso, David, Suresh, Hamsini, Castro-Pacheco, Nathan, Krienen, Fenna M, Yanny, Anna Marie, Close, Jennie, Gelfand, Emily, Long, Brian, Seeman, Stephanie C, Travaglini, Kyle J, Basu, Soumyadeep, Beaudin, Marc, Bertagnolli, Darren, Crow, Megan, Ding, Song-Lin, Eggermont, Jeroen, Glandon, Alexandra, Goldy, Jeff, Kiick, Katelyn, Kroes, Thomas, McMillen, Delissa, Pham, Trangthanh, Rimorin, Christine, Siletti, Kimberly, Somasundaram, Saroja, Tieu, Michael, Torkelson, Amy, Feng, Guoping, Hopkins, William D, Höllt, Thomas, Keene, C Dirk, Linnarsson, Sten, McCarroll, Steven A, Lelieveldt, Boudewijn P, Sherwood, Chet C, Smith, Kimberly, Walsh, Christopher A, Dobin, Alexander, Gillis, Jesse, Lein, Ed S, Hodge, Rebecca D, Bakken, Trygve E (October 2023) Comparative transcriptomics reveals human-specific cortical features. Science, 382 (6667). eade9516. ISSN 0036-8075

Judge, Sean J, Ghalambor, Tara, Cavnar, Michael J, Lidsky, Michael E, Merkow, Ryan P, Cho, May, Dominguez-Rosado, Ismael, Karanicolas, Paul J, Mayo, Skye C, Rocha, Flavio G, Fields, Ryan C, Patel, Reema A, Kennecke, Hagen F, Koerkamp, Bas Groot, Yopp, Adam C, Petrowsky, Henrik, Mahalingam, Devalingham, Kemeny, Nancy, D'Angelica, Michael, Gholami, Sepideh (September 2023) Current Practices in Hepatic Artery Infusion (HAI) Chemotherapy: An International Survey of the HAI Consortium Research Network. Annals of Surgical Oncology. ISSN 1068-9265

Kaczmarzyk, Jakub R, Gupta, Rajarsi, Kurc, Tahsin M, Abousamra, Shahira, Saltz, Joel H, Koo, Peter K (September 2023) ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification. Computer Methods and Programs in Biomedicine, 239. p. 107631. ISSN 0169-2607

Kahng, Jessica A, Xavier, Andre M, Ferro, Austin, Auguste, Yohan SS, Cheadle, Lucas (August 2023) Integrated high-confidence and high-throughput approaches for quantifying synapse engulfment by oligodendrocyte precursor cells. bioRxiv. (Submitted)

Karthik, Srinivasa, Joseph, Jayaraj, Jayakumar, Jaikishan, Manoj, Rahul, Shetty, Mahesh, Bota, Mihail, Verma, Richa, Mitra, Partha, Sivaprakasam, Mohanasankar (September 2023) Wide field block face imaging using deep ultraviolet induced autofluorescence of the human brain. Journal of Neuroscience Methods, 397. p. 109921. ISSN 0165-0270

Katcher, Arielle, Yueh, Brian, Ozler, Kadir, Nizam, Aaron, Kredentser, Ariel, Chung, Charlie, Frimer, Marina, Goldberg, Gary L, Beyaz, Semir (2023) Establishing patient-derived organoids from human endometrial cancer and normal endometrium. Frontiers in Endocrinology, 14. p. 1059228. ISSN 1664-2392

Kim, Young Jin, Krainer, Adrian R (January 2023) Antisense Oligonucleotide Therapeutics for Cystic Fibrosis: Recent Developments and Perspectives. Molecules and Cells, 46 (1). pp. 10-20. ISSN 1016-8478

Kinney, Brian, Sahu, Shubham, Stec, Natalia, Hills-Muckey, Kelly, Adams, Dexter W, Wang, Jing, Jaremko, Matt, Joshua-Tor, Leemor, Keil, Wolfgang, Hammell, Christopher M (August 2023) A circadian-like gene network programs the timing and dosage of heterochronic miRNA transcription during C. elegans development. Developmental Cell. S1534-5807(23)00402. ISSN 1534-5807

Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Battle, Alexis, Aganezov, Sergey, Schatz, Michael C (March 2023) Jasmine and Iris: population-scale structural variant comparison and analysis. Nature Methods, 20 (3). pp. 408-417. ISSN 1548-7091

Kitagawa, Munenori, Tran, Thu M, Jackson, David (June 2023) Traveling with purpose: cell-to-cell transport of plant mRNAs. Trends in Cell Biology. S0962-8924(23)00106. ISSN 0962-8924

Kleeman, Sam O, Thakir, Tuba Mansoor, Demestichas, Breanna, Mourikis, Nicholas, Loiero, Dominik, Ferrer, Miriam, Bankier, Sean, Riazat-Kesh, Yosef JRA, Lee, Hassal, Chantzichristos, Dimitrios, Regan, Claire, Preall, Jonathan, Sinha, Sarthak, Rosin, Nicole, Yipp, Bryan, de Almeida, Luiz GN, Biernaskie, Jeff, Dufour, Antoine, Tober-Lau, Pinkus, Ruusalepp, Arno, Bjorkegren, Johan LM, Ralser, Markus, Kurth, Florian, Demichev, Vadim, Heywood, Todd, Gao, Qing, Johannsson, Gudmundur, Koelzer, Viktor H, Walker, Brian R, Meyer, Hannah V, Janowitz, Tobias (August 2023) Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy. Cell Genomics, 3 (8). p. 100347. ISSN 2666-979X

Klindt, David, Sanborn, Sophia, Acosta, Francisco, Poitevin, Frédéric, Miolane, Nina (October 2023) Identifying Interpretable Visual Features in Artificial and Biological Neural Systems. arXiv. (Submitted)

Koo, Peter K, Ploenzke, Matt, Anand, Praveen, Paul, Steffan, Majdandzic, Antonio (2023) ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks. Methods in Molecular Biology, 2586. pp. 197-215. ISSN 1064-3745

Kovaka, Sam, Ou, Shujun, Jenike, Katharine M, Schatz, Michael C (January 2023) Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing. Nature Methods, 20 (1). pp. 12-16. ISSN 1548-7091

Kovaleva, Vasilisa A, Pattinson, David J, Barton, Carl, Chapin, Sarah R, Minervina, Anastasia A, Richards, Katherine A, Sant, Andrea J, Thomas, Paul G, Pogorelyy, Mikhail V, Meyer, Hannah V (November 2023) copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling. bioRxiv. (Submitted)

Kuderna, Lukas FK, Ulirsch, Jacob C, Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J, Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J, Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C, Kuhlwilm, Martin, Orkin, Joseph D, Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S, Horvath, Julie E, Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G, de Melo, Fabiano R, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria NF, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J, Zaramody, Alphonse, Jolly, Clifford J, Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H, Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D, Knauf, Sascha, Le, Minh D, Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C, Zinner, Dietmar, Gut, Ivo, Melin, Amanda D, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin MD, Karakikes, Ioannis, Wang, Kevin C, Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P, Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, Farh, Kyle Kai-How (November 2023) Identification of constrained sequence elements across 239 primate genomes. Nature. ISSN 0028-0836

Kumarasami, Ramdayalan, Verma, Richa, Pandurangan, Karthika, Ramesh, Jivitha Jyothi, Pandidurai, Sathish, Savoia, Stephen, Jayakumar, Jaikishan, Bota, Mihail, Mitra, Partha, Joseph, Jayaraj, Sivaprakasam, Mohanasankar (2023) A technology platform for standardized cryoprotection and freezing of large-volume brain tissues for high-resolution histology. Frontiers in Neuroanatomy, 17. p. 1292655. ISSN 1662-5129

Lammertse, E, Li, S, Kendall, J, Kim, C, Morris, P, Ranade, N, Levy, D, Wigler, M, Brouzes, E (January 2023) Magnetically Functionalized Hydrogels for High-Throughput Genomic Applications. Advanced Materials Technologies. ISSN 2365-709X

Lanctot, Amy (November 2023) A high-yielding recipe: Cytokinin signaling in soybean roots affects phosphorus uptake efficiency and crop production. Plant Physiology. kiad616. ISSN 0032-0889

Lanctot, Amy (August 2023) The root of the mystery: The role of long non-coding RNAs in regulating transcription. Plant Physiology. kiad434. ISSN 0032-0889

