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Maxwell Ma, Fahad Paryani, Kelly Jakubiak, Shengnan Xia, Susumu Antoku, Adithya Kannan, Jaeseung Lee, Nacoya Madden, Shailesh Kumar, Juncheng Li, David Chen, Gunnar Hargus, Aayushi Mahajan, Xena Flowers, Ashley Harms, David Sulzer, James Goldman, Peter Sims, Osama Al-Dalahmah .  2025.   The spatial landscape of glial pathology and T cell response in Parkinson's disease substantia nigra.. Nature communications. 16 (1) :7146 ▶ Go to Pubmed
Sneha Rao, Zhixiong Sun, Francesco Brundu, Yannan Chen, Yan Sun, Huixiang Zhu, Robert Shprintzen, Raju Tomer, Raul Rabadan, Kam Leong, Sander Markx, Steven Kushner, Bin Xu, Joseph Gogos .  2025.   Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome-associated schizophrenia.. Nature communications. 16 (1) :6986 ▶ Go to Pubmed
Alexander Wang, Luca Zanella, Yosuke Ochiai, Leonardo Golinelli, Andrea Califano, Ermanno Malagola, Alessandro Vasciaveo .  2025.   Protocol for automated graph-based clustering of single-cell RNA-seq data with application in mouse intestinal stem cells.. STAR protocols. 6 (3) :104000 ▶ Go to Pubmed
John Tuddenham, Masashi Fujita, Emily Lee, Nivedita Nimmagadda, Anthony Khairallah, Claire Harbison, Xena Flowers, Guillermo Coronas-Samano, Silas Maniatis, Aidan Daly, Julie Schneider, Andrew Teich, Jean Vonsattel, Peter Sims, Wassim Elyaman, Elizabeth Bradshaw, Lyle Ostrow, Hemali Phatnani, Neil Shneider, David Bennett, Philip De Jager, Serge Przedborski, Vilas Menon, Marta Olah .  2025.   Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord.. Acta neuropathologica. 150 (1) :10 ▶ Go to Pubmed
Carlotta Ronda, Tyler Perdue, Logan Schwanz, Diego Gelsinger, Leonie Brockmann, Andrew Kaufman, Yiming Huang, Samuel Sternberg, Harris Wang .  2025.   Precise virulence inactivation using a CRISPR-associated transposase for combating Enterobacteriaceae gut pathogens.. Nature biomedical engineering. 9 (12) :2017-2027 ▶ Go to Pubmed
Yun Lin, Andrea Clark-Sevilla, Mahdi Loodaricheh, Itsik Pe'er, Anita Raja, Ronald Wapner, Ansaf Salleb-Aouissi .  2025.   Differential Predictability of Preterm Birth Types: Strong Signals for Indicated Cases versus Limited Success in Spontaneous Preterm Birth.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Alyssa Ekdahl, Tatiana Julien, Sahana Suraj, Judith Kribelbauer-Swietek, Saeed Tavazoie, Lydia Freddolino, Lydia Contreras .  2025.   Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.. Nucleic acids research. 53 (13) ▶ Go to Pubmed
Dapeng Xiong, Mateo Torres, Diana Murray, Le Li, Aniket Naravane, Robert Fragoza, Barry Honig, Haiyuan Yu .  2025.   Integrating structural homology with deep learning to achieve highly accurate protein-protein interface prediction for the human interactome.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Amir Momen-Roknabadi, Panos Oikonomou, Saeed Tavazoie .  2025.   Adaptation by stochastic tuning of gene expression in mammalian cells.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Zicheng Wang, Yufeng Shen .  2025.   G2VTCR: predicting antigen binding specificity by Weisfeiler-Lehman graph embedding of T cell receptor sequences.