Aghi, K, Anderson, BM, Castellano, BM, Cunningham, A, Delano, M, Dickinson, ES, von Diezmann, L, Forslund-Startceva, SK, Grijseels, DM, Groh, SS, Guthman, EM, Jayasinghe, I, Johnston, J, Long, S, McLaughlin, JF, McLaughlin, M, Miyagi, M, Rajaraman, B, Sancheznieto, F, Scheim, AI, Sun, SD, Titmuss, FD, Walsh, RJ, Weinberg, ZY (March 2024) Rigorous science demands support of transgender scientists. Cell, 187 (6). pp. 1327-1334. ISSN 0092-8674
Aghi, K, Goetz, TG, Pfau, DR, Sun, SD, Guthman, EM, Roepke, TA (January 2024) Using Animal Models for Gender-Affirming Hormone Therapy. Journal of the Endocrine Society, 8 (1). ISSN 2472-1972
Aguado, Brian A, Jeffries, Daniel L, Jordan-Young, Rebecca, Klein, Sabra L, Lett, Elle, Stachenfeld, Nina, Tollkuhn, Jessica, Xu, Xiaohong (March 2024) The future of sex and gender in research. Cell, 187 (6). pp. 1354-1357. ISSN 0092-8674
Aguzzoli Heberle, Bernardo, 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 (May 2024) Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nature Biotechnology. ISSN 1087-0156 (Public Dataset)
Alpsoy, Aktan, Wu, Xiaoli S, Pal, Sujay, Klingbeil, Olaf, Kumar, Pramod, El Demerdash, Osama, Nalbant, Benan, Vakoc, Christopher R (January 2024) IκBζ is a dual-use coactivator of NF-κB and POU transcription factors. Molecular Cell. S1097-2765(24)00008. ISSN 1097-2765 (Public Dataset)
Amit, Moran, Anastasaki, Corina, Dantzer, Robert, Demir, Ihsan Ekin, Deneen, Benjamin, Dixon, Karen O, Egeblad, Mikala, Gibson, Erin M, Hervey-Jumper, Shawn L, Hondermarck, Hubert, Magnon, Claire, Monje, Michelle, Na'ara, Shorook, Pan, Yuan, Repasky, Elizabeth A, Scheff, Nicole N, Sloan, Erica K, Talbot, Sebastien, Tracey, Kevin J, Trotman, Lloyd C, Valiente, Manuel, Van Aelst, Linda, Venkataramani, Varun, Venkatesh, Humsa S, Vermeer, Paola D, Winkler, Frank, Wong, Richard J, Gutmann, David H, Borniger, Jeremy C (April 2024) Next Directions in the Neuroscience of Cancers Arising outside the CNS. Cancer Discovery, 14 (4). pp. 669-673. ISSN 2159-8274
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 (January 2024) Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Nature Aging. ISSN 2662-8465 (Public Dataset)
Asiimwe, Rebecca, Alexander, Dobin (February 2024) STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads. bioRxiv. (Submitted)
Avissar-Whiting, Michele, Belliard, Frédérique, Bertozzi, Stefano M, Brand, Amy, Brown, Katherine, Clément-Stoneham, Géraldine, Dawson, Stephanie, Dey, Gautam, Ecer, Daniel, Edmunds, Scott C, Farley, Ashley, Fischer, Tara D, Franko, Maryrose, Fraser, James S, Funk, Kathryn, Ganier, Clarisse, Harrison, Melissa, Hatch, Anna, Hazlett, Haley, Hindle, Samantha, Hook, Daniel W, Hurst, Phil, Kamoun, Sophien, Kiley, Robert, Lacy, Michael M, LaFlamme, Marcel, Lawrence, Rebecca, Lemberger, Thomas, Leptin, Maria, Lumb, Elliott, MacCallum, Catriona J, Marcum, Christopher Steven, Marinello, Gabriele, Mendonça, Alex, Monaco, Sara, Neves, Kleber, Pattinson, Damian, Polka, Jessica K, Puebla, Iratxe, Rittman, Martyn, Royle, Stephen J, Saderi, Daniela, Sever, Richard, Shearer, Kathleen, Spiro, John E, Stern, Bodo, Taraborelli, Dario, Vale, Ron, Vasquez, Claudia G, Waltman, Ludo, Watt, Fiona M, Weinberg, Zara Y, Williams, Mark (February 2024) Recommendations for accelerating open preprint peer review to improve the culture of science. PLoS Biology, 22 (2). e3002502. ISSN 1544-9173
Badger, Jonathan H, Giordano, Rosanna, Zimin, Aleksey, Wappel, Robert, Eskipehlivan, Senem M, Muller, Stephanie, Donthu, Ravikiran, Soto-Adames, Felipe, Vieira, Paulo, Zasada, Inga, Goodwin, Sara (February 2024) Direct sequencing of insect symbionts via nanopore adaptive sampling. Current Opinion in Insect Science, 61. p. 101135. ISSN 2214-5745
Banerjee, Amitava, Pattinson, David J, Wincek, Cornelia L, Bunk, Paul, Chapin, Sarah R, Navlakha, Saket, Meyer, Hannah V (January 2024) BATMAN: Improved T cell receptor cross-reactivity prediction benchmarked on a comprehensive mutational scan database. bioRxiv. (Submitted)
Banerjee, Arkarup, Chen, Feng, Druckmann, Shaul, Long, Michael A (January 2024) Temporal scaling of motor cortical dynamics reveals hierarchical control of vocal production. Nature Neuroscience. ISSN 1097-6256
Boelaars, Kelly, Rodriguez, Ernesto, Huinen, Zowi R, Liu, Chang, Wang, Di, Springer, Babet O, Olesek, Katarzyna, Goossens-Kruijssen, Laura, van Ee, Thomas, Lindijer, Dimitri, Tak, Willemijn, de Haas, Aram, Wehry, Laetitia, Nugteren-Boogaard, Joline P, Mikula, Aleksandra, de Winde, Charlotte M, Mebius, Reina E, Tuveson, David A, Giovannetti, Elisa, Bijlsma, Maarten F, Wuhrer, Manfred, van Vliet, Sandra J, van Kooyk, Yvette (April 2024) Pancreatic cancer-associated fibroblasts modulate macrophage differentiation via sialic acid-Siglec interactions. Communications Biology, 7 (1). p. 430. ISSN 2399-3642 (Public Dataset)
Boire, Adrienne, Burke, Katy, Cox, Thomas R, Guise, Theresa, Jamal-Hanjani, Mariam, Janowitz, Tobias, Kaplan, Rosandra, Lee, Rebecca, Swanton, Charles, Vander Heiden, Matthew G, Sahai, Erik (June 2024) Why do patients with cancer die? Nature Reviews Cancer. ISSN 1474-175X