Langdon, Christopher, Genkin, Mikhail, Engel, Tatiana A (April 2023) A unifying perspective on neural manifolds and circuits for cognition. Nature Reviews Neuroscience. ISSN 1471-003X

Langer, Henning Tim, Ramsamooj, Shakti, Dantas, Ezequiel, Murthy, Anirudh, Ahmed, Mujmmail, Hwang, Seo-Kyoung, Grover, Rahul, Pozovskiy, Rita, Liang, Roger J, Queiroz, Andre Lima, Brown, Justin C, White, Eileen P, Janowitz, Tobias, Goncalves, And Marcus D (August 2023) Restoring adiponectin via rosiglitazone ameliorates tissue wasting in mice with lung cancer. bioRxiv. (Submitted)

Langlieb, Jonah, Sachdev, Nina S, Balderrama, Karol S, Nadaf, Naeem M, Raj, Mukund, Murray, Evan, Webber, James T, Vanderburg, Charles, Gazestani, Vahid, Tward, Daniel, Mezias, Chris, Li, Xu, Cable, Dylan M, Norton, Tabitha, Mitra, Partha, Chen, Fei, Macosko, Evan Z (March 2023) The cell type composition of the adult mouse brain revealed by single cell and spatial genomics. bioRxiv. (Submitted)

Langlieb, Jonah, Sachdev, Nina S, Balderrama, Karol S, Nadaf, Naeem M, Raj, Mukund, Murray, Evan, Webber, James T, Vanderburg, Charles, Gazestani, Vahid, Tward, Daniel, Mezias, Chris, Li, Xu, Flowers, Katelyn, Cable, Dylan M, Norton, Tabitha, Mitra, Partha, Chen, Fei, Macosko, Evan Z (December 2023) The molecular cytoarchitecture of the adult mouse brain. Nature, 624 (7991). pp. 333-342. ISSN 0028-0836

Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D, Rabbani, Keon, Balacco, Jennifer R, Chaisson, Mark, Cheng, Haoyu, Collins, Joanna, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, Jain, Nivesh, Johnson, Cassidy, Kim, Heebal, Lee, Chul, Marques-Bonet, Tomas, O'Toole, Brian, Rhie, Arang, Secomandi, Simona, Sozzoni, Marcella, Tilley, Tatiana, Uliano-Silva, Marcela, van den Beek, Marius, Waterhouse, Robert M, Phillippy, Adam M, Jarvis, Erich D, Schatz, Michael C, Nekrutenko, Anton, Formenti, Giulio (June 2023) Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. (Submitted)

Lee, Eun Song, Heo, Jung, Bang, Woo Young, Chougule, Kapeel M, Waminal, Nomar Espinosa, Hong, Nguyen Thi, Kim, Min Ji, Beak, Hong Kwan, Kim, Yong Jun, Priatama, Ryza A, Jang, Ji In, Cha, Kang Il, Son, Seung Han, Rajendran, Sujeevan, Choo, Young-Kug, Bae, Jong Hyang, Kim, Chul Min, Lee, Young Koung, Bae, Sangsu, Jones, Jonathan DG, Sohn, Kee Hoon, Lee, Jiyoung, Kim, Hyun Hee, Hong, Jong Chan, Ware, Doreen, Kim, Keunhwa, Park, Soon Ju (August 2023) Engineering homoeologs provide a fine scale for quantitative traits in polyploid. Plant Biotechnology Journal. pp. 1-15. ISSN 1467-7644 (Public Dataset)

Lee, Hassal, Bates, Alexander, Marshall, Andrea, Callier, Shawneequa, Chambwe, Nyasha, Janowitz, Tobias (2023) Analysis and optimization of equitable US cancer clinical trial center access by travel time. Journal of Clinical Oncology, 41 (16). ISSN 0732-183X

Lee, JS, Lowell, JL, Whitewater, K, Roane, TM, Miller, CS, Chan, AP, Sylvester, AW, Jackson, D, Hunter, LE (September 2023) Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework. Molecular Ecology Resources. ISSN 1755-098X

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (May 2023) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome Biology, 24 (1). p. 105. ISSN 1474-760X

Lee, Seung Cho, Adams, Dexter W, Ipsaro, Jonathan J, Cahn, Jonathan, Lynn, Jason, Kim, Hyun-Soo, Berube, Benjamin, Major, Viktoria, Calarco, Joseph P, LeBlanc, Chantal, Bhattacharjee, Sonali, Ramu, Umamaheswari, Grimanelli, Daniel, Jacob, Yannick, Voigt, Philipp, Joshua-Tor, Leemor, Martienssen, Robert A (August 2023) Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Cell, 186 (19). 4100-4116.e15. ISSN 0092-8674 (Public Dataset)

Lee, Seung Cho, Adams, Dexter W, Ipsaro, Jonathan J, Cahn, Jonathan, Lynn, Jason, Kim, Hyun-Soo, Berube, Benjamin, Major, Viktoria, Calarco, Joseph P, LeBlanc, Chantal, Bhattacharjee, Sonali, Ramu, Umamaheswari, Grimanelli, Daniel, Jacob, Yannick, Voigt, Philipp, Joshua-Tor, Leemor, Martienssen, Robert A (August 2023) Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation. bioRxiv. (Submitted)

Lee, YK, Olson, A, Kim, K, Ohme-Takagi, M, Ware, D (January 2023) HB31 and HB21 regulate floral architecture through miRNA396/GRF modules in Arabidopsis. Plant Biotechnology Reports. ISSN 1863-5466

Lee, Hassal, Ciabatti, Ernesto, González-Rueda, Ana, Williams, Elena, Nugent, Fiona, Mookerjee, Souradip, Morgese, Fabio, Tripodi, Marco (March 2023) Combining long-term circuit mapping and network transcriptomics with SiR-N2c. Nature Methods. ISSN 1548-7091 (Public Dataset)

Lei, Pin-Ji, Pereira, Ethel R, Andersson, Patrik, Amoozgar, Zohreh, Van Wijnbergen, Jan Willem, O'Melia, Meghan J, Zhou, Hengbo, Chatterjee, Sampurna, Ho, William W, Posada, Jessica M, Kumar, Ashwin S, Morita, Satoru, Menzel, Lutz, Chung, Charlie, Ergin, Ilgin, Jones, Dennis, Huang, Peigen, Beyaz, Semir, Padera, Timothy P (September 2023) Cancer cell plasticity and MHC-II-mediated immune tolerance promote breast cancer metastasis to lymph nodes. Journal of Experimental Medicine, 220 (9). e20221847. ISSN 0022-1007 (Public Dataset)

Li, Bin E, Li, Grace Y, Cai, Wenqing, Zhu, Qian, Seruggia, Davide, Fujiwara, Yuko, Vakoc, Christopher R, Orkin, Stuart (July 2023) In vivo CRISPR/Cas9 Screening Identifies Pbrm1 as a Regulator of Mouse Myeloid Leukemia Development. Blood Advances, 7 (18). pp. 5281-5293. ISSN 2473-9529 (Public Dataset)

Lindsay, Penelope, Swentowsky, Kyle W, Jackson, David (December 2023) Cultivating Potential: Harnessing Plant Stem Cells for Agricultural Crop Improvement. Molecular Plant. ISSN 1674-2052

Liu, Hao, Caballero-Florán, René N, Hergenreder, Ty, Yang, Tao, Hull, Jacob M, Pan, Geng, Li, Ruonan, Veling, Macy W, Isom, Lori L, Kwan, Kenneth Y, Huang, Z Josh, Fuerst, Peter G, Jenkins, Paul M, Ye, Bing (April 2023) DSCAM gene triplication causes excessive GABAergic synapses in the neocortex in Down syndrome mouse models. PLoS Biology, 21 (4). e3002078. ISSN 1544-9173

Liu, Lingjie, Zhao, Yixin, Siepel, Adam (December 2023) DNA-sequence and epigenomic determinants of local rates of transcription elongation. bioRxiv. (Submitted)

Liu, Ying, Dantas, Ezequiel, Ferrer, Miriam, Liu, Yifang, Comjean, Aram, Davidson, Emma E, Hu, Yanhui, Goncalves, Marcus D, Janowitz, Tobias, Perrimon, Norbert (May 2023) Tumor Cytokine-Induced Hepatic Gluconeogenesis Contributes to Cancer Cachexia: Insights from Full Body Single Nuclei Sequencing. bioRxiv. (Submitted)