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Jiayu Su, Yiming Qu, Megan Schertzer, Haochen Yang, Jiahao Jiang, Tenzin Lhakhang, Theodore Nelson, Stella Park, Qiliang Lai, Xi Fu, Seung-Won Choi, David Knowles, Raul Rabadan .  2025.   A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Scott Watkins, Edgar Hernandez, Thomas Miller, Nathan Blue, Raquel Zimmerman, Eric Griffiths, Erwin Frise, Daniel Bernstein, Marko Boskovski, Martina Brueckner, Wendy Chung, William Gaynor, Bruce Gelb, Elizabeth Goldmuntz, Peter Gruber, Jane Newburger, Amy Roberts, Sarah Morton, John Mayer, Christine Seidman, Jonathan Seidman, Yufeng Shen, Michael Wagner, Joseph Yost, Mark Yandell, Martin Tristani-Firouzi .  2025.   Genome sequencing is critical for forecasting outcomes following congenital cardiac surgery.. Nature communications. 16 (1) :6365 ▶ Go to Pubmed
Ye Zheng, Daniel Caron, Ju Kim, Seong-Hwan Jun, Yuan Tian, Florian Mair, Kenneth Stuart, Peter Sims, Raphael Gottardo .  2025.   ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets.. Nature communications. 16 (1) :5852 ▶ Go to Pubmed
Yoonhee Nam, Karen Gomez, Jean-Baptiste Reynier, Cole Khamnei, Michael Aitken, Vivian Zheng, Tenzin Lhakhang, Milena Casula, Giuseppe Palmieri, Antonio Cossu, Arnold Levine, Enrico Tiacci, Raul Rabadan .  2025.   Genomic landscape of virus-associated cancers.. Nature communications. 16 (1) :5887 ▶ Go to Pubmed
Panfeng Bao, Wenjun Yi, Yue Zhu, Yufeng Shen, Haotian Peng .  2025.   A Spectral Interpretable Bearing Fault Diagnosis Framework Powered by Large Language Models.. Sensors (Basel, Switzerland). 25 (12) ▶ Go to Pubmed
Daniel Moakley, Melissa Campbell, Miquel Anglada-Girotto, Huijuan Feng, Andrea Califano, Edmund Au, Chaolin Zhang .  2025.   Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes.. Cell reports. 44 (7) :115898 ▶ Go to Pubmed
Daniel Moakley, Melissa Campbell, Miquel Anglada-Girotto, Huijuan Feng, Andrea Califano, Edmund Au, Chaolin Zhang .  2025.   Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes.. Cell reports. 44 (7) :115898 ▶ Go to Pubmed
Pasquale Laise, Gideon Bosker, Mariana Babor, Xiaoyun Sun, Stuart Andrews, Lorenzo Tomassoni, Andrea Califano, Mariano Alvarez .  2025.   Systematic identification and targeting of master regulator checkpoints (MRC) governing tumor microenvironment-mediated immune evasion.. Journal for immunotherapy of cancer. 13 (6) ▶ Go to Pubmed
Noah Fierer, Pok Leung, Rachael Lappan, Raphael Eisenhofer, Francesco Ricci, Sophie Holland, Nicholas Dragone, Linda Blackall, Xiyang Dong, Cristina Dorador, Belinda Ferrari, Jacqueline Goordial, Susan Holmes, Fumio Inagaki, Tal Korem, Simone Li, Thulani Makhalanyane, Jessica Metcalf, Niranjan Nagarajan, William Orsi, Erin Shanahan, Alan Walker, Laura Weyrich, Jack Gilbert, Amy Willis, Benjamin Callahan, Ashley Shade, Julian Parkhill, Jillian Banfield, Chris Greening .  2025.   Guidelines for preventing and reporting contamination in low-biomass microbiome studies.. Nature microbiology. 10 (7) :1570-1580 ▶ Go to Pubmed
Daniel Caron, William Specht, David Chen, Steven Wells, Peter Szabo, Peter Sims, Donna Farber .  2025.   Tissue signatures of human macrophages during homeostasis and activation.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