Boyer, Jacob A, Sharma, Malvika, Dorso, Madeline, Mai, Nicholas, Amor, Corina, Reiter, Jason M, Kannan, Ram, Gadal, Sunyana, Xu, Jianing, Miele, Matthew, Zhuoning, Li, Chen, Xiaoping, Chang, Qing, Pareja, Fresia, Worland, Stephan, Warner, Douglas, Sperry, Sam, Chiang, Gary G, Thompson, Peggy A, Yang, Guangli, Ouerfelli, Ouathek, De Stanchina, Elisa, Wendel, Hans G, Rosen, Ezra Y, Chandarlapaty, Sarat, Rosen, Neal (May 2024) eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer. bioRxiv. (Submitted)
Burbridge, Timothy J, Ratliff, Jacob M, Dwivedi, Deepanjali, Vrudhula, Uma, Alvarado-Huerta, Francisco, Sjulson, Lucas, Ibrahim, Leena Ali, Cheadle, Lucas, Fishell, Gordon, Batista-Brito, Renata (April 2024) Disruption of Cholinergic Retinal Waves Alters Visual Cortex Development and Function. bioRxiv. (Public Dataset) (Submitted)
Chen, Xiaoyin, Fischer, Stephan, Rue, Mara CP, Zhang, Aixin, Mukherjee, Didhiti, Kanold, Patrick O, Gillis, Jesse, Zador, Anthony M (April 2024) Whole-cortex in situ sequencing reveals input-dependent area identity. Nature. ISSN 0028-0836
Chorbadjiev, Liubomir, Cokol, Murat, Weinstein, Zohar, Shi, Kevin, Fleisch, Chris, Dimitrov, Nikolay, Mladenov, Svetlin, Xu, Simon, Hall, Jake, Ford, Steven, Lee, Yoon-Ha, Yamrom, Boris, Marks, Steven, Munoz, Adriana, Lash, Alex, Volfovsky, Natalia, Iossifov, Ivan (February 2024) The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI. bioRxiv. (Submitted)
Ciren, Danielle, Zebell, Sophia, Lippman, Zachary B (March 2024) Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. PLoS Genetics, 20 (3). e1011174. ISSN 1553-7390
Colucci, Manuel, Zumerle, Sara, Bressan, Silvia, Gianfanti, Federico, Troiani, Martina, Valdata, Aurora, D'Ambrosio, Mariantonietta, Pasquini, Emiliano, Varesi, Angelica, Cogo, Francesca, Mosole, Simone, Dongilli, Cristina, Desbats, Maria Andrea, Contu, Liliana, Revankdar, Ajinkya, Chen, Jingjing, Kalathur, Madhuri, Perciato, Maria Luna, Basilotta, Rossella, Endre, Laczko, Schauer, Stefan, Othman, Alaa, Guccini, Ilaria, Saponaro, Miriam, Maraccani, Luisa, Bancaro, Nicolò, Lai, Ping, Liu, Lei, Pernigoni, Nicolò, Mele, Federico, Merler, Sara, Trotman, Lloyd C, Guarda, Greta, Calì, Bianca, Montopoli, Monica, Alimonti, Andrea (February 2024) Retinoic acid receptor activation reprograms senescence response and enhances anti-tumor activity of natural killer cells. Cancer Cell. S1535-6108(24)00048. ISSN 1535-6108 (Public Dataset)
Comen, Elizabeth, Budhu, Sadna, Elhanati, Yuval, Page, David, Rasalan-Ho, Teresa, Ritter, Erika, Wong, Phillip, Plitas, George, Patil, Sujata, Brogi, Edi, Jochelson, Maxine, Bryce, Yolanda, Solomon, Stephen B, Norton, Larry, Merghoub, Taha, McArthur, Heather L (February 2024) Preoperative immune checkpoint inhibition and cryoablation in early-stage breast cancer. iScience, 27 (2). p. 108880. ISSN 2589-0042
Cowley, Benjamin R, Calhoun, Adam J, Rangarajan, Nivedita, Ireland, Elise, Turner, Maxwell H, Pillow, Jonathan W, Murthy, Mala (May 2024) Mapping model units to visual neurons reveals population code for social behaviour. Nature. ISSN 0028-0836 (Public Dataset)
Critical Assessment of Genome Interpretation Consortium (February 2024) CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology, 25 (1). p. 53. ISSN 1474-7596
Dai, Enyong, Chen, Xin, Linkermann, Andreas, Jiang, Xuejun, Kang, Rui, Kagan, Valerian E, Bayir, Hülya, Yang, Wan Seok, Garcia-Saez, Ana J, Ioannou, Maria S, Janowitz, Tobias, Ran, Qitao, Gu, Wei, Gan, Boyi, Krysko, Dmitri V, Zhu, Xiaofeng, Wang, Jiayi, Krautwald, Stefan, Toyokuni, Shinya, Xie, Yangchun, Greten, Florian R, Yi, Qing, Schick, Joel, Liu, Jiao, Gabrilovich, Dmitry I, Liu, Jinbao, Zeh, Herbert J, Zhang, Donna D, Yang, Minghua, Iovanna, Juan, Kopf, Manfred, Adolph, Timon E, Chi, Jen-Tsan, Li, Changfeng, Ichijo, Hidenori, Karin, Michael, Sankaran, Vijay G, Zou, Weiping, Galluzzi, Lorenzo, Bush, Ashley I, Li, Binghui, Melino, Gerry, Baehrecke, Eric H, Lotze, Michael T, Klionsky, Daniel J, Stockwell, Brent R, Kroemer, Guido, Tang, Daolin (February 2024) A guideline on the molecular ecosystem regulating ferroptosis. Nature Cell Biology. ISSN 1465-7392
Damoci, Chris B, Merrill, Joseph R, Sun, Yanping, Lyons, Scott K, Olive, Kenneth P (March 2024) Addressing Biological Questions with Preclinical Cancer Imaging. Cold Spring Harbor Perspectives in Medicine. a041378-a041378. ISSN 2157-1422
Daruwalla, Kyle, Lipasti, Mikko (May 2024) Information bottleneck-based Hebbian learning rule naturally ties working memory and synaptic updates. Frontiers in Computational Neuroscience, 18. p. 1240348. ISSN 1662-5188
Daruwalla, Kyle, Martin, Irene Nozal, Frankel, Andrew, Naglic, Diana, Ahmad, Zainab, Hou, Xun Helen (May 2024) A 3D whole-face movement analysis system to uncover underlying physiology in mice. bioRxiv. (Submitted)
Dzien, Piotr, Raffo Iraolagoitia, Ximena, May, Stephanie, Stevenson, David, McGarry, Lynn, Soloviev, Dmitry, Brown, Gavin, Nixon, Colin, Kapeni, Chrysa, De La Roche, Maike, Blyth, Karen, Lyons, Scott, Bird, Thomas, Strathdee, Douglas, Fruhwirth, Gilbert, Carlin, Leo, Lewis, David (April 2024) Multi-scale in vivo imaging of tumour development using a germline conditional triple-reporter system. Res Sq.