Loh, Liyen, Carcy, Salomé, Krovi, Harsha S, Domenico, Joanne, Spengler, Andrea, Lin, Yong, Torres, Joshua, Palmer, William, Norman, Paul J, Stone, Matthew, Brunetti, Tonya, Meyer, Hannah V, Gapin, Laurent (December 2023) Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models. bioRxiv. (Submitted)

Lu, Guang-An, Zhang, Jinning, Zhao, Yixin, Chen, Qingjian, Lin, Pei, Tang, Tian, Tang, Zhixiong, Wen, Haijun, Liufu, Zhongqi, Wu, Chung-I (January 2023) Canalization of Phenotypes-When the Transcriptome is Constantly but Weakly Perturbed. Molecular Biology and Evolution, 40 (1). msad005. ISSN 0737-4038

Lyon, Gholson J, Longo, Joseph, Garcia, Andrew, Inusa, Fatima, Marchi, Elaine, Shi, Daniel, Dörfel, Max, Arnesen, Thomas, Aldabe, Rafael, Lyons, Scott, Nashat, Melissa, Bolton, David (April 2023) Evaluating possible maternal effect lethality of Naa10 knockout mice, and modulation of phenotypes for embryonic and neonatal lethality by genetic background and environment. (Submitted)

Ma, Hai-Li, Bizet, Martin, Soares Da Costa, Christelle, Murisier, Frédéric, de Bony, Eric James, Wang, Meng-Ke, Yoshimi, Akihide, Lin, Kuan-Ting, Riching, Kristin M, Wang, Xing, Beckman, John I, Arya, Shailee, Droin, Nathalie, Calonne, Emilie, Hassabi, Bouchra, Zhang, Qing-Yang, Li, Ang, Putmans, Pascale, Malbec, Lionel, Hubert, Céline, Lan, Jie, Mies, Frédérique, Yang, Ying, Solary, Eric, Daniels, Danette L, Gupta, Yogesh K, Deplus, Rachel, Abdel-Wahab, Omar, Yang, Yun-Gui, Fuks, François (December 2023) SRSF2 plays an unexpected role as reader of m5C on mRNA, linking epitranscriptomics to cancer. Molecular Cell, 83 (23). 4239-4254.e10. ISSN 1097-2765 (Public Dataset)

Maia-Silva, Diogo, Schier, Allison C, Skopelitis, Damianos, Kechejian, Vahag, Alpsoy, Aktan, Liverpool, Jynelle, Taatjes, Dylan J, Vakoc, Christopher R (October 2023) Marker-based CRISPR screening reveals a MED12-p63 interaction that activates basal identity in pancreatic ductal adenocarcinoma. bioRxiv. (Submitted)

Majdandzic, Antonio, Rajesh, Chandana, Koo, Peter K (May 2023) Correcting gradient-based interpretations of deep neural networks for genomics. Genome Biology, 24 (1). p. 109. ISSN 1474-760X

Mateo-Elizalde, Cristian, Lynn, Jason, Ernst, Evan, Martienssen, Rob (February 2023) Duckweeds. Current Biology, 33 (3). R89-R91. ISSN 0960-9822

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Mou, Haiwei, Eskiocak, Onur, Özler, Kadir A, Gorman, Megan, Yue, Junjiayu, Jin, Ying, Wang, Zhikai, Gao, Ya, Janowitz, Tobias, Meyer, Hannah V, Yu, Tianxiong, Wilkinson, John E, Kucukural, Alper, Ozata, Deniz M, Beyaz, Semir (January 2023) CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer. Journal of Pathology. ISSN 0022-3417

Mousset, Alexandra, Lecorgne, Enora, Bourget, Isabelle, Lopez, Pascal, Jenovai, Kitti, Cherfils-Vicini, Julien, Dominici, Chloé, Rios, Géraldine, Girard-Riboulleau, Cédric, Liu, Bodu, Spector, David L, Ehmsen, Sidse, Renault, Shufang, Hego, Caroline, Mechta-Grigoriou, Fatima, Bidard, François-Clément, Terp, Mikkel Green, Egeblad, Mikala, Gaggioli, Cédric, Albrengues, Jean (April 2023) Neutrophil extracellular traps formed during chemotherapy confer treatment resistance via TGF-β activation. Cancer Cell, 41 (4). 757-775.e10. ISSN 1535-6108 (Public Dataset)

Musall, Simon, Sun, Xiaonan R, Mohan, Hemanth, An, Xu, Gluf, Steven, Li, Shu-Jing, Drewes, Rhonda, Cravo, Emma, Lenzi, Irene, Yin, Chaoqun, Kampa, Björn M, Churchland, Anne K (January 2023) Pyramidal cell types drive functionally distinct cortical activity patterns during decision-making. Nature Neuroscience. ISSN 1097-6256

Nocini, Riccardo, Tondulli, Luca, D'Ambrosio, Consuelo, Luchini, Claudio, Biankin, Andrew V, Casolino, Raffaella, Scarpa, Aldo, ICGC-ARGO, Milella, Michele, Lawlor, Rita T (August 2023) ICGC ARGO precision medicine: genomic profiling-informed prediction of immunotherapy response in two patients with metastatic head and neck squamous cell carcinoma. The Lancet Oncology, 24 (8). pp. 851-853. ISSN 1470-2045

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Ntakirutimana, Fabrice, Tranchant-Dubreuil, Christine, Cubry, Philippe, Chougule, Kapeel, Zhang, Jianwei, Wing, Rod A, Adam, Hélène, Lorieux, Mathias, Jouannic, Stefan (August 2023) Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3: Genes, Genomes, Genetics. jkad174. ISSN 2160-1836 (Public Dataset)

Ogawa, Yuki, Lim, Brian C, George, Shanu, Oses-Prieto, Juan A, Rasband, Joshua M, Eshed-Eisenbach, Yael, Hamdan, Hamdan, Nair, Supna, Boato, Francesco, Peles, Elior, Burlingame, Alma L, Van Aelst, Linda, Rasband, Matthew N (October 2023) Antibody-directed extracellular proximity biotinylation reveals that Contactin-1 regulates axo-axonic innervation of axon initial segments. Nature Communications, 14 (1). p. 6797. ISSN 2041-1723

Ogawa, Yuki, Lim, Brian C, George, Shanu, Oses-Prieto, Juan A, Rasband, Joshua M, Eshed-Eisenbach, Yael, Nair, Supna, Boato, Francesco, Peles, Elior, Burlingame, Alma L, Van Aelst, Linda, Rasband, Matthew N (March 2023) Antibody-directed extracellular proximity biotinylation reveals Contactin-1 regulates axo-axonic innervation of axon initial segments. (Submitted)

Ortiz, Jenelys Ruiz, Lewis, Steven M, Ciccone, Michael F, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila O (September 2023) Single-cell transcription mapping of murine and human mammary organoids responses to female hormones. bioRxiv. (Public Dataset) (Submitted)

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Pandey, Kiran, Bessières, Benjamin, Sheng, Susan L, Taranda, Julian, Osten, Pavel, Sandovici, Ionel, Constancia, Miguel, Alberini, Cristina M (December 2023) Neuronal activity drives IGF2 expression from pericytes to form long-term memory. Neuron, 111 (23). 3819-3836.e8. ISSN 0896-6273

Passalacqua, Michael John, Gillis, Jesse (November 2023) Coexpression enhances cross-species integration of scRNA-seq across diverse plant species. bioRxiv. (Submitted)

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Perlee, Sarah, Kikuchi, Sota, Nakadai, Tomoyoshi, Masuda, Takeshi, Ohtsuki, Sumio, Matsumoto, Makoto, Rahmutulla, Bahityar, Fukuyo, Masaki, Cifani, Paolo, Kentsis, Alex, Roeder, Robert G, Kaneda, Atsushi, Hoshii, Takayuki (October 2023) SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3. EMBO Reports, 24 (10). e57108. ISSN 1469-221X

Pinto, Brendan J, O'Connor, Brian, Schatz, Michael C, Zarate, Samantha, Wilson, Melissa A (February 2023) Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants. (Public Dataset) (Submitted)

