Items where Year is 2025

Paper

Alexander, Katherine A, Yu, Ruofan, Skuli, Nicolas, Coffey, Nathan J, Nguyen, Son, Faunce, Christine L, Huang, Hua, Dardani, Ian P, Good, Austin L, Lim, Joan, Li, Catherine Y, Biddle, Nicholas, Joyce, Eric F, Raj, Arjun, Lee, Daniel, Keith, Brian, Simon, M Celeste, Berger, Shelley L (January 2025) Nuclear speckles regulate functional programs in cancer. Nature Cell Biology. ISSN 1465-7392 (Public Dataset)

Alsaloum, Matthew, Dib-Hajj, Sulayman D, Page, Dana A, Ruben, Peter C, Krainer, Adrian R, Waxman, Stephen G (February 2025) Voltage-gated sodium channels in excitable cells as drug targets. Nature Reviews Drug Discovery. ISSN 1474-1776

Altea-Manzano, Patricia, Decker-Farrell, Amanda, Janowitz, Tobias, Erez, Ayelet (January 2025) Metabolic interplays between the tumour and the host shape the tumour macroenvironment. Nature Reviews Cancer. ISSN 1474-175X

Avizemer, Ziv, Martí-Gómez, Carlos, Hoch, Shlomo Yakir, McCandlish, David M, Fleishman, Sarel J (April 2025) Evolutionary paths that link orthogonal pairs of binding proteins. Cell Systems, 32 (12). p. 101262. ISSN 0961-8368 (Public Dataset)

Battison, Alexandria S, Merrill, Joseph R, Borniger, Jeremy C, Lyons, Scott K (March 2025) The regulation of reporter transgene expression for diverse biological imaging applications. npj Imaging, 3 (1). ISSN 2948-197X

Benoit, Matthias, Jenike, Katharine M, Satterlee, James W, Ramakrishnan, Srividya, Gentile, Iacopo, Hendelman, Anat, Passalacqua, Michael J, Suresh, Hamsini, Shohat, Hagai, Robitaille, Gina M, Fitzgerald, Blaine, Alonge, Michael, Wang, Xingang, Santos, Ryan, He, Jia, Ou, Shujun, Golan, Hezi, Green, Yumi, Swartwood, Kerry, Karavolias, Nicholas G, Sierra, Gina P, Orejuela, Andres, Roda, Federico, Goodwin, Sara, McCombie, W Richard, Kizito, Elizabeth B, Gagnon, Edeline, Knapp, Sandra, Särkinen, Tiina E, Frary, Amy, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B (March 2025) Solanum pan-genetics reveals paralogues as contingencies in crop engineering. Nature. ISSN 0028-0836 (Public Dataset)

Berntsen, Leslie, Courtney, Emma, Delawalla, Colette, Flores, JP, Goldstein, Samantha, Payne, Charlotte (March 2025) Why we organized 'Stand Up For Science'. Nature Human Behaviour. ISSN 2397-3374

Bhattacharya, Swarnabh, Tei, Guodong, Singh, Pratik Narendra Pratap, Malagola, Ermanno, Eskiocak, Onur, He, Ruiyang, Kraiczy, Judith, Gu, Wei, Perlov, Yakov, Beyaz, Semir, Wang, Timothy Cragin, Zhou, Qiao, Shivdasani, Ramesh Arjun (February 2025) Niche-driven phenotypic plasticity and cis-regulatory dynamics of a revised model for intestinal secretory differentiation. bioRxiv. ISSN 2692-8205 (Public Dataset)

Bhattacharya, Swarnabh, Tie, Guodong, Singh, Pratik NP, Malagola, Ermanno, Eskiocak, Onur, He, Ruiyang, Kraiczy, Judith, Gu, Wei, Perlov, Yakov, Alici-Garipcan, Aybuke, Beyaz, Semir, Wang, Timothy C, Zhou, Qiao, Shivdasani, Ramesh A (April 2025) Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell. Cell Stem Cell. ISSN 1934-5909 (Public Dataset)

Brady, Meghan J, Gupta, Anjali, Gent, Jonathan I, Swentowsky, Kyle W, Unckless, Robert L, Dawe, R Kelly (February 2025) Antagonistic kinesin-14s within a single chromosomal drive haplotype. bioRxiv. ISSN 2692-8205 (Public Dataset) (Submitted)