Ecker, DJ, Aiello, CD, Arron, JR, Bennett, CF, Bernard, A, Breakefield, XO, Broderick, TJ, Callier, SL, Canton, B, Chen, JS, Fishburn, CS, Garrett, B, Hecht, SM, Janowitz, T, Kliegman, M, Krainer, A, Louis, CU, Lowe, C, Sehgal, A, Tozan, Y, Tracey, KJ, Urnov, F, Wattendorf, D, Williams, TW, Zhao, X, Hayden, MR (February 2024) Opportunities and challenges for innovative and equitable healthcare. Nature Reviews Drug Discovery. ISSN 1474-1776
Elkin, Rena, Oh, Jung Hun, Dela Cruz, Filemon, Norton, Larry, Deasy, Joseph O, Kung, Andrew L, Tannenbaum, Allen R (January 2024) Dynamic network curvature analysis of gene expression reveals novel potential therapeutic targets in sarcoma. Scientific Reports, 14 (1). p. 488. ISSN 2045-2322 (Public Dataset)
Eskiocak, Onur, Chowdhury, Saria, Shah, Vyom, Nnuji-John, Emmanuella, Chung, Charlie, Boyer, Jacob A, Harris, Alexander S, Habel, Jill, Sadelain, Michel, Beyaz, Semir, Amor, Corina (March 2024) Senolytic CAR T cells reverse aging-associated defects in intestinal regeneration and fitness. bioRxiv. (Submitted)
Ferro, Austin, Arshad, Anosha, Boyd, Leah, Stanley, Tess, Berisha, Adrian, Vrudhula, Uma, Gomez, Adrian M, Borniger, Jeremy C, Cheadle, Lucas M (April 2024) The cytokine receptor Fn14 is a molecular brake on neuronal activity that mediates circadian function in vivo. bioRxiv. (Submitted)
Gao, Yuan, Vakoc, Christopher R (February 2024) Therapeutic index of targeting select chromatin complexes in human cancer patients. Current Opinion in Genetics and Development, 85. p. 102162. ISSN 0959-437X
Garg, Ankur, Shang, Renfu, Cvetanovic, Todor, Lai, Eric C, Joshua-Tor, Leemor (May 2024) The structural landscape of Microprocessor Mediated pri-let-7 miRNAs processing. bioRxiv. (Submitted)
Gaudino, Stephen J, Singh, Ankita, Huang, Huakang, Padiadpu, Jyothi, Jean-Pierre, Makheni, Kempen, Cody, Bahadur, Tej, Shiomitsu, Kiyoshi, Blumberg, Richard, Shroyer, Kenneth R, Beyaz, Semir, Shulzhenko, Natalia, Morgun, Andrey, Kumar, Pawan (February 2024) Intestinal IL-22RA1 signaling regulates intrinsic and systemic lipid and glucose metabolism to alleviate obesity-associated disorders. Nature Communications, 15 (1). p. 1597. ISSN 2041-1723 (Public Dataset)
Goto, Norihiro, Westcott, Peter MK, Goto, Saori, Imada, Shinya, Taylor, Martin S, Eng, George, Braverman, Jonathan, Deshpande, Vikram, Jacks, Tyler, Agudo, Judith, Yilmaz, Ömer H (February 2024) SOX17 enables immune evasion of early colorectal adenomas and cancers. Nature. ISSN 0028-0836 (Public Dataset)
Guo, Guangran, Amor, Corina (June 2024) SGLT2 regulates immune-mediated senolysis. Nature Aging. ISSN 2662-8465
Gustafson, Jonas A, Gibson, Sophia B, Damaraju, Nikhita, Zalusky, Miranda Pg, Hoekzema, Kendra, Twesigomwe, David, Yang, Lei, Snead, Anthony A, Richmond, Phillip A, De Coster, Wouter, Olson, Nathan D, Guarracino, Andrea, Li, Qiuhui, Miller, Angela L, Goffena, Joy, Anderson, Zachery, Storz, Sophie Hr, Ward, Sydney A, Sinha, Maisha, Gonzaga-Jauregui, Claudia, Clarke, Wayne E, Basile, Anna O, Corvelo, Andre, Reeves, Catherine E, Helland, Adrienne, Musunuri, Rajeeva Lochan, Revsine, Mahler, Patterson, Karynne E, Paschal, Cate, Zakarian, Christina, Goodwin, Sara, Jensen, Tanner D, Robb, Esther, 1000 Genomes ONT Sequencing Consortium, University of Washington Center for Rare Disease Research (UW-CR, Genomics Research to Elucidate the Genetics of Rare Diseases (GR, McCombie, W Richard, Sedlazeck, Fritz J, Zook, Justin M, Montgomery, Stephen B, Garrison, Erik, Kolmogorov, Mikhail, Schatz, Michael C, McLaughlin, Richard N, Dashnow, Harriet, Zody, Michael C, Loose, Matthew, Jain, Miten, Eichler, Evan E, Miller, Danny E (March 2024) Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. medRxiv. (Public Dataset) (Submitted)
Habowski, Amber N, Budagavi, Deepthi P, Scherer, Sandra D, Aurora, Arin B, Caligiuri, Giuseppina, Flynn, William F, Langer, Ellen M, Brody, Jonathan R, Sears, Rosalie C, Foggetti, Giorgia, Arnal Estape, Anna, Nguyen, Don X, Politi, Katerina A, Shen, Xiling, Hsu, David S, Peehl, Donna M, Kurhanewicz, John, Sriram, Renuka, Suarez, Milagros, Xiao, Sophie, Du, Yuchen, Li, Xiao-Nan, Navone, Nora M, Labanca, Estefania, Willey, Christopher D (January 2024) Patient-Derived Models of Cancer in the NCI PDMC Consortium: Selection, Pitfalls, and Practical Recommendations. Cancers, 16 (3). p. 565. ISSN 2072-6694
Hackett, Jennifer, Pepenella, Sharon, Marco, Cristina Fernandez, Bodt, Louise, Grajales, Lina Ruiz, Petracca, Jeffry, Burke, Justin, Mayle, Allison, Nash, Bruce, Micklos, David A (April 2024) Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification. Methods in molecular biology (Clifton, N.J.), 2744. pp. 119-127. ISSN 1064-3745
He, Tongchen, Xiao, Lanbo, Qiao, Yuanyuan, Klingbeil, Olaf, Young, Eleanor, Wu, Xiaoli S, Mannan, Rahul, Mahapatra, Somnath, Eyunni, Sanjana, Tien, Jean Ching-Yi, Wang, Xiaoju, Zheng, Yang, Kim, NamHoon, Zheng, Heng, Hou, Siyu, Su, Fengyun, Miner, Stephanie J, Mehra, Rohit, Cao, Xuhong, Sekhar, A Chandra, Samajdar, Susanta, Ramachandra, Murali, Parolia, Abhijit, Vakoc, Christopher R, Chinnaiyan, Arul M (January 2024) Targeting the mSWI/SNF Complex in POU2F-POU2AF Transcription Factor-Driven Malignancies. bioRxiv. (Submitted)
He, Xue-Yan, Gao, Yuan, Ng, David, Michalopoulou, Evdokia, George, Shanu, Adrover, Jose M, Sun, Lijuan, Albrengues, Jean, Daßler-Plenker, Juliane, Han, Xiao, Wan, Ledong, Wu, Xiaoli Sky, Shui, Longling S, Huang, Yu-Han, Liu, Bodu, Su, Chang, Spector, David L, Vakoc, Christopher R, Van Aelst, Linda, Egeblad, Mikala (February 2024) Chronic stress increases metastasis via neutrophil-mediated changes to the microenvironment. Cancer Cell. ISSN 1535-6108
Henry, Samantha, Lewis, Steven Macauley, Cyrill, Samantha Leeanne, Callaway, Mackenzie Kate, Chatterjee, Deeptiman, Hanasoge Somasundara, Amritha Varshini, Jones, Gina, He, Xue-Yan, Caligiuri, Giuseppina, Ciccone, Michael Francis, Diaz, Isabella Andrea, Biswas, Amelia, Hernandez, Evelyn, Ha, Taehoon, Wilkinson, John Erby, Egeblad, Mikala, Tuveson, David Arthur, Oresco dos Santos, Camila (February 2024) Host response during unresolved urinary tract infection alters mammary tissue homeostasis through collagen deposition and TIMP1. bioRxiv. (Public Dataset) (Submitted)