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Pomella, Silvia, Cassandri, Matteo, D'Archivio, Lucrezia, Porrazzo, Antonella, Cossetti, Cristina, Phelps, Doris, Perrone, Clara, Pezzella, Michele, Cardinale, Antonella, Wachtel, Marco, Aloisi, Sara, Milewski, David, Colletti, Marta, Sreenivas, Prethish, Walters, Zoë S, Barillari, Giovanni, Di Giannatale, Angela, Milano, Giuseppe Maria, De Stefanis, Cristiano, Alaggio, Rita, Rodriguez-Rodriguez, Sonia, Carlesso, Nadia, Vakoc, Christopher R, Velardi, Enrico, Schafer, Beat W, Guccione, Ernesto, Gatz, Susanne A, Wasti, Ajla, Yohe, Marielle, Ignatius, Myron, Quintarelli, Concetta, Shipley, Janet, Miele, Lucio, Khan, Javed, Houghton, Peter J, Marampon, Francesco, Gryder, Berkley E, De Angelis, Biagio, Locatelli, Franco, Rota, Rossella (December 2023) MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57Kip2 targeting. Nature Communications, 14 (1). p. 8373. ISSN 2041-1723

Qian, Zhe, Song, Dongyan, Ipsaro, Jonathan J, Bautista, Carmelita, Joshua-Tor, Leemor, Yeh, Johannes T-H, Tonks, Nicholas K (September 2023) Manipulating PTPRD function with ectodomain antibodies. Genes and Development. ISSN 0890-9369

Qiu, Yongrong, Klindt, David A, Szatko, Klaudia P, Gonschorek, Dominic, Hoefling, Larissa, Schubert, Timm, Busse, Laura, Bethge, Matthias, Euler, Thomas (April 2023) Efficient coding of natural scenes improves neural system identification. PLoS Computational Biology, 19 (4). e1011037-e1011037. ISSN 1553-7358

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Roach, James P, Churchland, Anne K, Engel, Tatiana A (January 2023) Choice selective inhibition drives stability and competition in decision circuits. Nature Communications, 14 (1). p. 147. ISSN 2041-1723

Rozhoňová, Hana, Martí-Gómez, Carlos, McCandlish, David M, Payne, Joshua L (June 2023) Protein evolvability under rewired genetic codes. bioRxiv. (Submitted)

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Rupert, Deborah D, Pagliaro, Alexa, Choe, Jane, Shea, Stephen D (August 2023) Selective deletion of Methyl CpG binding protein 2 from parvalbumin interneurons in the auditory cortex delays the onset of maternal retrieval in mice. The Journal of Neuroscience. JN-RM-0838-23. ISSN 0270-6474

San Martin, Rebeca, Moffitt, Andrea, Loveless, Theresa, Brixius-Anderko, Simone (February 2023) Recruiting women faculty through inclusive, family-friendly practices. Trends in Biochemical Sciences. ISSN 0968-0004

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Schwörer, Simon, Cimino, Francesco V, Ros, Manon, Tsanov, Kaloyan M, Ng, Charles, Lowe, Scott W, Carmona-Fontaine, Carlos, Thompson, Craig B (May 2023) Hypoxia Potentiates the Inflammatory Fibroblast Phenotype Promoted by Pancreatic Cancer Cell-Derived Cytokines. Cancer Research, 83 (10). pp. 1596-1610. ISSN 0008-5472

Seitz, Evan E, McCandlish, David M, Kinney, Justin B, Koo, Peter K (November 2023) Interpreting cis -regulatory mechanisms from genomic deep neural networks using surrogate models. bioRxiv. (Submitted)

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Shi, Hai, Ernst, Evan, Heinzel, Nicolas, McCorkle, Sean, Rolletschek, Hardy, Borisjuk, Ljudmilla, Ortleb, Stefan, Martienssen, Robert, Shanklin, John, Schwender, Jorg (October 2023) Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis. BMC Plant Biology, 23 (1). p. 458. ISSN 1471-2229 (Public Dataset)

Shi, Xi, Lu, Congyi, Corman, Alba, Nikish, Alexandra, Zhou, Yang, Platt, Randy J, Iossifov, Ivan, Zhang, Feng, Pan, Jen Q, Sanjana, Neville E (October 2023) Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction. American Journal of Human Genetics, 110 (10). pp. 1750-1768. ISSN 0002-9297 (Public Dataset)

Shi, Xiaoya, Cao, Shuo, Wang, Xu, Huang, Siyang, Wang, Yue, Liu, Zhongjie, Liu, Wenwen, Leng, Xiangpeng, Peng, Yanling, Wang, Nan, Wang, Yiwen, Ma, Zhiyao, Xu, Xiaodong, Zhang, Fan, Xue, Hui, Zhong, Haixia, Wang, Yi, Zhang, Kekun, Velt, Amandine, Avia, Komlan, Holtgräwe, Daniela, Grimplet, Jérôme, Matus, José Tomás, Ware, Doreen, Wu, Xinyu, Wang, Haibo, Liu, Chonghuai, Fang, Yuling, Rustenholz, Camille, Cheng, Zongming, Xiao, Hua, Zhou, Yongfeng (May 2023) The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Horticulture Research, 10 (5). uhad061. ISSN 2662-6810

Shi, YL, Zeraati, R, Levina, A, Engel, TA (January 2023) Spatial and temporal correlations in neural networks with structured connectivity. Physical Review Research, 5 (1). ISSN 2643-1564

Shimada, Atsushi, Cahn, Jonathan, Ernst, Evan, Lynn, Jason, Grimanelli, Daniel, Henderson, Ian, Kakutani, Tetsuji, Martienssen, Robert A (August 2023) Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs. (Public Dataset) (Submitted)

Shrestha, Padmina, Jaganathan, Anbalagan, Huilgol, Dhananjay, Ballon, Carlos, Hwangbo, Yon, Mills, Alea A (January 2023) Chd5 regulates the transcription factor Six3 to promote neuronal differentiation. Stem Cells. sxad002. ISSN 1066-5099 (Public Dataset)

Shuvaev, Sergey, Amelchenko, Evgeny, Smagin, Dmitry, Kudryavtseva, Natalia, Enikolopov, Grigori, Koulakov, Alexei (March 2023) A normative theory of social conflict. (Submitted)

Simhal, Anish K, Maclachlan, Kylee H, Elkin, Rena, Zhu, Jiening, Norton, Larry, Deasy, Joseph O, Oh, Jung Hun, Usmani, Saad Z, Tannenbaum, Allen (November 2023) Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival. Blood Cancer Journal, 13 (1). p. 175. ISSN 2044-5385

Simner, Patricia J, Bergman, Yehudit, Fan, Yunfan, Jacobs, Emily B, Ramakrishnan, Srividya, Lu, Jennifer, Lewis, Shawna, Hanlon, Ann, Tamma, Pranita D, Schatz, Michael C, Timp, Winston, Carroll, Karen C (June 2023) Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids. JAC-Antimicrobial Resistance, 5 (3). dlad061. ISSN 2632-1823

Smedley, Christopher J, Giel, Marie‐Claire, Fallon, Thomas, Moses, John E (July 2023) Ethene‐1,1‐disulfonyl Difluoride (EDSF) for SuFEx Click Chemistry: Synthesis of SuFExable 1,1‐Bissulfonylfluoride Substituted Cyclobutene Hubs. Angewandte Chemie International Edition, 135 (30). ISSN 0044-8249

Smiley, Kristina O, Munley, Kathleen M, Aghi, Krisha, Lipshutz, Sara E, Patton, Tessa M, Pradhan, Devaleena S, Solomon-Lane, Tessa K, Sun, Simón ED (November 2023) Sex diversity in the 21st century: Concepts, frameworks, and approaches for the future of neuroendocrinology. Hormones and Behaviour, 157. p. 105445. ISSN 0018-506X

Soto-Feliciano, Yadira M, Sánchez-Rivera, Francisco J, Perner, Florian, Barrows, Douglas W, Kastenhuber, Edward R, Ho, Yu-Jui, Carroll, Thomas, Xiong, Yijun, Anand, Disha, Soshnev, Alexey A, Gates, Leah, Beytagh, Mary Clare, Cheon, David, Gu, Shengqing, Liu, X Shirley, Krivtsov, Andrei V, Meneses, Maximiliano, de Stanchina, Elisa, Stone, Richard M, Armstrong, Scott A, Lowe, Scott W, Allis, C David (January 2023) A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin-MLL Inhibition. Cancer Discovery, 13 (1). pp. 146-169. ISSN 2159-8274