Buchanan, JoAnn, Cheadle, Lucas (April 2025) The Many Lives of an Oligodendrocyte Precursor Cell. Annual Review of Neuroscience. ISSN 0147-006X

Cannon, Ethalinda KS, Molik, David C, Wright, Adam J, Zhang, Huiting, Honaas, Loren, Chougule, Kapeel, Dyer, Sarah (January 2025) Guidelines for Gene and Genome Assembly Nomenclature. Genetics. iyaf006. ISSN 0016-6731 (Public Dataset)

Chang, Mario C, Malut, Vinay R, Mahar, Rohit, Rushin, Anna, McLeod, Marc A, Pierre, Geraldine L, Malut, Indu R, Staklinski, Stephen J, Glanz, Max E, Ragavan, Mukundan, Sharma, Gaurav, Madheswaran, Manoj, Badar, Arshee, Rao, Aparna D, Law, Brian K, Kilberg, Michael S, Collins, James HP, Kodibagkar, Vikram D, Bankson, James A, DeBerardinis, Ralph J, Merritt, Matthew E (March 2025) Assessing cancer therapeutic efficacy in vivo using [2H7]glucose deuterium metabolic imaging. Science Advances, 11 (13). eadr0568. ISSN 2375-2548

Contreras-Moreira, Bruno, Sharma, Eshan, Saraf, Shradha, Naamati, Guy, Gupta, Parul, Elser, Justin, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Wei, Sharon, Olson, Andrew, Tsang, Ian, Lodha, Disha, Zhou, Yong, Yu, Zhichao, Zhao, Wen, Zhang, Jianwei, Amberkar, Sandeep, Sue-Ob, Kawinnat, Martin, Maria, McNally, Kenneth L, Ware, Doreen, Sun, Zhi, Deutsch, Eric W, Copetti, Dario, Wing, Rod A, Jaiswal, Pankaj, Dyer, Sarah, Jones, Andrew R (February 2025) A pan-gene catalogue of Asian cultivated rice. bioRxiv. ISSN 2692-8205 (Submitted)

Ernst, Evan, Abramson, Bradley, Acosta, Kenneth, Hoang, Phuong TN, Mateo-Elizalde, Cristian, Schubert, Veit, Pasaribu, Buntora, Albert, Patrice S, Hartwick, Nolan, Colt, Kelly, Aylward, Anthony, Ramu, Umamaheswari, Birchler, James A, Schubert, Ingo, Lam, Eric, Michael, Todd P, Martienssen, Robert A (March 2025) Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction. Current Biology. ISSN 0960-9822 (Public Dataset)

Ferguson, L Paige, Tuveson, David A (April 2025) Road Map to Defeat Pancreatic Cancer. Annual Review of Cancer Biology, 9 (1). pp. 1-20. ISSN 2472-3428

Fiorini, Elena, Malinova, Antonia, Schreyer, Daniel, Pasini, Davide, Bevere, Michele, Alessio, Giorgia, Rosa, Diego, D'Agosto, Sabrina, Azzolin, Luca, Milite, Salvatore, Andreani, Silvia, Lupo, Francesca, Veghini, Lisa, Grimaldi, Sonia, Pedron, Serena, Castellucci, Monica, Nourse, Craig, Salvia, Roberto, Malleo, Giuseppe, Ruzzenente, Andrea, Guglielmi, Alfredo, Milella, Michele, Lawlor, Rita T, Luchini, Claudio, Agostini, Antonio, Carbone, Carmine, Pilarsky, Christian, Sottoriva, Andrea, Scarpa, Aldo, Tuveson, David A, Bailey, Peter, Corbo, Vincenzo (March 2025) MYC ecDNA promotes intratumour heterogeneity and plasticity in PDAC. Nature. ISSN 0028-0836 (Public Dataset)

Franklin, Reuben, Zhang, Brian, Frazier, Jonah, Chen, Meijuan, Do, Brian T, Padayao, Sally, Wu, Kun, Vander Heiden, Matthew G, Vakoc, Christopher R, Roe, Jae-Seok, Ninova, Maria, Murn, Jernej, Sykes, David B, Cheloufi, Sihem (April 2025) Histone chaperones coupled to DNA replication and transcription control divergent chromatin elements to maintain cell fate. Genes & Development. ISSN 0890-9369 (Public Dataset)

