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

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)

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)

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)

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)

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

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)

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)

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)

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

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

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

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)

Uner, Burcu, Akyildiz, Erdogan Oguzhan, Kolci, Kubra, Eskiocak, Onur, Reis, Rengin, Beyaz, Semir (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

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.

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)