Henry, Samantha, Lewis, Steven Macauley, Cyrill, Samantha Leeanne, Callaway, Mackenzie Kate, Chatterjee, Deeptiman, Hanasoge Somasundara, Amritha Varshini, Jones, Gina, He, Xue-Yan, Caligiuri, Giuseppina, Ciccone, Michael Francis, Diaz, Isabella Andrea, Biswas, Amelia Aumalika, Hernandez, Evelyn, Ha, Taehoon, Wilkinson, John Erby, Egeblad, Mikala, Tuveson, David Arthur, Dos Santos, Camila Oresco (April 2024) Host response during unresolved urinary tract infection alters female mammary tissue homeostasis through collagen deposition and TIMP1. Nature Communications, 15 (1). p. 3282. ISSN 2041-1723 (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 (February 2024) 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). BMC Cancer, 24 (1). p. 201. ISSN 1471-2407
Homer, Joshua A, Koelln, Rebecca A, Barrow, Andrew S, Gialelis, Timothy L, Boiarska, Zlata, Steinohrt, Nikita S, Lee, Erinna F, Yang, Wen-Hsuan, Johnson, Robert M, Chung, Taemoon, Habowski, Amber N, Vishwakarma, Dharmendra S, Bhunia, Debmalya, Avanzi, Charlotte, Moorhouse, Adam D, Jackson, Mary, Tuveson, David A, Lyons, Scott K, Lukey, Michael J, Fairlie, W Douglas, Haider, Shozeb M, Steinmetz, Michel O, Prota, Andrea E, Moses, John E (March 2024) Modular synthesis of functional libraries by accelerated SuFEx click chemistry. Chemical Science, 15 (11). pp. 3879-3892. ISSN 2041-6520 (Public Dataset)
Homer, Joshua A, Sun, Shoujun, Koelln, Rebecca A, Moses, John E (January 2024) Protocol for producing phosphoramidate using phosphorus fluoride exchange click chemistry. STAR Protocols, 5 (1). p. 102824. ISSN 2666-1667
Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya M, McCandlish, David M, Krainer, Adrian R, Kinney, Justin B (February 2024) Specificity, synergy, and mechanisms of splice-modifying drugs. Nature Communications, 15 (1). p. 1880. ISSN 2041-1723 (Public Dataset)
Karakaya, Eda, Oleinik, Natalia, Edwards, Jazlyn, Tomberlin, Jensen, Barker, Randy Bent, Berber, Burak, Ericsson, Maria, Alsudani, Habeeb, Ergul, Adviye, Beyaz, Semir, Lemasters, John J, Ogretmen, Besim, Albayram, Onder (February 2024) p17/C18-ceramide-mediated mitophagy is an endogenous neuroprotective response in preclinical and clinical brain injury. PNAS Nexus, 3 (2). ISSN 2752-6542
Khalid, Abdullah, Amini, Neda, Pasha, Shamsher A, Demyan, Lyudmyla, Newman, Elliot, King, Daniel A, DePeralta, Danielle, Gholami, Sepideh, Deutsch, Gary B, Melis, Marcovalerio, Weiss, Matthew J (May 2024) Impact of Postoperative Pancreatic Fistula on Outcomes in Pancreatoduodenectomy: A Comprehensive Analysis of ACS-NSQIP Data. Journal of Gastrointestinal Surgery. S1091-255X(24)00483. ISSN 1091-255X
Klindt, David A, Hyvärinen, Aapo, Levy, Axel, Miolane, Nina, Poitevin, Frédéric (March 2024) Towards Interpretable Cryo-EM: Disentangling Latent Spaces of Molecular Conformations. bioRxiv. (Submitted)
Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Alpsoy, Aktan, Minicozzi, Francesca, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Spector, David L, Tuveson, David A, Cifani, Paolo, Vakoc, Christopher R (February 2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. bioRxiv. (Submitted)
Koren, Sergey, Bao, Zhigui, Guarracino, Andrea, Ou, Shujun, Goodwin, Sara, Jenike, Katharine M, Lucas, Julian, McNulty, Brandy, Park, Jimin, Rautianinen, Mikko, Rhie, Arang, Roelofs, Dick, Schneiders, Harrie, Vrijenhoek, Ilse, Nijbroek, Koen, Ware, Doreen, Schatz, Michael C, Garrison, Erik, Huang, Sanwen, McCombie, William Richard, Miga, Karen H, Wittenberg, Alexander HJ, Phillippy, Adam M (March 2024) Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. bioRxiv. (Submitted)
Kotagama, Kasuen, Grimme, Acadia L, Braviner, Leah, Yang, Bing, Sakhawala, Rima M, Yu, Guoyun, Benner, Lars Kristian, Joshua-Tor, Leemor, McJunkin, Katherine (March 2024) Catalytic residues of microRNA Argonautes play a modest role in microRNA star strand destabilization in C. elegans. Nucleic Acids Research (NAR). gkae170. ISSN 0305-1048 (Public Dataset)
Kotagama, Kasuen, Grimme, Acadia L, Braviner, Leah, Yang, Bing, Sakhawala, Rima M, Yu, Guoyun, Benner, Lars Kristian, Joshua-Tor, Leemor, McJunkin, Katherine (January 2024) The catalytic activity of microRNA Argonautes plays a modest role in microRNA star strand destabilization in C. elegans. bioRxiv. (Submitted)
Lanctot, Amy (January 2024) On the cutting edge of development: Laser-assisted microdissection of the Arabidopsis gynoecium reveals tissue-specific gene expression patterns. Plant Physiology. ISSN 0032-0889
Langer, Henning Tim, Ramsamooj, Shakti, Dantas, Ezequiel, Murthy, Anirudh, Ahmed, Mujmmail, Ahmed, Tanvir, Hwang, Seo-Kyoung, Grover, Rahul, Pozovskiy, Rita, Liang, Roger J, Queiroz, Andre Lima, Brown, Justin C, White, Eileen P, Janowitz, Tobias, Goncalves, Marcus D (May 2024) Restoring adiponectin via rosiglitazone ameliorates tissue wasting in mice with lung cancer. Acta Physiologica. e14167. ISSN 1748-1708
Lee, YK, Kim, K, Ware, D (April 2024) Role of moss and Arabidopsis zinc-finger homeodomain transcription factors in regulating plant architecture. Plant Biotechnology Reports, 18 (2). pp. 223-231. ISSN 1863-5466
Leibold, Josef, Tsanov, Kaloyan M, Amor, Corina, Ho, Yu-Jui, Sánchez-Rivera, Francisco J, Feucht, Judith, Baslan, Timour, Chen, Hsuan-An, Tian, Sha, Simon, Janelle, Wuest, Alexandra, Wilkinson, John E, Lowe, Scott W (January 2024) Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease. Nature Cancer. ISSN 2662-1347
Liu, Yu, Li, Huinan, Liu, Jie, Wang, Yuebin, Jiang, Chenglin, Zhou, Ziqi, Zhuo, Lin, Li, Wenqiang, Fernie, Alisdair R, Jackson, David, Yan, Jianbing, Luo, Yun (May 2024) The additive function of YIGE2 and YIGE1 in regulating maize ear length. The Plant Journal. ISSN 0960-7412
Livesey, Benjamin J, Badonyi, Mihaly, Dias, Mafalda, Frazer, Jonathan, Kumar, Sushant, Lindorff-Larsen, Kresten, McCandlish, David M, Orenbuch, Rose, Shearer, Courtney A, Muffley, Lara, Foreman, Julia, Glazer, Andrew M, Lehner, Ben, Marks, Debora S, Roth, Frederick P, Rubin, Alan F, Starita, Lea M, Marsh, Joseph A (April 2024) Guidelines for releasing a variant effect predictor. ArXiv. ISSN 2331-8422 (Submitted)