Fuller, Sophia, Alexeeff, Stacey, Caan, Bette, Dasilva Goncalves, Marcus, Dunne, Richard F, Janowitz, Tobias, Jamal-Hanjani, Mariam, Sundaresan, Tilak K, Cespedes Feliciano, Elizabeth M (February 2025) Early identification of weight loss trajectories in advanced cancer and associations with survival. Journal of the National Cancer Institute. djaf030. ISSN 0027-8874

Garg, Ankur, On, Kin Fan, Xiao, Yang, Elkayam, Elad, Cifani, Paolo, David, Yael, Joshua-Tor, Leemor (January 2025) The molecular basis of Human FN3K mediated phosphorylation of glycated substrates. Nature Communications, 16 (1). p. 941. ISSN 2041-1723 (Public Dataset)

Goncalves, Marcus D, Dunne, Richard F, Moore, Amy C, Phillips, Wendy, Heymsfield, Steven B, Brown, Justin C, Talbert, Erin E, Janowitz, Tobias (January 2025) Call to Improve Coding of Cancer-Associated Cachexia. JCO Oncology Practice. OP2400781. ISSN 2688-1527

Goncalves, Marcus D, Janowitz, Tobias (March 2025) Reply to: Overcoming Barriers to Cancer-Associated Cachexia Diagnosis and Management. JCO Oncology Practice. OP2500108. ISSN 2688-1527

Gutmann, David H, Anastasaki, Corina, Gupta, Aditi, Hou, Yang, Morris, Stephanie M, Payne, Jonathan M, Raber, Jacob, Tomchik, Seth M, Van Aelst, Linda, Walker, James A, Yohay, Kaleb H, CABIN Task Force (March 2025) Cognition and behavior in neurofibromatosis type 1: report and perspective from the Cognition and Behavior in NF1 (CABIN) Task Force. Genes & Development. ISSN 0890-9369

Hernandez, Diego E, Ciuparu, Andrei, Garcia da Silva, Pedro, Velasquez, Cristina M, Rebouillat, Benjamin, Gross, Michael D, Davis, Martin B, Chae, Honggoo, Muresan, Raul C, Albeanu, Dinu F (January 2025) Fast updating feedback from piriform cortex to the olfactory bulb relays multimodal identity and reward contingency signals during rule-reversal. Nature Communications, 16 (1). p. 937. ISSN 2041-1723 (Public Dataset)

Huilgol, Dhananjay, Levine, Jesse M, Galbavy, William, Wang, Bor-Shuen, Huang, Z Josh (March 2025) Orderly specification and precise laminar deployment of mouse cortical projection neuron types through intermediate progenitors. Developmental Cell. S1534-5807(25)00114. ISSN 1534-5807

IIT-Concerned, Klincewicz, Michał, Cheng, Tony, Schmitz, Michael, Sebastián, Miguel Ángel, Snyder, Joel S (April 2025) What makes a theory of consciousness unscientific? Nature Neuroscience, 28 (4). pp. 689-693. ISSN 1097-6256

Ibrahim, Maria, Gomez-Jenkins, Maria, Scheinfeld, Adina, Zhao, Zhengqiao, Lopes, Eduardo Cararo, Sawant, Akshada, Hu, Zhixian, Dharani, Aditya, Sun, Michael, Siddiqui, Sarah, Mirek, Emily T, Abram-Saliba, Johan, Lattime, Edmund C, Su, Xiaoyang, Janowitz, Tobias, Goncalves, Marcus D, Dunn, Steven M, Pritykin, Yuri, Anthony, Tracy G, Rabinowitz, Joshua D, White, Eileen (February 2025) Autophagy Suppresses CCL2 to Preserve Appetite and Prevent Lethal Cachexia. bioRxiv. ISSN 2692-8205 (Submitted)

Kaczmarzyk, Jakub, Sharma, Rishul, Koo, Peter, Saltz, Joel (January 2025) Reusable specimen-level inference in computational pathology. arXiv. ISSN 2331-8422 (Public Dataset) (Submitted)