James Swann, Jun Fung, Ziwei Chen, Oakley Olson, Amélie Collins, Tenzin Lhakhang, Melissa Proven, Ruiyuan Zhang, Raul Rabadan, Emmanuelle Passegué .  2025.   Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Benjamin Joffe, John Christin, Clémentine Le Coz, Prakash Gorroochurn, Jamie Pak, Caroline Laplaca, Helena Reyes, Joel DeCastro, Christopher Anderson, Cory Abate-Shen, Michael Shen, James McKiernan, Andrew Lenis .  2025.   Combination regimen of intravesical docetaxel, gemcitabine, and cisplatin in patients with BCG-unresponsive bladder cancer: clinical outcomes and genomic correlations.. Urologic oncology. 43 (10) :594.e1-594.e7 ▶ Go to Pubmed
H Zhao, C Velez, A Navarene, A Saha, J Feldman, J Skolnick, D Murray, B Honig .  2025.   Combining structural modeling and deep learning to calculate the protein interactome and functional networks.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Aziz Zafar .  2025.   Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant effect predictors.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Verena Haage .  2025.   HDAC inhibitors engage MITF and the disease-associated microglia signature to enhance amyloid β uptake.. Brain, behavior, and immunity. 129 :279-293 ▶ Go to Pubmed
John Lee, Alina Sergeeva, Goran Ahlsen, Seetha Mannepalli, Fabiana Bahna, Kerry Goodman, Runzhe Xu, Baljit Khakh, Joshua Weiner, Lawrence Shapiro, Barry Honig, Lawrence Zipursky .  2025.   Astrocyte morphogenesis requires self-recognition.. Nature. 644 (8075) :164-172 ▶ Go to Pubmed
Lu Rao, Wenxing Li, Yufeng Shen, Wendy Chung, Arne Gennerich .  2025.   Distinct Clinical Phenotypes in KIF1A-Associated Neurological Disorders Result from Different Amino Acid Substitutions at the Same Residue in KIF1A.. Biomolecules. 15 (5) ▶ Go to Pubmed
Nicole Edwards, Scott Rankin, Adhish Kashyap, Alissa Warren, Zachary Agricola, Alan Kenny, Matthew Kofron, Yufeng Shen, Wendy Chung, Aaron Zorn .  2025.   Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in Xenopus trachea-esophageal morphogenesis.. Developmental cell. 60 (18) :2487-2502.e4 ▶ Go to Pubmed
Giovanni Valenti, Pasquale Laise, Feijing Wu, Ryota Takahashi, Tuo Ruan, Alessandro Vasciaveo, Zhengyu Jiang, Hiroki Kobayashi, Masaki Sunagawa, Moritz Middelhoff, Henrik Nienhüser, Na Fu, Ermanno Malagola, Osmel Companioni, Yoku Hayakawa, Alina Iuga, Andrea Califano, Timothy Wang .  2025.   Regulatory network analysis of Dclk1 gene expression reveals a tuft cell-ILC2 axis that inhibits pancreatic tumor progression.. Cell reports. 44 (6) :115734 ▶ Go to Pubmed
Yige Zhao, Tian Lan, Guojie Zhong, Jake Hagen, Hongbing Pan, Wendy Chung, Yufeng Shen .  2025.   A probabilistic graphical model for estimating selection coefficients of nonsynonymous variants from human population sequence data.. Nature communications. 16 (1) :4670 ▶ Go to Pubmed
Brooke Dirvin, Heeju Noh, Lorenzo Tomassoni, Danting Cao, Yizhuo Zhou, Xiangyi Ke, Jun Qian, Sonia Jangra, Michael Schotsaert, Adolfo García-Sastre, Charles Karan, Andrea Califano, Wellington Cardoso V .  2025.   Identification and targeting of regulators of SARS-CoV-2-host interactions in the airway epithelium.. Science advances. 11 (20) :eadu2079 ▶ Go to Pubmed