Srinivasan, Shyam, Daste, Simon, Modi, Mehrab N, Turner, Glenn C, Fleischmann, Alexander, Navlakha, Saket (October 2023) Effects of stochastic coding on olfactory discrimination in flies and mice. PLoS Biology, 21 (10). e3002206. ISSN 1545-7885

Sroka, Martyna W, Skopelitis, Damianos, Vermunt, Marit W, Preall, Jonathan B, El Demerdash, Osama, de Almeida, Larissa MN, Chang, Kenneth, Utama, Raditya, Gryder, Berkley, Caligiuri, Giuseppina, Ren, Diqiu, Nalbant, Benan, Milazzo, Joseph P, Tuveson, David A, Dobin, Alexander, Hiebert, Scott W, Stengel, Kristy R, Mantovani, Roberto, Khan, Javed, Kohli, Rahul M, Shi, Junwei, Blobel, Gerd A, Vakoc, Christopher R (September 2023) Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proceedings of the National Academy of Sciences of USA, 120 (36). e2303859120. ISSN 0027-8424 (Public Dataset)

Staklinski, Stephen J, Chang, Mario C, Ahrens-Nicklas, Rebecca C, Kaur, Shagun, Stefanatos, Arianna K, Dudenhausen, Elizabeth E, Merritt, Matthew E, Kilberg, Michael S (March 2023) Characterizing asparagine synthetase deficiency variants in lymphoblastoid cell lines. JIMD Reports, 64 (2). pp. 167-179. ISSN 2192-8304

Staklinski, Stephen J, Scheben, Armin, Siepel, Adam, Kilberg, Michael S (November 2023) Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification. bioRxiv. (Submitted)

Standring, Oliver, Gholami, Sepideh (September 2023) Adjuvant hepatic artery infusion pump chemotherapy for resected colorectal cancer liver metastases. Surgery, 174 (3). pp. 747-749. ISSN 0039-6060

Stevenson, Dennis Wm, Ramakrishnan, Srividya, Alves, Cristiane de Santis, Coelho, Laís Araujo, Kramer, Melissa, Goodwin, Sara, Ramos, Olivia Mendevil, Eshel, Gil, Sondervan, Veronica M, Frangos, Samantha, Zumajo-Cardona, Cecilia, Jenike, Katherine, Ou, Shujun, Wang, Xiaojin, Lee, Yin Peng, Loke, Stella, Rossetto, Maurizio, McPherson, Hannah, Nigris, Sebastiano, Moschin, Silvia, Little, Damon P, Katari, Manpreet S, Varala, Kranthi, Kolokotronis, Sergios-Orestis, Ambrose, Barbara, Croft, Larry J, Coruzzi, Gloria M, Schatz, Michael, McCombie, W Richard, Martienssen, Robert A (August 2023) The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. bioRxiv. (Public Dataset) (Submitted)

Sun, S, Homer, JA, Smedley, CJ, Cheng, QQ, Sharpless, KB, Moses, JE (August 2023) Phosphorus fluoride exchange: Multidimensional catalytic click chemistry from phosphorus connective hubs. Chem, 9 (8). pp. 2128-2143. ISSN 2451-9308

Sun, Shenghuan, Torok, Justin, Mezias, Christopher, Ma, Daren, Raj, Ashish (October 2023) Spatial cell-type enrichment predicts mouse brain connectivity. Cell Reports, 42 (10). p. 113258. ISSN 2211-1247

Sun, Qingtao, van de Lisdonk, Daniëlle, Ferrer, Miriam, Gegenhuber, Bruno, Wu, Melody, Tollkuhn, Jessica, Janowitz, Tobias, Li, Bo (January 2023) Area postrema neurons mediate interleukin-6 function in cancer-associated cachexia. bioRxiv. (Unpublished)

Suresh, Hamsini, Crow, Megan, Jorstad, Nikolas, Hodge, Rebecca, Lein, Ed, Dobin, Alexander, Bakken, Trygve, Gillis, Jesse (September 2023) Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution. Nature Ecology and Evolution. ISSN 2397-334X

Swentowsky, Kyle W (November 2023) Multifactor Agitation: Several Minor Stresses Severely Compromise Crop Growth When Combined. Plant Physiology. kiad608. ISSN 0032-0889

Swentowsky, Kyle W, Robil, Janlo M (April 2023) Timekeeper's Dilemma: How Photo-Thermal Cues Alter Flowering Duration. Plant Physiology. kiad240. ISSN 0032-0889

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Werner, Jonathan M, Gillis, Jesse (October 2023) Preservation of co-expression defines the primary tissue fidelity of human neural organoids. bioRxiv. (Submitted)

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Westcott, Peter MK, Muyas, Francesc, Hauck, Haley, Smith, Olivia C, Sacks, Nathan J, Ely, Zackery A, Jaeger, Alex M, Rideout, William M, Zhang, Daniel, Bhutkar, Arjun, Beytagh, Mary C, Canner, David A, Jaramillo, Grissel C, Bronson, Roderick T, Naranjo, Santiago, Jin, Abbey, Patten, JJ, Cruz, Amanda M, Shanahan, Sean-Luc, Cortes-Ciriano, Isidro, Jacks, Tyler (September 2023) Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity. Nature Genetics. ISSN 1061-4036

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Wroten, Mathew, Yoon, Seungtai, Andrews, Peter, Yamrom, Boris, Ronemus, Michael, Buja, Andreas, Krieger, Abba M, Levy, Dan, Ye, Kenny, Wigler, Michael, Iossifov, Ivan (June 2023) Sharing parental genomes by siblings concordant or discordant for autism. Cell Genomics, 3 (6). p. 100319. ISSN 2666-979X (Public Dataset)

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Xu, Jihao, Roe, Jae-Seok, Lee, EunJung, Tonelli, Claudia, Ji, Keely Y, Younis, Omar W, Somervile, Tim DD, Yao, Melissa, Milazzo, Joseph P, Tiriac, Herve, Kolarzyk, Anna M, Lee, Esak, Grem, Jean L, Lazenby, Audrey J, Grunkemeyer, James A, Hollingsworth, Michael A, Grandgenett, Paul M, Borowsky, Alexander D, Park, Youngkyu, Vakoc, Christopher R, Tuveson, David A, Hwang, Chang-Il (December 2023) Engrailed-1 Promotes Pancreatic Cancer Metastasis. Advanced Science. e2308537. ISSN 2198-3844

Yaeger, Rona, Mezzadra, Riccardo, Sinopoli, Jenna, Bian, Yu, Marasco, Michelangelo, Kaplun, Esther, Gao, Yijun, Zhao, HuiYong, Paula, Arnaud Da Cruz, Zhu, Yingjie, Perez, Almudena Chaves, Chadalavada, Kalyani, Tse, Edison, Chowdhry, Sudhir, Bowker, Sydney, Chang, Qing, Qeriqi, Besnik, Weigelt, Britta, Nanjangud, Gouri J, Berger, Michael F, Der-Torossian, Hirak, Anderes, Kenna, Socci, Nicholas D, Shia, Jinru, Riely, Gregory J, Murciano-Goroff, Yonina R, Li, Bob T, Christensen, James G, Reis-Filho, Jorge S, Solit, David B, de Stanchina, Elisa, Lowe, Scott W, Rosen, Neal, Misale, Sandra (January 2023) Molecular Characterization of Acquired Resistance to KRASG12C-EGFR Inhibition in Colorectal Cancer. Cancer Discovery, 13 (1). pp. 41-55. ISSN 2159-8274

Yan, Ran, Moresco, Philip, Gegenhuber, Bruno, Fearon, Douglas T (June 2023) T cell-Mediated Development of Stromal Fibroblasts with an Immune-Enhancing Chemokine Profile. Cancer Immunology Research. OF1-OF11. ISSN 2326-6066