Kang, Hyunook, Epstein, Max, Banke, Tue G, Perszyk, Riley, Simorowski, Noriko, Paladugu, Srinu, Liotta, Dennis C, Traynelis, Stephen F, Furukawa, Hiro (February 2025) Structural basis for channel gating and blockade in tri-heteromeric GluN1-2B-2D NMDA receptor. Neuron. ISSN 0896-6273

Klindt, David, O'Neill, Charles, Reizinger, Patrik, Maurer, Harald, Miolane, Nina (March 2025) From superposition to sparse codes: interpretable representations in neural networks. arXiv. ISSN 2331-8422 (Submitted)

Koh, Kexin, Scott, Rachel, Cespedes Feliciano, Elizabeth M, Janowitz, Tobias, Goncalves, Marcus D, White, Eileen P, Laird, Barry JA, Haase, Kerstin, Jamal-Hanjani, Mariam (April 2025) Cancer-Associated Cachexia: Bridging Clinical Findings with Mechanistic Insights in Human Studies. Cancer Discovery. OF1-OF26. ISSN 2159-8290

Koh, Matthew, Anselmi, Francesca, Kaushalya, Sanjeev K, Hernandez, Diego E, Bast, Walter Germán, Villar, Pablo S, Chae, Honggoo, Davis, Martin B, Teja, Sadhu Sai, Qu, Zhe, Gradinaru, Viviana, Gupta, Priyanka, Banerjee, Arkarup, Albeanu, Dinu F (March 2025) Axially decoupled photo-stimulation and two photon readout (ADePT) for mapping functional connectivity of neural circuits. bioRxiv. ISSN 2692-8205 (Submitted)

Kral, Alexander, Jia, Lu, Sim, GeunYoung, Wan, Ledong, Krainer, Adrian (April 2025) Splice-switching ASOs targeting an Alu-derived exon in the AURKA 5'UTR collapse an SRSF1-AURKA-MYC oncogenic circuit in pancreatic cancer. bioRxiv. ISSN 2692-8205 (Submitted)

Lanctot, Amy, Hendelman, Anat, Udilovich, Peter, Robitaille, Gina M, Lippman, Zachary B (February 2025) Antagonizing cis-regulatory elements of a conserved flowering gene mediate developmental robustness. Proceedings of the National Academy of Sciences of the United States of America, 122 (8). e2421990122. ISSN 0027-8424

Lanctot, Amy, Ramos Báez, Román, Moss, Britney L (March 2025) Synthetic Biology Approaches to Study Maize Signaling Pathways. Cold Spring Harbor Protocols. ISSN 1940-3402

Langdon, Christopher, Engel, Tatiana A (February 2025) Latent circuit inference from heterogeneous neural responses during cognitive tasks. Nature Neuroscience. ISSN 1097-6256 (Public Dataset)

Li, Katrina, Mathew, Brandon, Saldanha, Ethan, Ghosh, Puja, Krainer, Adrian R, Dasarathy, Srinivasan, Huang, Hai, Xiang, Xiyan, Mishra, Lopa (April 2025) New insights into biomarkers and risk stratification to predict hepatocellular cancer. Molecular Medicine, 31 (1). p. 152. ISSN 1528-3658

Liu, Hai-Jun, Liu, Jie, Zhai, Zhiwen, Dai, Mingqiu, Tian, Feng, Wu, Yongrui, Tang, Jihua, Lu, Yanli, Wang, Haiyang, Jackson, David, Yang, Xiaohong, Qin, Feng, Xu, Mingliang, Fernie, Alisdair R, Zhang, Zuxin, Yan, Jianbing (January 2025) Maize2035: A decadal vision for intelligent maize breeding. Molecular Plant. S1674-2052(25)00033. ISSN 1674-2052

Liu, Lingjie, Zhao, Yixin, Hassett, Rebecca, Toneyan, Shushan, Koo, Peter K, Siepel, Adam (February 2025) Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data. Nucleic Acids Research (NAR), 53 (4). ISSN 1362-4962 (Public Dataset)

Liu, Ying, Dantas, Ezequiel, Ferrer, Miriam, Miao, Ting, Qadiri, Mujeeb, Liu, Yifang, Comjean, Aram, Davidson, Emma E, Perrier, Tiffany, Ahmed, Tanvir, Hu, Yanhui, Goncalves, Marcus D, Janowitz, Tobias, Perrimon, Norbert (April 2025) Hepatic gluconeogenesis and PDK3 upregulation drive cancer cachexia in flies and mice. Nature Metabolism, 7 (4). pp. 823-841. ISSN 2522-5812 (Public Dataset)