Brooke Dirvin, Heeju Noh, Lorenzo Tomassoni, Danting Cao, Yizhuo Zhou, Xiangyi Ke, Jun Qian, Sonia Jangra, Michael Schotsaert, Adolfo García-Sastre, Charles Karan, Andrea Califano, Wellington Cardoso V .  2025.   Identification and targeting of regulators of SARS-CoV-2-host interactions in the airway epithelium.. Science advances. 11 (20) :eadu2079 ▶ Go to Pubmed
Yimeng Zhu, Angelina Li, Suvrajit Maji, Brian Lee, Sophie Korn, Jake Gertie, Tyler Dorrity, Jianhua Wang, Kyle Wang, Amandine Pelletier, Daniel Moakley, Rachel Kelly, Antony Holmes, Raul Rabadan, David Edgell, Caroline Poulter, Mauro Modesti, Anna-Lena Steckelberg, Eric Hendrickson, Hachung Chung, Chaolin Zhang, Shan Zha .  2025.   Ku limits RNA-induced innate immunity to allow Alu-expansion in primates.. Nature. ▶ Go to Pubmed
Gulam Manji, Liam Stanton, Angela Hirbe, Liner Ge, Sarah Ana, Shiny Titus, Brian Labadie, Michael May, Yang Lyu, John Chrisinger, Naomi Sender, Varun Monga, Mohammed Milhem, Rashmi Chugh, Peter Sims, Aik Tan, Shing Lee, Brian Van Tine, Gary Schwartz .  2025.   Phase II Study of Pexidartinib Plus Sirolimus in Unresectable Malignant Peripheral Nerve Sheath Tumors Identifies M2 Macrophage Activation.. JCO oncology advances. 2 (1) :e2400083 ▶ Go to Pubmed
Shino Murakami, Anthony Olarerin-George, Jianheng Liu, Sara Zaccara, Ben Hawley, Samie Jaffrey .  2025.   mA alters ribosome dynamics to initiate mRNA degradation.. Cell. 188 (14) :3728-3743.e20 ▶ Go to Pubmed
Shino Murakami, Anthony Olarerin-George, Jianheng Liu, Sara Zaccara, Ben Hawley, Samie Jaffrey .  2025.   mA alters ribosome dynamics to initiate mRNA degradation.. Cell. ▶ Go to Pubmed
George Austin, Tal Korem .  2025.   Compositional transformations can reasonably introduce phenotype-associated values into sparse features.. mSystems. :e0002125 ▶ Go to Pubmed
George Austin, Tal Korem .  2025.   Compositional transformations can reasonably introduce phenotype-associated values into sparse features.. mSystems. 10 (5) :e0002125 ▶ Go to Pubmed
Wen Huang, Xiaoting Li, Feifang Zhang, Yufeng Shen, Bingcheng Yang .  2025.   Simultaneous determination of cations in nuclear power plant water by conductometric ion chromatography equipped with fluorescence detector.. Journal of chromatography. A. 1752 :465984 ▶ Go to Pubmed
Menghan Liu, Sydney Blattman, Mai Takahashi, Nandan Mandayam, Wenyan Jiang, Panos Oikonomou, Sohail Tavazoie, Saeed Tavazoie .  2025.   Conserved genetic basis for microbial colonization of the gut.. Cell. 188 (10) :2823-2824 ▶ Go to Pubmed
Maria Alvarez-Torres, Xi Fu, Raul Rabadan .  2025.   Illuminating the Noncoding Genome in Cancer using Artificial Intelligence.. Cancer research. ▶ Go to Pubmed
Stephanie Herrlinger, Jiayao Wang, Bovey Rao, Jonathan Chang, Joseph Gogos, Attila Losonczy, Dennis Vitkup .  2025.   Rare mutations implicate CGE interneurons as a vulnerable axis of cognitive deficits across psychiatric disorders.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Bo Li, Mariano Alvarez, Hui Zhao, Napon Chirathivat, Andrea Califano, Michael Shen .  2025.   The regulatory architecture of the primed pluripotent cell state.. Nature communications. 16 (1) :3351 ▶ Go to Pubmed
