Items where Year is 2023

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

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.

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

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

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)

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.

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

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.

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

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.

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)

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.

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

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

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, 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.

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

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, 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.

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)

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.

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

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

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

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.

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

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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, 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.

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

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

Mattick, John S, Amaral, Paulo P, Carninci, Piero, Carpenter, Susan, Chang, Howard Y, Chen, Ling-Ling, Chen, Runsheng, Dean, Caroline, Dinger, Marcel E, Fitzgerald, Katherine A, Gingeras, Thomas R, Guttman, Mitchell, Hirose, Tetsuro, Huarte, Maite, Johnson, Rory, Kanduri, Chandrasekhar, Kapranov, Philipp, Lawrence, Jeanne B, Lee, Jeannie T, Mendell, Joshua T, Mercer, Timothy R, Moore, Kathryn J, Nakagawa, Shinichi, Rinn, John L, Spector, David L, Ulitsky, Igor, Wan, Yue, Wilusz, Jeremy E, Wu, Mian (January 2023) Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews Molecular Cell Biology. ISSN 1471-0072

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.

McDonald, Hannah G, Patel, Reema A, Ellis, Carleton S, Gholami, Sepideh, Barry-Hundeyin, Mautin, Pandalai, Prakash K, Kim, Joseph, Cavnar, Michael J (July 2023) Starting a successful hepatic artery infusion pump program: A practical guide. Surgery, 174 (1). pp. 101-105. ISSN 0039-6060

Medwig-Kinney, Taylor N, Kinney, Brian A, Martinez, Michael AQ, Yee, Callista, Sirota, Sydney S, Mullarkey, Angelina A, Somineni, Neha, Hippler, Justin, Zhang, Wan, Shen, Kang, Hammell, Christopher, Pani, Ariel M, Matus, David Q (December 2023) Dynamic compartmentalization of the pro-invasive transcription factor NHR-67 reveals a role for Groucho in regulating a proliferative-invasive cellular switch in C. elegans. eLife, 12. RP84355. ISSN 2050-084X

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Mitra, Partha P, Sire, Clément (December 2023) AI without networks. bioRxiv. (Submitted)

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Mohan, Hemanth, An, Xu, Xu, X Hermione, Kondo, Hideki, Zhao, Shengli, Matho, Katherine S, Wang, Bor-Shuen, Musall, Simon, Mitra, Partha, Huang, Z Josh (January 2023) Cortical glutamatergic projection neuron types contribute to distinct functional subnetworks. Nature Neuroscience. ISSN 1097-6256

Moorhouse, AD, Homer, JA, Moses, JE (August 2023) The certainty of a few good reactions. Chem, 9 (8). pp. 2063-2077. ISSN 2451-9308

Morris, Van K, Kennedy, Erin B, Baxter, Nancy N, Benson, Al B, Cercek, Andrea, Cho, May, Ciombor, Kristen K, Cremolini, Chiara, Davis, Anjee, Deming, Dustin A, Fakih, Marwan G, Gholami, Sepideh, Hong, Theodore S, Jaiyesimi, Ishmael, Klute, Kelsey, Lieu, Christopher, Sanoff, Hanna, Strickler, John H, White, Sarah, Willis, Jason A, Eng, Cathy (January 2023) Treatment of Metastatic Colorectal Cancer: ASCO Guideline. Journal of Clinical Oncology, 41 (3). pp. 678-700. ISSN 0732-183X

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

Norén Lindbäck, Louise, Ji, Yan, Cervela-Cardona, Luis, Jin, Xu, Pedmale, Ullas V, Strand, Åsa (August 2023) An interplay between bZIP16, bZIP68, and GBF1 regulates nuclear photosynthetic genes during photomorphogenesis in Arabidopsis. New Phytologist. ISSN 0028-646X

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)

Ottonello, Alessandra, Wyllie, Jessica A, Yahiaoui, Oussama, Sun, Shoujun, Koelln, Rebecca A, Homer, Joshua A, Johnson, Robert M, Murray, Ewan, Williams, Paul, Bolla, Jani R, Robinson, Carol V, Fallon, Thomas, Soares da Costa, Tatiana P, Moses, John E (April 2023) Shapeshifting bullvalene-linked vancomycin dimers as effective antibiotics against multidrug-resistant gram-positive bacteria. Proceedings of the National Academy of Sciences of USA, 120 (15). e2208737120. ISSN 0027-8424

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.

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)

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.