Yang, Ning, Wang, Yuebin, Luo, Yun, Guo, Xing, Li, Yunfu, Yan, Jiali, Shao, Wenwen, Wei, Wenjie, Jackson, David, Zhang, Zuxin, Yan, Jianbing, Liu, Huan, Liu, Lei (June 2023) A spatial transcriptome map of developing maize ear. Research square. (Public Dataset) (Submitted)

Yang, Xiangyu, Wang, Xuankai, Zou, Yawen, Zhang, Shilong, Xia, Manying, Fu, Lianting, Vollger, Mitchell R, Chen, Nae-Chyun, Taylor, Dylan J, Harvey, William T, Logsdon, Glennis A, Meng, Dan, Shi, Junfeng, McCoy, Rajiv C, Schatz, Michael C, Li, Weidong, Eichler, Evan E, Lu, Qing, Mao, Yafei (July 2023) Characterization of large-scale genomic differences in the first complete human genome. Genome Biology, 24 (1). p. 157. ISSN 1474-760X

Yao, M, Tudi, A, Jiang, T, An, X, Sun, Q, Li, A, Huang, ZJ, Gong, H, Li, X (April 2023) Long-range connectome of pyramidal neurons in the sensorimotor cortex. iScience, 26 (4). p. 106316. ISSN 2589-0042

Yao, Min, Preall, Jonathan, Yeh, Johannes, Pappin, Darryl J, Cifani, Paolo, Zhao, Yixin, Shen, Sophia, Moresco, Philip, He, Brian, Patel, Hardik, Habowski, Amber N, King, Daniel A, Raphael, Kara L, Rishi, Arvind, Sejpal, Divyesh V, Weiss, Matthew, Tuveson, David, Fearon, Douglas T (September 2023) Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens. JCI Insight. e172449. ISSN 2379-3708 (Public Dataset)

Yoo, Hye-Been, Moon, Jin Woo, Kim, Hwa-Ryeon, Lee, Hee Seung, Miyabayashi, Koji, Park, Chan Hee, Ge, Sabrina, Zhang, Amy, Tae, Yoo Keung, Sub, Yujin, Park, Hyun-Woo, Gee, Heon Yung, Notta, Faiyaz, Tuveson, David A, Bang, Seungmin, Kim, Mi-Young, Roe, Jae-Seok (July 2023) A TEAD2-Driven Endothelial-Like Program Shapes Basal-Like Differentiation and Metastasis of Pancreatic Cancer. Gastroenterology, 165 (1). 133-148.e17. ISSN 0016-5085

Yu, Ruofan, Roseman, Shelby, Siegenfeld, Allison P, Nguyen, Son C, Joyce, Eric F, Liau, Brian B, Krantz, Ian D, Alexander, Katherine A, Berger, Shelley L (July 2023) CTCF/cohesin organize the ground state of chromatin-nuclear speckle association. bioRxiv. (Submitted)

Yuan, Li, Chen, Xiaoyin, Zhan, Huiqing, Gilbert, Henry L, Zador, Anthony M (February 2023) Massive Multiplexing of Spatially Resolved Single Neuron Projections with Axonal BARseq. bioRxiv. (Submitted)

Zador, Anthony, Escola, Sean, Richards, Blake, Ölveczky, Bence, Bengio, Yoshua, Boahen, Kwabena, Botvinick, Matthew, Chklovskii, Dmitri, Churchland, Anne, Clopath, Claudia, DiCarlo, James, Ganguli, Surya, Hawkins, Jeff, Körding, Konrad, Koulakov, Alexei, LeCun, Yann, Lillicrap, Timothy, Marblestone, Adam, Olshausen, Bruno, Pouget, Alexandre, Savin, Cristina, Sejnowski, Terrence, Simoncelli, Eero, Solla, Sara, Sussillo, David, Tolias, Andreas S, Tsao, Doris (March 2023) Catalyzing next-generation Artificial Intelligence through NeuroAI. Nature Communications, 14 (1). p. 1597. ISSN 2041-1723

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Zeisler, Zachary R, London, Liza, Janssen, William G, Fredericks, J Megan, Elorette, Catherine, Fujimoto, Atsushi, Zhan, Huiqing, Russ, Brian E, Clem, Roger L, Hof, Patrick R, Stoll, Frederic M, Rudebeck, Peter H (October 2023) Single basolateral amygdala neurons in macaques exhibit distinct connectional motifs with frontal cortex. Neuron, 111 (20). 3307-3320.e5. ISSN 0896-6273

Zeraati, Roxana, Shi, Yan-Liang, Steinmetz, Nicholas A, Gieselmann, Marc A, Thiele, Alexander, Moore, Tirin, Levina, Anna, Engel, Tatiana A (April 2023) Intrinsic timescales in the visual cortex change with selective attention and reflect spatial connectivity. Nature Communications, 14 (1). p. 1858. ISSN 2041-1723

Zhang, Anqi, Zador, Anthony M (December 2023) Neurons in the primary visual cortex of freely moving rats encode both sensory and non-sensory task variables. PLoS Biology, 21 (12). e3002384. ISSN 1545-7885

Zhang, Lifang, Braynen, Janeen, Fahey, Audrey, Chopra, Kriti, Cifani, Paolo, Tadesse, Dimiru, Regulski, Michael, Hu, Fangle, van Dam, Hubertus JJ, Xie, Meng, Ware, Doreen, Blaby-Haas, Crysten E (2023) Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. Frontiers in Plant Science, 14. p. 1237722. ISSN 1664-462X

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Zhao, Guodong, Ge, Qinyu, Lan, Wenjun, Zheng, Bo, Liang, Yuting (December 2023) Editorial: Advance in translational genomics based biomarkers for cancer management: discovery and application. Frontiers in Genetics, 14. p. 1342616. ISSN 1664-8021

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Zhou, Yong, Yu, Zhichao, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Rivera, Luis F, Kathiresan, Nagarajan, Al-Bader, Noor, Mohammed, Nahed, Alsantely, Aseel, Mussurova, Saule, Santos, João, Thimma, Manjula, Troukhan, Maxim, Fornasiero, Alice, Green, Carl D, Copetti, Dario, Kudrna, David, Llaca, Victor, Lorieux, Mathias, Zuccolo, Andrea, Ware, Doreen, McNally, Kenneth, Zhang, Jianwei, Wing, Rod A (March 2023) Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nature Communications, 14 (1). p. 1567. ISSN 2041-1723

Zhu, Jiening, Oh, Jung Hun, Simhal, Anish K, Elkin, Rena, Norton, Larry, Deasy, Joseph O, Tannenbaum, Allen (September 2023) Geometric graph neural networks on multi-omics data to predict cancer survival outcomes. Computers in Biology and Medicine, 163. p. 107117. ISSN 0010-4825

Zilbauer, Matthias, James, Kylie R, Kaur, Mandeep, Pott, Sebastian, Li, Zhixin, Burger, Albert, Thiagarajah, Jay R, Burclaff, Joseph, Jahnsen, Frode L, Perrone, Francesca, Ross, Alexander D, Matteoli, Gianluca, Stakenborg, Nathalie, Sujino, Tomohisa, Moor, Andreas, Bartolome-Casado, Raquel, Bækkevold, Espen S, Zhou, Ran, Xie, Bingqing, Lau, Ken S, Din, Shahida, Magness, Scott T, Yao, Qiuming, Beyaz, Semir, Arends, Mark, Denadai-Souza, Alexandre, Coburn, Lori A, Gaublomme, Jellert T, Baldock, Richard, Papatheodorou, Irene, Ordovas-Montanes, Jose, Boeckxstaens, Guy, Hupalowska, Anna, Teichmann, Sarah A, Regev, Aviv, Xavier, Ramnik J, Simmons, Alison, Snyder, Michael P, Wilson, Keith T, Gut Cell Atlas Consortium, Human Cell Atlas Gut Biological Network Consortium (September 2023) A Roadmap for the Human Gut Cell Atlas. Nature Reviews Gastroenterology & Hepatology, 20 (9). pp. 597-614. ISSN 1759-5045

de Ruiter Swain, Jed, Michalopoulou, Evdokia, Noch, Evan K, Lukey, Michael J, Van Aelst, Linda (August 2023) Metabolic partitioning in the brain and its hijacking by glioblastoma. Genes and Development, 37. pp. 681-702. ISSN 0890-9369

Book Section

Sun, SD, Tollkuhn, J (January 2023) Regulation of gene expression in the brain by sex hormones. In: Principles of Gender-Specific Medicine: Sex and Gender-Specific Biology in the Postgenomic Era. UNSPECIFIED, pp. 117-127. ISBN 9780323885348

Conference or Workshop Item

Abuhadra, Nour, Chen, Yuan, Plitas, George, Razavi, Pedram, Pareja, Fresia, Reis-Filho, Jorge S, Wen, Hannah Yong, Khan, Atif J, Traina, Tiffany A, Downs-Canner, Stephanie, Robson, Mark E, Norton, Larry, Montagna, Giacomo (2023) Prospective evaluation of pathologic response with neoadjuvant chemo-immunotherapy in metaplastic breast cancer. In: UNSPECIFIED.