Vineetha Mathew, Raiyan Khan, Amanda Jowell, Qi Yan, Itsik Pe'er, Buu Truong, Pradeep Natarajan, Lynn Yee, Sadiya Khan, Garima Sharma, Aniruddh Patel, So Cho, Maria Pabon, Rebecca McNeil, Jillyn Spencer, Robert Silver, Lisa Levine, William Grobman, Janet Catov, David Haas, Michael Honigberg .  2025.   Genetic Risk and First-Trimester Cardiovascular Health Predict Hypertensive Disorders of Pregnancy in Nulliparous Women.. Journal of the American College of Cardiology. 85 (14) :1488-1500 ▶ Go to Pubmed
Victoria Marshe, John Tuddenham, Kevin Chen, Rebecca Chiu, Verena Haage, Yiyi Ma, Annie Lee, Neil Shneider, Julian Agin-Liebes, Roy Alcalay, Andrew Teich, Peter Canoll, Claire Riley, Dirk Keene, Julie Schneider, David Bennett, Vilas Menon, Mariko Taga, Hans-Ulrich Klein, Marta Olah, Masashi Fujita, Ya Zhang, Peter Sims, Philip De Jager .  2025.   A factor-based analysis of individual human microglia uncovers regulators of an Alzheimer-related transcriptional signature.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Menghan Liu, Sydney Blattman, Mai Takahashi, Nandan Mandayam, Wenyan Jiang, Panos Oikonomou, Sohail Tavazoie, Saeed Tavazoie .  2025.   Conserved genetic basis for microbial colonization of the gut.. Cell. 188 (9) :2505-2520.e22 ▶ Go to Pubmed
Menghan Liu, Sydney Blattman, Mai Takahashi, Nandan Mandayam, Wenyan Jiang, Panos Oikonomou, Sohail Tavazoie, Saeed Tavazoie .  2025.   Conserved genetic basis for microbial colonization of the gut.. Cell. 188 (9) :2505-2520.e22 ▶ Go to Pubmed
Harris Wang, Derek Rubadeux, Andrew Trout, Cara Morin, Alexander Opotowsky, Alexandra Glenn, Joseph Palermo, Khurram Bari, Jonathan Dillman .  2025.   Ultrasound-MRI Agreement in Individuals Undergoing Surveillance of Fontan-associated Liver Disease.. Journal of computer assisted tomography. 49 (5) :705-713 ▶ Go to Pubmed
Xinlong He, Yufeng Shen, Ye Feng, Zhifang Gao, Hanbing Xue, Huimin Chen .  2025.   Latest possible timing for endoscopic-assisted intervention in capsule endoscopy.. Gastroenterology report. 13 :goaf011 ▶ Go to Pubmed
Xinlong He, Yufeng Shen, Ye Feng, Zhifang Gao, Hanbing Xue, Huimin Chen .  2025.   Latest possible timing for endoscopic-assisted intervention in capsule endoscopy.. Gastroenterology report. 13 :goaf011 ▶ Go to Pubmed
Yuxuan Liu, Ted Piorczynski, Brian Estrella, Edd Ricker, Manuel Pazos, Yulissa Gonzalez, Seda Tolu, Yun Tiger, Charles Karan, Serge Cremers, Renu Nandakumar, Barry Honig, Howook Hwang, Neil Kelleher, Jeannie Camarillo, Nebiyu Abshiru, Jennifer Amengual .  2025.   Targeting Monoallelic / Mutations in Germinal Center-Derived B-Cell Lymphoma with a First-in-Class Histone Acetyltransferase Activator.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Ioanna Mosialou, Abdullah Ali, Rossella Labella, Brygida Bisikirska, Alvaro Cuesta-Dominguez, Paraskevi Vgenopoulou, Ismarc Reyes, Sanjana Rao, Anqi Wang, Na Luo, Marta Galán-Díez, Junfei Zhao, Brian Chernak, Jan Bewersdorf, Kazuya Fukasawa, Jiayu Su, Jason Higa, Rachel Adams, Adam Corper, Sergey Pampou, Catherine Woods, Xiaomin Fan, Roshan Shah, Julie Feldstein, Na Liu, Cui Liang, Maël Heiblig, Steven Kornblau, Guillermo Garcia-Manero, Ellin Berman, Joseph Jurcic, Raul Rabadan, Azra Raza, Stavroula Kousteni .  2025.   A niche driven mechanism determines response and a mutation-independent therapeutic approach for myeloid malignancies.. Cancer cell. 43 (6) :1007-1024.e13 ▶ Go to Pubmed