Lobo, Anandi, Mishra, Sourav K, Jha, Shilpy, Tiwari, Ankit, Kapoor, Rahul, Sharma, Shivani, Kaushal, Seema, Kiranmai, N Sri, Das, M Rakshitha, Peddinti, Kamal P, Sharma, Shailendra K, Bhardwaj, Nitin, Arora, Samriti, Jain, Deepika, Jain, Ekta, Munjal, Gauri, Shinde, Sayali, Malik, Vipra, Singh, Hena, Varshney, Juhi, Pradhan, Dinesh, Dixit, Mallika, Pattnaik, Niharika, Sharma, Ashish K, Barapatre, Yogesh R, Pradhan, Manas, Satapathy, Kaliprasad, Rath, Debadarshi, Jaiswal, Sunil, Das, Stithi, Khadenga, Chiraranjan, Routa, Sudhasmita, Baisakh, Manas R, Tiwari, Romila, Sampat, Nakul Y, Chakrabarti, Indranil, Parwani, Anil V, Mohanty, Sambit K (January 2024) Evaluation of programmed cell death ligand 1 expression in a contemporary cohort of penile squamous cell carcinoma and its correlation with clinicopathologic and survival parameters: A study of 134 patients. American Journal of Clinical Pathology. aqad107. ISSN 0002-9173
Lou, Emil, Xiu, Joanne, Baca, Yasmine, Saeed, Anwaar, Prakash, Ajay, Gholami, Sepideh, Subramanian, Subbaya, Starr, Timothy K, Fontana, Elisa, Pandey, Ritu, Lenz, Heinz-Josef, Shields, Anthony F, Nabhan, Chadi, Oberley, Matthew, Seeber, Andreas, El-Deiry, Wafik (March 2024) Differential landscape of immune evasion in oncogenic RAS-driven primary and metastatic colorectal cancers. Mol Ther Oncol, 32 (1). p. 200786. ISSN 2950-3299
Lupo, Francesca, Pezzini, Francesco, Pasini, Davide, Fiorini, Elena, Adamo, Annalisa, Veghini, Lisa, Bevere, Michele, Frusteri, Cristina, Delfino, Pietro, D'agosto, Sabrina, Andreani, Silvia, Piro, Geny, Malinova, Antonia, Wang, Tian, De Sanctis, Francesco, Lawlor, Rita Teresa, Hwang, Chang-Il, Carbone, Carmine, Amelio, Ivano, Bailey, Peter, Bronte, Vincenzo, Tuveson, David, Scarpa, Aldo, Ugel, Stefano, Corbo, Vincenzo (April 2024) Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC. Gut. gutjnl-2023. ISSN 0017-5749
Lyon, Gholson J, Longo, Joseph, Garcia, Andrew, Inusa, Fatima, Marchi, Elaine, Shi, Daniel, Dörfel, Max, Arnesen, Thomas, Aldabe, Rafael, Lyons, Scott, Nashat, Melissa A, Bolton, David (May 2024) Evaluating possible maternal effect lethality and genetic background effects in Naa10 knockout mice. PLoS ONE, 19 (5). e0301328. ISSN 1932-6203
M. Swamynathan, Manojit, Mathew, Grinu, Aziz, Andrei, Gordon, Chris, Hillowe, Andrew, Wang, Hehe, Jhaveri, Aashna, Kendall, Jude, Cox, Hilary, Giarrizzo, Michael, Azabdaftari, Gissou, Rizzo, Robert C, Diermeier, Sarah D, Ojima, Iwao, Bialkowska, Agnieszka B, Kaczocha, Martin, Trotman, Lloyd C (2024) FABP5 Inhibition against PTEN-Mutant Therapy Resistant Prostate Cancer. Cancers, 16 (1). p. 60. ISSN 2072-6694
Mai, Nicholas, Dos Anjos, Carlos H, Razavi, Pedram, Safonov, Anton, Patil, Sujata, Chen, Yuan, Drago, Joshua Z, Modi, Shanu, Bromberg, Jacqueline F, Dang, Chau T, Liu, Dazhi, Norton, Larry, Robson, Mark, Chandarlapaty, Sarat, Jhaveri, Komal (May 2024) Predictors of Response to CDK4/6i Retrial After Prior CDK4/6i Failure in ER+ Metastatic Breast Cancer. Res Sq.
Maia-Silva, Diogo, Cunniff, Patrick J, Schier, Allison C, Skopelitis, Damianos, Trousdell, Marygrace C, Moresco, Philip, Gao, Yuan, Kechejian, Vahag, He, Xue-Yan, Sahin, Yunus, Wan, Ledong, Alpsoy, Aktan, Liverpool, Jynelle, Krainer, Adrian R, Egeblad, Mikala, Spector, David L, Fearon, Douglas T, Dos Santos, Camila O, Taatjes, Dylan J, Vakoc, Christopher R (June 2024) Interaction between MED12 and ΔNp63 activates basal identity in pancreatic ductal adenocarcinoma. Nature Genetics. ISSN 1061-4036
Michalski, Kevin, Furukawa, Hiro (April 2024) Structure and function of GluN1-3A NMDA receptor excitatory glycine receptor channel. Science Advances, 10 (15). eadl5952. ISSN 2375-2548
Miller, Eric D, Klamer, Brett G, Cloyd, Jordan M, Pawlik, Timothy M, Williams, Terence M, Hitchcock, Kathryn E, Romesser, Paul B, Mamon, Harvey J, Ng, Kimmie, Gholami, Sepideh, Chang, George J, Anker, Christopher J (January 2024) Consideration of Metastasis-Directed Therapy for Patients With Metastatic Colorectal Cancer: Expert Survey and Systematic Review. Clinical Colorectal Cancer. S1533-0028(24)00004. ISSN 1533-0028
Mitra, Partha, Mezias, Chris, Huo, Bingxing, Bota, Mihail, Jayakumar, Jaikishan (May 2024) Establishing neuroanatomical correspondences across mouse and marmoset brain structures. Research Square. (Submitted)
Mohanasundaram, Boominathan, Palit, Shirsa, Bhide, Amey J, Pala, Madhusmita, Rajoria, Kanishka, Girigosavi, Payal, Banerjee, Anjan K (February 2024) PpSCARECROW1 (PpSCR1) regulates leaf blade and mid-vein development in Physcomitrium patens. Plant Molecular Biology, 114 (1). ISSN 0167-4412 (Public Dataset)
Nie, Yongxin, Wang, Hui, Zhang, Guan, Ding, Haiping, Han, Beibei, Liu, Lei, Shi, Jian, Du, Jiyuan, Li, Xiaohu, Li, Xinzheng, Zhao, Yajie, Zhang, Xiaocong, Liu, Changlin, Weng, Jianfeng, Li, Xinhai, Zhang, Xiansheng, Zhao, Xiangyu, Pan, Guangtang, Jackson, David, Li, Qin-Bao, Stinard, Philip S, Arp, Jennifer, Sachs, Martin M, Moose, Steven, Hunter, Charles T, Wu, Qingyu, Zhang, Zhiming (January 2024) The maize PLASTID TERMINAL OXIDASE (PTOX) locus controls the carotenoid content of kernels. The Plant Journal. ISSN 0960-7412
Nogueira, Marcelo S, Gunther, Jacqueline E, Komolibus, Katarzyna, Ryan, Sinéad M, Murray, Brian S, Jezzini, Moises A, Kennedy, Declan, Andersson-Engels, Stefan (April 2024) Teaching and learning in biophotonics: Crossing the bridge between educators and students. Journal of Biophotonics. e202300491. ISSN 1864-063X
Ortiz, Jenelys Ruiz, Lewis, Steven M, Ciccone, Michael, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila O (January 2024) Single-Cell Transcription Mapping of Murine and Human Mammary Organoids Responses to Female Hormones. Journal of Mammary Gland Biology and Neoplasia, 29 (1). p. 3. ISSN 1083-3021 (Public Dataset)
Pandurangan, Karthika, Jayakumar, Jaikishan, Savoia, Stephen, Nanda, Reetuparna, Lata, S, Kumar, E Harish, S, Suresh, Vasudevan, Sudha, Srinivasan, Chitra, Joseph, Jayaraj, Sivaprakasam, Mohanasankar, Verma, Richa (February 2024) Systematic development of immunohistochemistry protocol for large cryosections-specific to non-perfused fetal brain. Journal of Neuroscience Methods, 405. p. 110085. ISSN 0165-0270
Patel, H, Zanos, T, Hewitt, DB (January 2024) Deep Learning Applications in Pancreatic Cancer. Cancers, 16 (2). p. 436. ISSN 2072-6694
Paul, Saikat, Jackson, David, Kitagawa, Munenori (April 2024) Tracking the messengers: Emerging advances in mRNA-based plant communication. Current Opinion in Plant Biology, 79. p. 102541. ISSN 1369-5266
Posfai, Anna, McCandlish, David M, Kinney, Justin B (May 2024) Symmetry, gauge freedoms, and the interpretability of sequence-function relationships. bioRxiv. (Submitted)
Posfai, Anna, Zhou, Juannan, McCandlish, David M, Kinney, Justin B (May 2024) Gauge fixing for sequence-function relationships. bioRxiv.