Balogun, Onyinye, Davis, Melissa, Mehallow, Michelle, Robine, Nicolas, Winterkorn, Lara, Oschwald, Dayna, Zody, Michael, Aparicio, Samuel, Maniatis, Tom, Varmus, Harold, Sawyers, Charles, Tuveson, David (2023) Polyethnic-1000: A New York-based initiative to advance cancer genomics through recruitment of diverse racial & ethnic populations. In: AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved.

Bast, Walter G, Aghamohammadi, Cina, Gupta, Priyanka, Engel, Tatiana A, Albeanu, Dinu F (2023) An optogenetic stimulation approach to quantify the contribution of individual glomeruli to olfactory percepts. In: UNSPECIFIED.

Belkhatir, Z, Berkane, S, Norton, L, Tannenbaum, A (November 2023) Nonlinear Impulsive Control Design for Biologically Grounded NSM Tumor Growth Model Using Exact Linearized Mapping. In: UNSPECIFIED.

Bhaloo, Shirin, Gazzo, Andrea, Paula, Arnaud Da Cruz, da Silva, Edaise M, Selenica, Pier, Zhu, Yingjie, Blanco-Heredia, Juan, Pei, Xin, Patel, Juber, Wen, Hannah, Riaz, Nadeem, Powell, Simon, Chandarlapaty, Sarat, Norton, Larry, Brown, David, Weigelt, Britta, Pareja, Fresia, Reis-Filho, Jorge (2023) Whole-genome Sequencing Analysis of Metaplastic Breast Cancers Shows Infrequent Homologous Recombination Deficiency. In: 112th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), MAR 11-16, 2023, Mexico.

Burr, Ansen, Ji, Junyi, Ozler, Kadir, Mentrup, Heather, Eskiocak, Onur, Cumberland, Rachel, Menk, Ashley, Zhang, Xiaoyi, Overacre-Delgoffe, Abigail, Rittenhouse, Natalie, Marshall, Chris, Cooper, Vaughn, Poholek, Amanda, Delgoffe, Greg, Beyaz, Semir, Hand, Timothy (2023) Excess dietary sugar alters colonocyte metabolism and impairs the early proliferative response to damage. In: Crohns and Colitis Congress, JAN 19-21, 2023, Denver, CO.

Cheadle, L (2023) Refinement of developing circuits through synaptic phagocytosis by oligodendrocyte precursor cells. In: Glia.

Chung, Charlie, Nizam, Aaron, Yueh, Brian, Subhash, Santhilal, Eskiocak, Onur, Frimer, Marina, Goldberg, Gary L, Beyaz, Semir (2023) Autologous patient-derived organoid-immune cell co-culture platform for therapeutic discovery in high-grade endometrial cancer. In: 114th Annual Meeting of the American Association for Cancer Research (AACR), APR 14-19, 2023, Orlando, FL.

Chung, Charlie, Ozcelik, Elif, Habel, Jill, Zhang, Jialin, Qin, Yihan, Garcia, Libia, Merrill, Joseph, Chung, Taemoon, Lyons, Scott, Shen, Zeli, Fox, James G, Westcott, Peter, Beyaz, Semir (2023) Microbial regulation of anti-tumor immunity in colorectal cancer. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024, 2024 Apr 5-10, San Diego, CA.

Ciubotaru, Mihai, Ionita, Elena, Koo, Peter (2023) RAG DNA recombinase mechanism investigated by single molecule assays; novel reaction mechanism derived from thermodynamics and statistical analysis. In: 25th International Analytical Ultracentrifugation Conference, July 10-15, 2022, Lethbridge, AB, Canada.

Demyan, Lyudmyla, Standring, Oliver, Chung, Taemoon, Gazzara, Emma, Lyons, Scott, Park, Youngkyu, King, Daniel, Jonas, Oliver, Tuveson, David, Weiss, Matthew (2023) Feasibility of Implantable Microdosing Devices to Perform in vivo Pharmacotyping in Pancreatic Cancer. In: Annual International Conference of the Society-of-Surgical-Oncology (SSO) on Surgical Cancer Care, MAR 22-25, 2023, Boston, MA.

Ferrer, Miriam, Mourikis, Nicholas, Davidson, Emma E, Kleeman, Sam O, Zaccaria, Marta, Habel, Jill, Rubino, Rachel, Flint, Thomas R, Connell, Claire M, Lukey, Michael J, White, Eileen P, Coll, Anthony P, Venkitaraman, Ashok R, Janowitz, Tobias (2023) Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023, 2023 Apr 14-19, Orlando, FL.

Gallo, NB, George, S, Boato, F, Berisha, A, Chan, S, Van Aelst, L (2023) Microglia Regulate Chandelier Cell Axo-axonic Synaptogenesis. In: UNSPECIFIED.

Garipcan, Aybuke, Eskiocak, Onur, Subhash, Santhilal, Ozler, Kadir, Yueh, Brian, Chung, Charlie, Ergin, Ilgin, Gautier, Nelson, Habel, Jill, Rubino, Rachel, Van der Velden, Adrianus WM, Beyaz, Semir (2023) Epigenetic mechanisms of epithelial - immune interactions that shape immune surveillance in the intestinal epithelium. In: UNSPECIFIED.

He, Xue-Yan, Ng, David, Gao, Yuan, Michalopoulou, Evdokia, George, Shanu, Adrover, Jose M, Sun, Lijuan, Albrengues, Jean, Wan, Ledong, Han, Xiao, Vakoc, Christopher, Van Aelst, Linda, Egeblad, Mikala (2023) Untangling the connection between stress and metastatic breast cancer. In: American Association for Cancer Research Annual Meeting 2023, 2023 Apr 14-19, Orlando, FL.

Kapoor, Muskan, Tuggle, Christopher K, Burdett, Tony, Tickle, Timothy, Harrison, Peter, Elsik, Christine, Provart, Nicholas, Libault, Marc, Warren, Wes, Koltes, James E, Sokolov, Alexey, Ventura, Enrique Sapena, Yordanova, Galabina, Papatheodorou, Irene, George, Nancy, Ware, Doreen, Kumari, Sunita, Daharsh, Lance, Cole, Benjamin (2023) Computational Tools and Resources for Analysis and Exploration of Single-Cell Rnaseq Data in Agriculture. In: UNSPECIFIED.

Katcher, Arielle, Chung, Charlie, Gorman, Megan, Yueh, Brian, Lyons, Scott, Merrill, Joseph, Garcia, Libia, Frimer, Marina, Goldberg, Gary L, Beyaz, Semir (2023) A clinically-relevant orthotopic endometrial carcinosarcoma mouse model using human patient-derived organoids. In: American Association for Cancer Research Annual Meeting 2023, 2023 Apr 14-19, Orlando, FL.

Kaur, Gagandeep, Selenica, Pier, Gazzo, Andrea, Cartagena, Lorraine Colon, Daaboul, Fayez, Dopeso, Higinio, da Silva, Edaise M, Ross, Dara, Zhang, Hong Amy, Wen, Hannah, Chandarlapaty, Sarat, Robson, Mark, Mandelker, Diana, Powell, Simon, Norton, Larry, Brogi, Edi, Reis-Filho, Jorge, Pareja, Fresia (2023) The Histologic and Genomic Features of Breast Cancers Harboring Genetic Alterations in RecQ DNA Helicases. In: 112th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), MAR 11-16, 2023, Mexico.

Klindt, D, Gaukstad, S, Vaupel, M, Hermansen, E, Dunn, B (January 2023) Topological Ensemble Detection with Differentiable Yoking. In: Proceedings of Machine Learning Research.