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 2025) Guidelines for releasing a variant effect predictor. Genome Biology, 26 (1). p. 97. ISSN 1474-7596

Martí-Gómez, Carlos, Zhou, Juannan, Chen, Wei-Chia, Kinney, Justin B, McCandlish, David M (March 2025) Inference and visualization of complex genotype-phenotype maps with gpmap-tools. bioRxiv. ISSN 2692-8205 (Submitted)

Medley, Jeffrey C, Perales, Roberto, Humada, Belén Gaete, Doerfel, Katja, Levine, Ariana, Panzade, Ganesh, Hammell, Christopher M, Zinovyeva, Anna (January 2025) LIN-67 functionally interacts with heterochronic miRNAs and regulates developmental timing in Caenorhabditis elegans. bioRxiv. ISSN 2692-8205 (Submitted)

Mitra, Partha, Jayakumar, Jaikishan, Sivaprakasam, Mohanasankar, Verma, Richa, Bota, Mihail, Joseph, Jayaraj, Mulay, Supriti, Kumutha, Jayaraman, Sriniva, Chitra, S, Suresh, S, Latha, Kumar, Harish, Bhaduri, Aparna, Nowakowski, Tomasz, Roy, Prasun, Savoia, Stephen, Bannerjee, Samik, Tward, Daniel (January 2025) A three-dimensional histological cell atlas of the developing human brain. Research Square. (Submitted)

Moresco, Philip, Kastan, Jonathan P, Yang, Jung-In, Prabakar, Rishvanth, Minicozzi, Francesca, Adams, Dexter W, Cifani, Paolo, Tuveson, David A, Fearon, Douglas T (January 2025) Signal peptide-independent secretion of keratin-19 by pancreatic cancer cells. bioRxiv. ISSN 2692-8205 (Submitted)

Moss, Britney L, Lanctot, Amy, Ramos Báez, Román (March 2025) Testing AuxInYeast Synthetic Biology Strains via Fluorescence Flow Cytometry. Cold Spring Harbor Protocols. ISSN 1940-3402

O'Neill, Kathryn, Shaw, Regina, Bolger, Isobel, NYGC ALS Consortium, Tam, Oliver H, Phatnani, Hemali, Gale Hammell, Molly (March 2025) ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers. Cell Reports, 44 (3). p. 115402. ISSN 2211-1247 (Public Dataset)

Posfai, A, McCandlish, DM, Kinney, JB (April 2025) Symmetry, gauge freedoms, and the interpretability of sequence-function relationships. Physical Review Research, 7 (2). ISSN 2643-1564

Posfai, Anna, Zhou, Juannan, McCandlish, David M, Kinney, Justin B (March 2025) Gauge fixing for sequence-function relationships. PLoS Computational Biology, 21 (3). e1012818. ISSN 1553-734X (Public Dataset)

Ramos Báez, Román, Lanctot, Amy, Moss, Britney L (March 2025) Building AuxInYeast Synthetic Biology Strains for Biochemical Characterization of Maize Auxin Hormone Signaling Components. Cold Spring Harbor Protocols. ISSN 1940-3402

Reed, Laura K, Kleinschmit, Adam J, Buonaccorsi, Vincent, Hunt, Arthur G, Chalker, Douglas, Williams, Jason, Jones, Christopher J, Martinez-Cruzado, Juan-Carlos, Rosenwald, Anne (January 2025) A genomics learning framework for undergraduates. PLoS ONE, 20 (1). e0313124. ISSN 1932-6203

Reizinger, Patrik, Balestriero, Randall, Klindt, David, Brendel, Wieland (April 2025) An Empirically Grounded Identifiability Theory Will Accelerate Self-Supervised Learning Research. bioRxiv. ISSN 2692-8205 (Submitted)

Robil, Janlo M, Straube, Henryk, Tran, Thu M (January 2025) A benzoxazinoid twist to boron homeostasis story in maize. Plant Physiology. kiaf007. ISSN 0032-0889

Ronemus, Michael, Bradford, Daniel, Laster, Zachary, Li, Siran (February 2025) Exploring genome-transcriptome correlations in cancer. Biochemical Society Transactions, 53 (1). ISSN 0300-5127