Ren, Zuen, Dharmaratne, Malindrie, Liang, Huizhi, Benard, Outhiriaradjou, Morales-Gallego, Miriam, Suyama, Kimita, Kumar, Viney, Fard, Atefeh Taherian, Kulkarni, Ameya S, Prystowsky, Michael, Mar, Jessica C, Norton, Larry, Hazan, Rachel B (January 2024) Redox signalling regulates breast cancer metastasis via phenotypic and metabolic reprogramming due to p63 activation by HIF1α. British Journal of Cancer. ISSN 0007-0920 (Public Dataset)
Renton, Angela I, Dao, Thuy T, Johnstone, Tom, Civier, Oren, Sullivan, Ryan P, White, David J, Lyons, Paris, Slade, Benjamin M, Abbott, David F, Amos, Toluwani J, Bollmann, Saskia, Botting, Andy, Campbell, Megan EJ, Chang, Jeryn, Close, Thomas G, Doerig, Monika, Eckstein, Korbinian, Egan, Gary F, Evas, Stefanie, Flandin, Guillaume, Garner, Kelly G, Garrido, Marta I, Ghosh, Satrajit S, Grignard, Martin, Halchenko, Yaroslav O, Hannan, Anthony J, Heinsfeld, Anibal S, Huber, Laurentius, Hughes, Matthew E, Kaczmarzyk, Jakub R, Kasper, Lars, Kuhlmann, Levin, Lou, Kexin, Mantilla-Ramos, Yorguin-Jose, Mattingley, Jason B, Meier, Michael L, Morris, Jo, Narayanan, Akshaiy, Pestilli, Franco, Puce, Aina, Ribeiro, Fernanda L, Rogasch, Nigel C, Rorden, Chris, Schira, Mark M, Shaw, Thomas B, Sowman, Paul F, Spitz, Gershon, Stewart, Ashley W, Ye, Xincheng, Zhu, Judy D, Narayanan, Aswin, Bollmann, Steffen (May 2024) Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods, 21 (2). pp. 804-808. ISSN 1548-7091
Rogava, Meri, Aprati, Tyler J, Chi, Wei-Yu, Melms, Johannes C, Hug, Clemens, Davis, Stephanie H, Earlie, Ethan M, Chung, Charlie, Deshmukh, Sachin K, Wu, Sharon, Sledge, George, Tang, Stephen, Ho, Patricia, Amin, Amit Dipak, Caprio, Lindsay, Gurjao, Carino, Tagore, Somnath, Ngo, Bryan, Lee, Michael J, Zanetti, Giorgia, Wang, Yiping, Chen, Sean, Ge, William, Melo, Luiza Martins Nascentes, Allies, Gabriele, Rösler, Jonas, Gibney, Goeffrey T, Schmitz, Oliver J, Sykes, Megan, Creusot, Rémi J, Tüting, Thomas, Schadendorf, Dirk, Röcken, Martin, Eigentler, Thomas K, Molotkov, Andrei, Mintz, Akiva, Bakhoum, Samuel F, Beyaz, Semir, Cantley, Lewis C, Sorger, Peter K, Meckelmann, Sven W, Tasdogan, Alpaslan, Liu, David, Laughney, Ashley M, Izar, Benjamin (January 2024) Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. Nature Cancer. ISSN 2662-1347 (Public Dataset)
Rogers, Crystal D, Amemiya, Chris, Arur, Swathi, Babonis, Leslie, Barresi, Michael, Bartlett, Madelaine, Behringer, Richard, Benham-Pyle, Blair, Bergmann, Dominique, Blackman, Ben, Brown, C Titus, Browne, Bill, Camacho, Jasmin, Chabu, Chiswili Yves, Chow, Ida, Cleaver, Ondine, Cool, Jonah, Dennis, Megan Y, Dickinson, Alexandra Jazz, Di Talia, Stefano, Frank, Margaret, Gillmor, Stewart, Haag, Eric S, Hariharan, Iswar, Harland, Richard, Husbands, Aman, Jerome-Majewska, Loydie, Koenig, Kristen, Labonne, Carole, Layden, Michael, Lowe, Chris, Mani, Madhav, Martik, Megan, McKown, Katelyn, Moens, Cecilia, Mosimann, Christian, Onyenedum, Joyce, Reed, Robert, Rivera, Ajna, Rokhsar, Dan, Royer, Loic, Rutaganira, Flora, Shahan, Rachel, Sinha, Neelima, Swalla, Billie, Van Norman, Jaimie M, Wagner, Daniel E, Wikramanayake, Athula, Zebell, Sophia, Brady, Siobhán M (February 2024) Pluripotency of a founding field: rebranding developmental biology. Development, 151 (3). ISSN 0950-1991
Romero, Rodrigo, Chu, Tinyi, González-Robles, Tania J, Smith, Perianne, Xie, Yubin, Kaur, Harmanpreet, Yoder, Sara, Zhao, Huiyong, Mao, Chenyi, Kang, Wenfei, Pulina, Maria V, Lawrence, Kayla E, Gopalan, Anuradha, Zaidi, Samir, Yoo, Kwangmin, Choi, Jungmin, Fan, Ning, Gerstner, Olivia, Karthaus, Wouter R, DeStanchina, Elisa, Ruggles, Kelly V, Westcott, Peter MK, Chaligné, Ronan, Pe'er, Dana, Sawyers, Charles L (April 2024) The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1. bioRxiv.