Peng, Hanchuan, Liu, Yufeng, Jiang, Shengdian, Li, Yingxin, Zhao, Sujun, Yun, Zhixi, Zhao, Zuo-Han, Zhang, Lingli, Wang, Gaoyu, Chen, Xin, Manubens-Gil, Linus, Hang, Yuning, Garcia-Forn, Marta, Wang, Wei, De Rubeis, Silvia, Wu, Zhuhao, Osten, Pavel, Gong, Hui, Hawrylycz, Michael, Mitra, Partha, Dong, Hong-Wei, Luo, Qingming, Ascoli, Giorgio, Zeng, Hongkui, Liu, Lijuan (July 2023) Full-Spectrum Neuronal Diversity and Stereotypy through Whole Brain Morphometry. (Submitted)

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)

Pinto, Brendan J, O'Connor, Brian, Schatz, Michael C, Zarate, Samantha, Wilson, Melissa A (September 2023) Concerning the eXclusion in human genomics: the choice of sex chromosome representation in the human genome drastically affects the number of identified variants. G3: Genes, Genomes, Genetics, 13 (10). jkad169. ISSN 2160-1836

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

Rhie, Arang, Nurk, Sergey, Cechova, Monika, Hoyt, Savannah J, Taylor, Dylan J, Altemose, Nicolas, Hook, Paul W, Koren, Sergey, Rautiainen, Mikko, Alexandrov, Ivan A, Allen, Jamie, Asri, Mobin, Bzikadze, Andrey V, Chen, Nae-Chyun, Chin, Chen-Shan, Diekhans, Mark, Flicek, Paul, Formenti, Giulio, Fungtammasan, Arkarachai, Garcia Giron, Carlos, Garrison, Erik, Gershman, Ariel, Gerton, Jennifer L, Grady, Patrick GS, Guarracino, Andrea, Haggerty, Leanne, Halabian, Reza, Hansen, Nancy F, Harris, Robert, Hartley, Gabrielle A, Harvey, William T, Haukness, Marina, Heinz, Jakob, Hourlier, Thibaut, Hubley, Robert M, Hunt, Sarah E, Hwang, Stephen, Jain, Miten, Kesharwani, Rupesh K, Lewis, Alexandra P, Li, Heng, Logsdon, Glennis A, Lucas, Julian K, Makalowski, Wojciech, Markovic, Christopher, Martin, Fergal J, Mc Cartney, Ann M, McCoy, Rajiv C, McDaniel, Jennifer, McNulty, Brandy M, Medvedev, Paul, Mikheenko, Alla, Munson, Katherine M, Murphy, Terence D, Olsen, Hugh E, Olson, Nathan D, Paulin, Luis F, Porubsky, David, Potapova, Tamara, Ryabov, Fedor, Salzberg, Steven L, Sauria, Michael EG, Sedlazeck, Fritz J, Shafin, Kishwar, Shepelev, Valery A, Shumate, Alaina, Storer, Jessica M, Surapaneni, Likhitha, Taravella Oill, Angela M, Thibaud-Nissen, Françoise, Timp, Winston, Tomaszkiewicz, Marta, Vollger, Mitchell R, Walenz, Brian P, Watwood, Allison C, Weissensteiner, Matthias H, Wenger, Aaron M, Wilson, Melissa A, Zarate, Samantha, Zhu, Yiming, Zook, Justin M, Eichler, Evan E, O'Neill, Rachel J, Schatz, Michael C, Miga, Karen H, Makova, Kateryna D, Phillippy, Adam M (September 2023) The complete sequence of a human Y chromosome. Nature, 621 (7978). pp. 344-354. ISSN 0028-0836

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)

Rozowsky, Joel, Gao, Jiahao, Borsari, Beatrice, Yang, Yucheng T, Galeev, Timur, Gürsoy, Gamze, Epstein, Charles B, Xiong, Kun, Xu, Jinrui, Li, Tianxiao, Liu, Jason, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Sun, Maxwell S, Wright, James, Chang, Justin, Cameron, Christopher JF, Shoresh, Noam, Gaskell, Elizabeth, Drenkow, Jorg, Adrian, Jessika, Aganezov, Sergey, Aguet, François, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo Barreto, Chee, Sora, Chhetri, Surya B, Cortez Martins, Gabriel Conte, Danyko, Cassidy, Davis, Carrie A, Farid, Daniel, Farrell, Nina P, Gabdank, Idan, Gofin, Yoel, Gorkin, David U, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin C, Issner, Robbyn, Jiang, Yunzhe, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita R, Li, Shantao, Li, Bian, Li, Xiqi, Lin, Khine Zin, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill E, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry E, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob M, Sedlazeck, Fritz J, See, Lei Hoon, Sherman, Rachel M, Shi, Xu, Shi, Minyi, Sloan, Cricket Alicia, Strattan, J Seth, Tan, Zhen, Tanaka, Forrest Y, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J Michael, Mendenhall, Eric M, Noble, William S, Weng, Zhiping, Levine, Morgan E, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard M, Snyder, Michael P, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael C, Bernstein, Bradley E, Guigó, Roderic, Gingeras, Thomas R, Gerstein, Mark (March 2023) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 186 (7). 1493-1511.e40. ISSN 0092-8674

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.

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

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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

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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.

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Werner, Jonathan M, Hover, John, Gillis, Jesse (October 2023) Population variability in X-chromosome inactivation across 9 mammalian species. (Submitted)

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