Sannigrahi, Achinta, De, Nayan, Bhunia, Debmalya, Bhadra, Jhuma (January 2025) Peptide nucleic acids: Recent advancements and future opportunities in biomedical applications. Bioorganic Chemistry, 155. p. 108146. ISSN 0045-2068

Shakiba, Mojdeh, Tuveson, David A (April 2025) Macrophages and fibroblasts as regulators of the immune response in pancreatic cancer. Nature Immunology. ISSN 1529-2908

Shen, Yang, Banerjee, Arkarup, Albeanu, Dinu F, Navlakha, Saket (February 2025) An evolutionarily conserved scheme for reformatting odor concentration in early olfactory circuits. bioRxiv. ISSN 2692-8205 (Submitted)

Stitzer, Michelle C, Seetharam, Arun S, Scheben, Armin, Hsu, Sheng-Kai, Schulz, Aimee J, AuBuchon-Elder, Taylor M, El-Walid, Mohamed, Ferebee, Taylor H, Hale, Charles O, La, Thuy, Liu, Zong-Yan, McMorrow, Sarah J, Minx, Patrick, Phillips, Alyssa R, Syring, Michael L, Wrightsman, Travis, Zhai, Jingjing, Pasquet, Rémy, McAllister, Christine A, Malcomber, Simon T, Traiperm, Paweena, Layton, Daniel J, Zhong, Jinshun, Costich, Denise E, Dawe, R Kelly, Fengler, Kevin, Harris, Charlotte, Irelan, Zach, Llaca, Victor, Parakkal, Praveena, Zastrow-Hayes, Gina, Woodhouse, Margaret R, Cannon, Ethalinda K, Portwood, John L, Andorf, Carson M, Albert, Patrice S, Birchler, James A, Siepel, Adam, Ross-Ibarra, Jeffrey, Romay, M Cinta, Kellogg, Elizabeth A, Buckler, Edward S, Hufford, Matthew B (January 2025) Extensive genome evolution distinguishes maize within a stable tribe of grasses. bioRxiv. ISSN 2692-8205 (Public Dataset) (Submitted)

Tajima, Yoko, Vargas, César DM, Ito, Keiichi, Wang, Wei, Luo, Ji-Dung, Xing, Jiawei, Kuru, Nurdan, Machado, Luiz Carlos, Siepel, Adam, Carroll, Thomas S, Jarvis, Erich D, Darnell, Robert B (February 2025) A humanized NOVA1 splicing factor alters mouse vocal communications. Nature Communications, 16 (1). p. 1542. ISSN 2041-1723 (Public Dataset)

Thompson, Mike, Martín, Mariano, Olmo, Trinidad Sanmartín, Rajesh, Chandana, Koo, Peter K, Bolognesi, Benedetta, Lehner, Ben (May 2025) Massive experimental quantification allows interpretable deep learning of protein aggregation. Science Advances, 11 (18). eadt5111. ISSN 2375-2548 (Public Dataset)

Tonelli, Claudia, Deschênes, Astrid, Gaeth, Victoria A, Jensen, Amanda, Vithlani, Nandan, Yao, Melissa A, Zhao, Zhen, Park, Youngkyu, Tuveson, David A (April 2025) FGFR2 Abrogation Intercepts Pancreatic Ductal Adenocarcinoma Development. Cancer Research. ISSN 0008-5472 (Public Dataset)

Uner, Burcu, Akyildiz, Erdogan Oguzhan, Kolci, Kubra, Reis, Rengin (March 2025) Nanoparticle Formulations for Intracellular Delivery in Colorectal Cancer Therapy. AAPS PharmSciTech, 26 (3). p. 81. ISSN 1530-9932

Vasan, Lakshmy, Chinchalongporn, Vorapin, Saleh, Fermisk, Zinyk, Dawn, Ke, Cao, Suresh, Hamsini, Ghazale, Hussein, Belfiore, Lauren, Touahri, Yacine, Oproescu, Ana-Maria, Patel, Shruti, Rozak, Matthew, Amemiya, Yutaka, Han, Sisu, Moffat, Alexandra, Black, Sandra E, McLaurin, JoAnne, Near, Jamie, Seth, Arun, Goubran, Maged, Reiner, Orly, Gillis, Jesse, Wang, Chao, Okawa, Satoshi, Schuurmans, Carol (January 2025) Examining the NEUROG2 lineage and associated gene expression in human cortical organoids. Development, 152 (2). dev.202703. ISSN 0950-1991 (Public Dataset)