Roux de Bézieux, Hector, Street, Kelly, Fischer, Stephan, Van den Berge, Koen, Chance, Rebecca, Risso, Davide, Gillis, Jesse, Ngai, John, Purdom, Elizabeth, Dudoit, Sandrine (May 2024) Improving replicability in single-cell RNA-Seq cell type discovery with Dune. BMC Bioinformatics, 25 (1). p. 198. ISSN 1471-2105 (Public Dataset)
Rozhoňová, Hana, Martí-Gómez, Carlos, McCandlish, David M, Payne, Joshua L (May 2024) Robust genetic codes enhance protein evolvability. PLoS Biology, 22 (5). e3002594. ISSN 1545-7885 (Public Dataset)
Sarkar, Anirban, Tang, Ziqi, Zhao, Chris, Koo, Peter (May 2024) Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion. bioRxiv. (Submitted)
Satterlee, James W, Alonso, David, Gramazio, Pietro, Jenike, Katharine M, He, Jia, Arrones, Andrea, Villanueva, Gloria, Plazas, Mariola, Ramakrishnan, Srividya, Benoit, Matthias, Gentile, Iacopo, Hendelman, Anat, Shohat, Hagai, Fitzgerald, Blaine, Robitaille, Gina M, Green, Yumi, Swartwood, Kerry, Passalacqua, Michael J, Gagnon, Edeline, Hilgenhof, Rebecca, Huggins, Trevis D, Eizenga, Georgia C, Gur, Amit, Rutten, Twan, Stein, Nils, Yao, Shengrui, Bellot, Clement, Bendahmane, Mohammed, Frary, Amy, Knapp, Sandra, Särkinen, Tiina, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Eshed, Yuval, Prohens, Jaime, Vilanova, Santiago, Lippman, Zachary B (February 2024) Convergent evolution of plant prickles is driven by repeated gene co-option over deep time. bioRxiv. (Submitted)
Segovia, D, Tepes, PS (May 2024) p160 nuclear receptor coactivator family members and their role in rare fusion‑driven neoplasms (Review). Oncology Letters, 27 (5). ISSN 1792-1074 (In Press)
Segovia, Danilo, Adams, Dexter W, Hoffman, Nickolas, Safaric Tepes, Polona, Wee, Tse-Luen, Cifani, Paolo, Joshua-Tor, Leemor, Krainer, Adrian R (May 2024) SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proceedings of the National Academy of Sciences of the United States of America, 121 (21). e2322974121. ISSN 0027-8424 (Public Dataset)
Stern, Shani, Zhang, Lei, Wang, Meiyan, Wright, Rebecca, Rosh, Idan, Hussein, Yara, Stern, Tchelet, Choudhary, Ashwani, Tripathi, Utkarsh, Reed, Patrick, Sadis, Hagit, Nayak, Ritu, Shemen, Aviram, Agarwal, Karishma, Cordeiro, Diogo, Peles, David, Hang, Yuqing, Mendes, Ana PD, Baul, Tithi D, Roth, Julien G, Coorapati, Shashank, Boks, Marco P, McCombie, W Richard, Hulshoff Pol, Hilleke, Brennand, Kristen J, Réthelyi, János M, Kahn, René S, Marchetto, Maria C, Gage, Fred H (May 2024) Monozygotic twins discordant for schizophrenia differ in maturation and synaptic transmission. Molecular Psychiatry. ISSN 1359-4184 (Public Dataset)
Stillman, Bruce (June 2024) Establishing a biochemical understanding of the initiation of chromosome replication in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 121 (23). e2400667121. ISSN 0027-8424
Sun, Simón ED, Levenstein, Daniel, Li, Boxing, Mandelberg, Nataniel, Chenouard, Nicolas, Suutari, Benjamin S, Sanchez, Sandrine, Tian, Guoling, Rinzel, John, Buzsáki, György, Tsien, Richard W (March 2024) Synaptic homeostasis transiently leverages Hebbian mechanisms for a multiphasic response to inactivity. Cell Reports, 43 (4). p. 113839. ISSN 2211-1247 (Public Dataset)
Sussillo, David, Kaifosh, Patrick, Reardon, Thomas (February 2024) A generic noninvasive neuromotor interface for human-computer interaction. bioRxiv. (Submitted)
Swentowsky, Kyle W (January 2024) A Bushel of WUSCHEL is Too Much: Uncovering the Role of Cytokinin cis-Regulatory Elements in the Maize WUSCHEL Promoter. Plant Physiology. kiae016. ISSN 0032-0889
Swentowsky, Kyle W (March 2024) Spud Buds: StAST1 antagonizes potato tuber development by suppressing the alternative Tuberization Activation Complex (aTAC). Plant Physiology. kiae180. ISSN 0032-0889
Swetnam, Tyson L, Antin, Parker B, Bartelme, Ryan, Bucksch, Alexander, Camhy, David, Chism, Greg, Choi, Illyoung, Cooksey, Amanda M, Cosi, Michele, Cowen, Cindy, Culshaw-Maurer, Michael, Davey, Robert, Davey, Sean, Devisetty, Upendra, Edgin, Tony, Edmonds, Andy, Fedorov, Dmitry, Frady, Jeremy, Fonner, John, Gillan, Jeffrey K, Hossain, Iqbal, Joyce, Blake, Lang, Konrad, Lee, Tina, Littin, Shelley, McEwen, Ian, Merchant, Nirav, Micklos, David, Nelson, Andrew, Ramsey, Ashley, Roberts, Sarah, Sarando, Paul, Skidmore, Edwin, Song, Jawon, Sprinkle, Mary Margaret, Srinivasan, Sriram, Stanzione, Dan, Strootman, Jonathan D, Stryeck, Sarah, Tuteja, Reetu, Vaughn, Matthew, Wali, Mojib, Wall, Mariah, Walls, Ramona, Wang, Liya, Wickizer, Todd, Williams, Jason, Wregglesworth, John, Lyons, Eric (February 2024) CyVerse: Cyberinfrastructure for open science. PLoS Computational Biology, 20 (2). e1011270. ISSN 1553-734X
Tang, Ziqi, Koo, Peter K (March 2024) Evaluating the representational power of pre-trained DNA language models for regulatory genomics. bioRxiv. (Public Dataset) (Submitted)
Tierney, Braden T, Kim, JangKeun, Overbey, Eliah G, Ryon, Krista A, Foox, Jonathan, Sierra, Maria A, Bhattacharya, Chandrima, Damle, Namita, Najjar, Deena, Park, Jiwoon, Garcia Medina, J Sebastian, Houerbi, Nadia, Meydan, Cem, Wain Hirschberg, Jeremy, Qiu, Jake, Kleinman, Ashley S, Al-Ghalith, Gabriel A, MacKay, Matthew, Afshin, Evan E, Dhir, Raja, Borg, Joseph, Gatt, Christine, Brereton, Nicholas, Readhead, Benjamin P, Beyaz, Semir, Venkateswaran, Kasthuri J, Wiseman, Kelly, Moreno, Juan, Boddicker, Andrew M, Zhao, Junhua, Lajoie, Bryan R, Scott, Ryan T, Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Church, George M, Mason, Christopher E (June 2024) Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight. Nature Microbiology. ISSN 2058-5276
Tollkuhn, Jessica (May 2024) Nuclear receptors - studying genes to understand hormones. Nature Reviews Genetics. ISSN 1471-0056
Tollkuhn, Jessica (May 2024) Parental-care puzzle in mice solved by thinking outside the brain. Nature. ISSN 0028-0836
Tonelli, Claudia, Yordanov, Georgi N, Hao, Yuan, Deschênes, Astrid, Hinds, Juliene, Belleau, Pascal, Klingbeil, Olaf, Brosnan, Erin, Doshi, Abhishek, Park, Youngkyu, Hruban, Ralph H, Vakoc, Christopher R, Dobin, Alexander, Preall, Jonathan, Tuveson, David A (January 2024) A mucus production programme promotes classical pancreatic ductal adenocarcinoma. Gut. ISSN 0017-5749