Klindt, David, Acosta, Francisco, Conwell, Colin, Sanborn, Sophia, Miolane, Nina (December 2023) Evaluation of Representational Similarity Scores Across Human Visual Cortex. In: UniReps: the First Workshop on Unifying Representations in Neural Models.

Lei, Pin-Ji, Pereira, Ethel, Andersson, Patrik, Amoozgar, Zohreh, Van Wijnbergen, Jan Willem, O'Melia, Meghan J, Zhou, Hengbo, Chatterjee, Sampurna, Ho, William Wee, Posada, Jessica M, Kumar, Ashwin Srinivasan, Morita, Satoru, Chuang, Charlie, Ergin, Ilgin, Jones, Dennis, Huang, Peigen, Beyaz, Semir, Padera, Timothy P (2023) Single cell analysis of breast cancer progression and metastasis to lymph nodes reveals cancer cell plasticity and MHC class II-mediated immune regulation. In: 114th Annual Meeting of the American Association for Cancer Research (AACR), APR 14-19, 2023, Orlando, FL.

McArthur, Heather L, Comen, Elizabeth Anne, Bryce, Yolanda, Solomon, Stephen Barnett, Leal, Jorge Henrique S, Abaya, Christina DiLauro, Martinez, Cristal, Basho, Reva K, McAndrew, Philomena, Larkin, Brigid, Page, David B, Mellinger, Staci L, Fredrich, Nicole, Moxon, Nicole, Reddy, Sangeetha M, Carter, Meredith, Patil, Sujata, Dogan, Basak, Gatti-Mays, Margaret Elena, Norton, Larry (2023) A single-arm phase 2 study of peri-operative immune checkpoint inhibition and cryoablation in women with hormone receptor-negative, HER2-negative, early-stage/resectable breast cancer. In: UNSPECIFIED.

Moffitt, Andrea B, Alexander, Joan, Stepansky, Asya, Boyle, Erin, Stauder, Danielle, Lopez, Carlos Alberto, Wu, Vernon, Hakim, Nausheen, Wang, Zihua, Kolitz, Jonathan E, Chiorazzi, Nicholas, Chitty, David W, Allen, Steven L, Levy, Dan, Wigler, Michael (November 2023) Personalized Residual Disease Detection in Acute Myeloid Leukemia with a Multiplexed Genomic Fingerprint Predicts Patient Outcomes. In: UNSPECIFIED.

Paul, S, Heinbaugh, A, Paul, A, Cifani, P, Pappin, D, Spratt, T (2023) Novel role of Translesion DNA synthesis polymerase kappa in the nucleolus and in nucleolar stress response recovery. In: Annual Meeting of the American-Society-for-Cell-Biology/ European-Molecular-Biology-Organisation, DEC 03-07, 2022, Washington, DC.

Safonov, A, Mehine, M, Ceyhan-Birsoy, O, Brown, D, Bandlamudi, C, Forbes, A, Gazzo, A, Selenica, P, Shen, R, Khurana, E, Norton, L, Solit, D, Chandarlapaty, S, Razavi, P, Robson, M, Weigelt, B, Berger, M, Ladanyi, M, Reis-Filho, JS, Mandelker, D (2023) Pan-cancer assessment of the impact of intronic variants on cancer development and progression. In: UNSPECIFIED.

Shen, Sherry, Solomon, Verna, Williams, Dominiq, Robson, Mark E, Norton, Larry, Traina, Tiffany A, Iyengar, Neil M (2023) The ARETHA study: A phase 2 randomized control trial of eribulin with evexomostat (SDX7320) or placebo for patients with metastatic triple-negative breast cancer (TNBC) and metabolic dysfunction. In: UNSPECIFIED.

Simhal, Anish Kumar, Maclachlan, Kylee H, Usmani, Saad Z, Norton, Larry, Deasy, Joseph O, Oh, Jung Hun, Tannenbaum, Allen (November 2023) Network Modeling of Apoptosis-Related Genes Reveal a High-Risk Cluster in Multiple Myeloma. In: UNSPECIFIED.

Sun, Sherine Xueqin, Klingbeil, Olaf, Vakoc, Christopher, Mills, Alea (2023) BRD8-driven EP400 complex hijacks H2AZ to maintain proliferation in glioblastoma. In: American Association for Cancer Research Annual Meeting 2023, 2023 Apr 14-19, Orlando, FL.

Trejo, Diego E Hernandez, Ciuparu, Andrei, da Silva, Pedro Garcia, Velasquez, Cristina M, Rebouillat, Benjamin, Gross, Michael, Davis, Martin B, Mureayan, Raul C, Albeanu, Dinu F (2023) Cortical-bulbar Feedback Supports Behavioral Flexibility During Rule Reversal. In: UNSPECIFIED.

Xiao, Lanbo, He, Tongchen, Klingbeil, Olaf, Eleanor, Young, Wu, Xiaoli, Qiao, Yuanyuan, Parolia, Abhijit, Eyunni, Sanjana, Mannan, Rahul, Mahapatra, Somnath, Kim, NamHoon, Zheng, Heng, Su, Fengyun, Cao, Xuhong, Samajdar, Susanta, Ramachandra, Murali, Vakoc, Christopher R, Chinnaiyan, Arul M (2023) Targeting the SWI/SNF complex in POU2F-POU2AF transcription factor-driven malignancies. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024, 2024 Apr 5-10, San Diego, CA.

Zhi, Iris, Lake, Diana E, Ehrich, Fiona, Chen, Yuan, Korc-Grodzicki, Beatriz, Norton, Larry, Robson, Mark E, Singh, Jasmeet Chadha (2023) Older patients with early-stage triple-negative breast cancer: The Memorial Sloan Kettering Cancer Center experience. In: UNSPECIFIED.

Thesis

Aguirre, Lyndsey (March 2023) Dissection of Quantitative Epistasis in Tomato Meristem Development. PhD thesis, Cold Spring Harbor Laboratory.

Boyle, Sara (May 2023) The Central Amygdala Encodes Nutritional Properties and Modulates Weight Gain. PhD thesis, Cold Spring Harbor Laboratory.

Corona, Alberto (March 2023) Sex-dependent neural activity underlying parenting behavior in mice. PhD thesis, Cold Spring Harbor Laboratory.

Ergin, Ilgin (May 2023) Metabolic regulation of anti-tumor immunity. PhD thesis, Cold Spring Harbor Laboratory.

Hu, Yuzhao (August 2023) Role of cryptochromes in chromatin remodeling and DNA damage repair. PhD thesis, Cold Spring Harbor Laboratory.

Lakhani, Asad A (March 2023) The Role of Recurrently Observed Aneuploidy in Tumorigenesis. PhD thesis, Cold Spring Harbor Laboratory.

Maia-Silva, Diogo (March 2023) MECHANISMS OF GENE TRANSCRIPTION BY TP63 AND THE MEDIATOR COMPLEX IN SQUAMOUS PANCREATIC CANCER. PhD thesis, Cold Spring Harbor Laboratory.

Pagliaro, Alexa H (May 2023) A disrupted parvalbumin network state impairs maternal behavior in a mouse model of Rett Syndrome. PhD thesis, Cold Spring Harbor Laboratory.

Ruiz-Ortiz, Jenelys (May 2023) Characterizing Models to Study Cellular Composition Changes in Response to Pregnancy Hormones in the Human Mammary Gland. PhD thesis, Cold Spring Harbor Laboratory.

Wang, Julia Huiming (June 2023) Interpretable Brain State Manifold for Characterizing Heterogeneity. PhD thesis, Cold Spring Harbor Laboratory.

Werner, Jonathan M (December 2023) Transcriptomic approaches for investigating developmental lineage: exploiting the X-chromosome as a marker for lineage specification and quantifying the lineage fidelity of neural organoid systems. PhD thesis, Cold Spring Harbor Laboratory.

Wunderlich, Cole (September 2023) Quantifying Transposable Element Expression in Single-Cell RNA Sequencing Data. PhD thesis, Cold Spring Harbor Laboratory.

Yuan, Chengxiang (March 2023) Applications of oligonucleotide ligation in sequencing. PhD thesis, Cold Spring Harbor Laboratory.

Other

Zador, Anthony M (February 2023) Charles F. Stevens (1934-2022). Springer Science and Business Media LLC.