Verma, Richa, Bota, Mihail, Ram, Keerthi, Jayakumar, Jaikishan, Folkerth, Rebecca, Pandurangan, Karthika, Ramesh, Jivitha Jyothi, Majumder, Moitrayee, Raveendran, Rakshika, Nanda, Reetuparna, K, Sivamani, S, Amal Dhivahar, Karthik, Srinivasa, Kumarasami, Ramdayalan, S, Suresh, Lata, S, Kumar, E Harish, Rangasami, Rajeswaran, Srinivasan, Chitra, Kumutha, Jayaraman, Vasudevan, Sudha, Bhat, Koushik, Sam C, Chrisline, Neelakantan, Sivathanu, Savoia, Stephen, Mitra, Partha P, Joseph, Jayaraj, Manger, Paul R, Sivaprakasam, Mohanasankar (February 2025) DHARANI: A 3D Developing Human-Brain Atlas Resource to Advance Neuroscience Internationally Integrated Multimodal Imaging and High-Resolution Histology of the Second Trimester. Journal of Comparative Neurology, 533 (2). e70006. ISSN 0021-9967 (Public Dataset)

Voss, Dillon M, Kral, Alexander J, Sim, GeunYoung, Utama, Raditya, Lin, Kuan-Ting, Cizmeciyan, Chris, Schafer, Balazs, Cunniff, Patrick J, Vakoc, Christopher R, Caruthers, Marvin H, Mishra, Lopa, Krainer, Adrian R (February 2025) PKM splice-switching ASOs induce upregulation of dual-specificity phosphatases and dephosphorylation of ERK1/2 in hepatocellular carcinoma. Journal of Biological Chemistry. p. 108345. ISSN 0021-9258

Vranken, Sofie, Wernberg, Thomas, Scheben, Armin, Pessarrodona, Albert, Batley, Jacqueline, Coleman, Melinda Ann (February 2025) Connectivity enhances resilience of marine forests after an extreme event. Scientific Reports, 15 (1). p. 5019. ISSN 2045-2322 (Public Dataset)

Wang, Hehe, Zhu, Chuanzhou, Swamynathan, Manojit M, Rajput, Shubhra, Jayanetti, Kalani, Rendina, Dominick, Takemura, Kathryn, Bogdan, Diane, Wang, Liqun, Rizzo, Robert C, Kaczocha, Martin, Trotman, Lloyd C, Bialkowska, Agnieszka B, Ojima, Iwao (May 2025) Fatty acid binding protein 5 inhibitors as novel anticancer agents against metastatic castration-resistant prostate cancer. Bioorganic and Medicinal Chemistry, 122. p. 118136. ISSN 0968-0896 (In Press)

Wang, Yuanting, Vakoc, Christopher R (February 2025) Sequential epigenetic therapy in AML. Blood, 145 (7). pp. 660-661. ISSN 0006-4971

Wang, Z, Vishwakarma, DS, Sun, S, Huang, Q, Pati, S, Johnson, RM, Rufrano, MR, Gembicky, M, Homer, JA, Moses, JE (January 2025) Phosphorus Fluoride Exchange (PFEx) Click Chemistry: 2-Substituted-Alkynyl-1-Cyclotriphosphazene (SACP) Hubs for Diversity Oriented Clicking. Advanced Synthesis and Catalysis. ISSN 1615-4150

Wei, Sharon, Chougule, Kapeel, Olson, Andrew, Lu, Zhenyuan, Tello-Ruiz, Marcela K, Kumar, Vivek, Kumari, Sunita, Zhang, Lifang, Olson, Audra, Kim, Catherine, Gladman, Nick, Ware, Doreen (April 2025) GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data. Database : the journal of biological databases and curation, 2025. ISSN 1758-0463 (Public Dataset)

Xavier, Andre M, Lin, Qianyu, Kang, Chris J, Cheadle, Lucas (February 2025) A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex. Development. dev.204244. ISSN 0950-1991 (Public Dataset)

Yu, Ruofan, Roseman, Shelby, Siegenfeld, Allison P, Gardner, Zachary, Nguyen, Son C, Tran, Khoa A, Joyce, Eric F, Jain, Rajan, Liau, Brian B, Krantz, Ian D, Alexander, Katherine A, Berger, Shelley L (February 2025) CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association. Nature Structural & Molecular Biology. ISSN 1545-9993 (Public Dataset)

Zador, Anthony (March 2025) How to communicate the value of curiosity-driven research. The Transmitter.