Ubhi, Tajinder, Zaslaver, Olga, Quaile, Andrew T, Plenker, Dennis, Cao, Pinjiang, Pham, Nhu-An, Békési, Angéla, Jang, Gun-Ho, O'Kane, Grainne M, Notta, Faiyaz, Moffat, Jason, Wilson, Julie M, Gallinger, Steven, Vértessy, Beáta G, Tuveson, David A, Röst, Hannes L, Brown, Grant W (March 2024) Cytidine deaminases APOBEC3C and APOBEC3D promote DNA replication stress resistance in pancreatic cancer cells. Nature Cancer. ISSN 2662-1347 (Public Dataset)
Verma, Richa, Jayakumar, Jaikishan, Folkerth, Rebecca, Manger, Paul R, Bota, Mihail, Majumder, Moitrayee, Pandurangan, Karthika, Savoia, Stephen, Karthik, Srinivasa, Kumarasami, Ramdayalan, Joseph, Jayaraj, Rohini, G, Vasudevan, Sudha, Srinivasan, Chitra, Lata, S, Kumar, E Harish, Rangasami, Rajeswaran, Kumutha, Jayaraman, Suresh, S, Šimić, Goran, Mitra, Partha P, Sivaprakasam, Mohanasankar (April 2024) Histological characterization and development of mesial surface sulci in the human brain at 13-15 gestational weeks through high-resolution histology. Journal of Comparative Neurology, 532 (4). e25612. ISSN 0021-9967
Wan, Ledong, Kral, Alexander J, Voss, Dillon, Schäfer, Balázs, Sudheendran, Kavitha, Danielsen, Mathias, Caruthers, Marvin H, Krainer, Adrian R (May 2024) Screening Splice-Switching Antisense Oligonucleotides in Pancreas-Cancer Organoids. Nucleic Acid Therapeutics. ISSN 2159-3337
Wang, Yuebin, Luo, Yun, Guo, Xing, Li, Yunfu, Yan, Jiali, Shao, Wenwen, Wei, Wenjie, Wei, Xiaofeng, Yang, Tao, Chen, Jing, Chen, Lihua, Ding, Qian, Bai, Minji, Zhuo, Lin, Li, Li, Jackson, David, Zhang, Zuxin, Xu, Xun, Yan, Jianbing, Liu, Huan, Liu, Lei, Yang, Ning (May 2024) A spatial transcriptome map of the developing maize ear. Nature Plants. ISSN 2055-0278 (Public Dataset)
Williams, Jason, Nash, Bruce, Ghiban, Cornel, Khalfan, Mohammed, Hilgert, Uwe, Lauter, Susan, Yang, Chun-Hua, Micklos, David Andrew (April 2024) Analysis of DNA Barcodes Using DNA Subway. Methods in molecular biology (Clifton, N.J.), 2744. pp. 551-560. ISSN 1064-3745
Xia, Ruobing, Chen, Xiaomo, Engel, Tatiana A, Moore, Tirin (February 2024) Common and distinct neural mechanisms of attention. Trends in Cognitive Sciences. ISSN 1364-6613
Xiang, Xiyan, Bhowmick, Krishanu, Shetty, Kirti, Ohshiro, Kazufumi, Yang, Xiaochun, Wong, Linda L, Yu, Herbert, Latham, Patricia S, Satapathy, Sanjaya K, Brennan, Christina, Dima, Richard J, Chambwe, Nyasha, Sharifova, Gulru, Cacaj, Fellanza, John, Sahara, Crawford, James M, Huang, Hai, Dasarathy, Srinivasan, Krainer, Adrian R, He, Aiwu R, Amdur, Richard L, Mishra, Lopa (2024) Mechanistically based blood proteomic markers in the TGF-β pathway stratify risk of hepatocellular cancer in patients with cirrhosis. Genes and Cancer, 15. pp. 1-14. ISSN 1947-6019
Yashaswini, Chittampalli N, Qin, Tianyue, Bhattacharya, Dipankar, Amor, Corina, Lowe, Scott, Lujambio, Amaia, Wang, Shuang, Friedman, Scott L (March 2024) Phenotypes and ontogeny of senescent hepatic stellate cells in metabolic dysfunction-associated steatotic liver disease. Journal of Hepatology. S0168-8278(24)00197. ISSN 0168-8278
Yu, Yiyang, Muthukumar, Shivani, Koo, Peter K (January 2024) EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. bioRxiv. (Submitted)
Yu, Yiyang, Muthukumar, Shivani, Koo, Peter K (February 2024) EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. Bioinformatics. ISSN 1367-4811
Zador, Anthony (February 2024) The origins of COSYNE: Building a community. The Transmitter. ISSN 2770-0976
Zhang, Jialin, Westcott, Peter MK (June 2024) Claudin 18 turns up the heat in cancer. Immunity, 57 (6). pp. 1187-1189. ISSN 1074-7613
Zhang, Xu, Duan, Shoufu, Apostolou, Panagiota E, Wu, Xiaoping, Watanabe, Jun, Gallitto, Matthew, Barron, Tara, Taylor, Kathryn R, Woo, Pamelyn J, Hua, Xu, Zhou, Hui, Wei, Hong-Jian, McQuillan, Nicholas, Kang, Kyung-Don, Friedman, Gregory K, Canoll, Peter D, Chang, Kenneth, Wu, Cheng-Chia, Hashizume, Rintaro, Vakoc, Christopher R, Monje, Michelle, McKhann, Guy M, Gogos, Joseph A, Zhang, Zhiguo (May 2024) CHD2 Regulates Neuron-glioma Interactions in Pediatric Glioma. Cancer Discovery. ISSN 2159-8274
Zhou, Yong, Kathiresan, Nagarajan, Yu, Zhichao, Rivera, Luis F, Yang, Yujian, Thimma, Manjula, Manickam, Keerthana, Chebotarov, Dmytro, Mauleon, Ramil, Chougule, Kapeel, Wei, Sharon, Gao, Tingting, Green, Carl D, Zuccolo, Andrea, Xie, Weibo, Ware, Doreen, Zhang, Jianwei, McNally, Kenneth L, Wing, Rod A (January 2024) A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset. BMC Biology, 22 (1). p. 13. ISSN 1741-7007
Chung, Taemoon, Merrill, Joseph R, Lyons, Scott K (2024) CRISPR/Cas for PET Reporter Gene Engineering. In: Methods in Molecular Biology. UNSPECIFIED, pp. 285-301. ISBN 9781071634981
Chougule, K, Tello-Ruiz, MK, Wei, S, Olson, A, Lu, Z, Kumari, S, Kumar, V, Contreras-Moreira, B, Naamati, G, Dyer, S, Papatheodorou, I, George, N, Elser, J, Naithani, S, Jaiswal, P, Ware, D (January 2024) Pan genome resources for grapevine. In: UNSPECIFIED.
Gazzara, Emma, Adrover, Jose, Liu, Alex, Han, Song, Rishi, Arvind, Chung, Charlie, Devoe, Craig, Huang, Hai, DePeralta, Danielle, Weiss, Matthew, Beyaz, Semir, Westcott, Peter, Taveson, Dave, Egeblad, Mikala, Gholami, Sepideh (2024) Neutrophil extracellular traps are an immunotherapeutic target in colorectal cancer. In: Annals of Surgical Oncology.
Klindt, David, Zimmermann, Roland, Brendel, Wieland (March 2024) Measuring Mechanistic Interpretability at Scale Without Humans. In: ICLR 2024 Workshop on Representational Alignment.
Lan, Wenjun, Sun, Shoujun, Nigri, Jeremy, Homer, Josh, Park, Young, Deschenes, Astrid, Cifani, Paolo, Cross, Justin, Gaeth, Victoria, Kim, Sunny, Ting, Shawn, Rubino, Rachel, Moses, John, Tuveson, David (January 2024) SOAT1 as a targetable KRAS dependency in PDAC. In: AACR Special Conference in Cancer Research: Pancreatic Cancer, 2023 Sep 27-30, Boston, Massachusetts.
Xu, Jihao, Roe, Jae-Seok, Lee, EunJung, Tonelli, Claudia, Somervile, Tim, Yao, Melissa, Milazzo, Joseph, Tiriac, Herve, Kolarzyk, Anna, Lee, Esak, Grem, Jeam, Lazenby, Audrey, Grunkemeyer, James, Hollingsworth, Michael, Grandgenett, Paul, Borowsky, Alexander, Park, Youngkyu, Vakoc, Christopher, Tuveson, David, Hwang, Chang-Il (January 2024) Engrailed-1 promotes pancreatic cancer metastasis. In: AACR Special Conference in Cancer Research: Pancreatic Cancer, 2023 Sep 27-30, Boston, Massachusetts.
Ciren, Danielle (February 2024) Decoding cis-regulatory control and evolution of conserved and divergent phenotypes in plants. PhD thesis, Cold Spring Harbor Laboratory.
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