Zali, Narges, El Damerash, Osama, Chougule, Kapeel, Lu, Zhenyuan, Ware, Doreen, Stillman, Bruce (March 2025) Genome sequence assembly and annotation of MATA and MATB strains of Yarrowia lipolytica. bioRxiv. ISSN 2692-8205 (Public Dataset) (Submitted)

Zebell, Sophia G, Martí-Gómez, Carlos, Fitzgerald, Blaine, Pinto Da Cunha, Camila, Lach, Michael, Seman, Brooke M, Hendelman, Anat, Sretenovic, Simon, Qi, Yiping, Bartlett, Madelaine, Eshed, Yuval, McCandlish, David M, Lippman, Zachary B (February 2025) Cryptic variation fuels plant phenotypic change through hierarchical epistasis. bioRxiv. ISSN 2692-8205 (Public Dataset) (Submitted)

Zheng, Xiaoyue Mike, Harpole, Clifford E, Davis, Martin B, Banerjee, Arkarup (April 2025) Parametric Modulation of a Shared Midbrain Circuit Drives Distinct Vocal Modes in a Singing Mouse. bioRxiv. ISSN 2692-8205 (Submitted)

Zhou, Edward, Yang, Jung-In, Habowski, Amber N, Deschênes, Astrid, Belleau, Pascal, Ha, Taehoon, Tzanavaris, Chris J, Boyd, Jeff, Hollweg, Christopher A, Zhu, Xinhua, Tuveson, David A, King, Daniel A (April 2025) GATA6 Amplification Is Associated With Improved Survival in TP53-Mutated Unresectable Pancreatic Cancer. Pancreas, 54 (4). e303-e309. ISSN 1536-4828

Zhu, Xiaoyue Aelita, Starosta, Sarah, Ferrer, Miriam, Hou, Junxiao, Chevy, Quentin, Lucantonio, Federica, Muñoz-Castañeda, Rodrigo, Zhang, Fengrui, Zang, Kaikai, Zhao, Xiang, Fiocchi, Francesca R, Bergstrom, Mason, Siebels, Aubrey A, Upin, Thomas, Wulf, Michael, Evans, Sarah, Kravitz, Alexxai V, Osten, Pavel, Janowitz, Tobias, Pignatelli, Marco, Kepecs, Adam (April 2025) A neuroimmune circuit mediates cancer cachexia-associated apathy. Science, 388 (6743). eadm8857. ISSN 0036-8075

Conference or Workshop Item

ElHarouni, Dina, Al-Jazrawe, Mushriq, Choi, Seongmin, Dede, Merve, Hinoue, Toshinori, Misek, Sean A, Noh, Heeju, Zanella, Luca, Tseng, Moony, Francies, Hayley E, Sridevi, Priya, Agarwal, Rachana, Kyi, Cindy W, Perez-Mayoral, Julyann, Stine, Megan J, Tonsing-Carter, Eva, Clinton, James M, Laird, Peter W, Kuo, Calvin J, Elemento, Olivier, Spector, David L, Cherniack, Andrew D, Ellrott, Kyle, Ferguson, Martin L, Beroukhim, Rameen, Hoadley, Katherine A, Robine, Nicolas, Garnett, Mathew, Califano, Andrea, Spellman, Paul T, Tuveson, David A, Ligon, Keith L, Gerhard, Daniela S, Staudt, Louis M, Boehm, Jesse (March 2025) Integrative clinical and molecular analysis of 665 next-generation in vitro cancer models generated by the the Human Cancer Models Initiative (HCMI) for advancing precision medicine and functional drug discovery. In: Proceedings of the AACR Special Conference in Cancer Research: Functional and Genomic Precision Medicine in Cancer: Different Perspectives, Common Goals, 2025 Mar 11-13, Boston, MA.