Ioanna Mosialou, Abdullah Ali, Rossella Labella, Brygida Bisikirska, Alvaro Cuesta-Dominguez, Paraskevi Vgenopoulou, Ismarc Reyes, Sanjana Rao, Anqi Wang, Na Luo, Marta Galán-Díez, Junfei Zhao, Brian Chernak, Jan Bewersdorf, Kazuya Fukasawa, Jiayu Su, Jason Higa, Rachel Adams, Adam Corper, Sergey Pampou, Catherine Woods, Xiaomin Fan, Roshan Shah, Julie Feldstein, Na Liu, Cui Liang, Maël Heiblig, Steven Kornblau, Guillermo Garcia-Manero, Ellin Berman, Joseph Jurcic, Raul Rabadan, Azra Raza, Stavroula Kousteni .  2025.   A niche driven mechanism determines response and a mutation-independent therapeutic approach for myeloid malignancies.. Cancer cell. ▶ Go to Pubmed
George Austin, Aya Kav, Shahd ElNaggar, Heekuk Park, Jana Biermann, Anne-Catrin Uhlemann, Itsik Pe'er, Tal Korem .  2025.   Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models.. Nature microbiology. 10 (4) :897-911 ▶ Go to Pubmed
George Austin, Aya Kav, Shahd ElNaggar, Heekuk Park, Jana Biermann, Anne-Catrin Uhlemann, Itsik Pe'er, Tal Korem .  2025.   Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models.. Nature microbiology. 10 (4) :897-911 ▶ Go to Pubmed
Danilo Fiore, Luca Cappelli, Liu Zhaoqi, Nikita Kotlov, Maria Sorokina, Jude Phillip, Paul Zumbo, Liron Yoffe, Paola Ghione, Anqi Wang, Xueshuai Han, Abigail Taylor, William Chiu, Valentina Fragliasso, Fabrizio Tabbò, Nahuel Zamponi, Nicolás Di Siervi, Clarisse Kayembe, Giovanni Medico, Ruchi Patel, Marcello Gaudiano, Rodolfo Machiorlatti, Giuseppina Astone, Maria Cacciapuoti, Giorgia Zanetti, Claudia Pignataro, Ruiz Eric, Sanjay Patel, Francesca Zammarchi, Claudio Zanettini, Lucio Queiroz, Anastasia Nikitina, Olga Kudryashova, Anton Karelin, Daniil Nikitin, Dmitry Tychinin, Ekaterina Postovalova, Alexander Bagaev, Viktor Svekolkin, Ekaterina Belova, Katerina Tikhonova, Sandrine Degryse, Chengqi Xu, Domenico Novero, Maurilio Ponzoni, Enrico Tiacci, Brunangelo Falini, Joo Song, Inna Khodos, Elisa de Stanchina, Gabriele Macari, Luciana Cafforio, Simone Gardini, Roberto Piva, Enzo Medico, Samuel Ng, Allison Moskowitz, Zachary Epstein, Andrew Intlekofer, Dogan Ahmed, Wing Chan, Peter Martin, Jia Ruan, Francesco Bertoni, Robin Foá, Joshua Brody, David Weinstock, Jaspreet Osan, Laura Santambrogio, Oliver Elemento, Doron Betel, Wayne Tam, Marco Ruella, Leandro Cerchietti, Raul Rabadan, Steven Horwitz, Giorgio Inghirami .  2025.   A patient-derived T cell lymphoma biorepository uncovers pathogenetic mechanisms and host-related therapeutic vulnerabilities.. Cell reports. Medicine. 6 (4) :102029 ▶ Go to Pubmed
Danilo Fiore, Luca Cappelli, Liu Zhaoqi, Nikita Kotlov, Maria Sorokina, Jude Phillip, Paul Zumbo, Liron Yoffe, Paola Ghione, Anqi Wang, Xueshuai Han, Abigail Taylor, William Chiu, Valentina Fragliasso, Fabrizio Tabbò, Nahuel Zamponi, Nicolás Di Siervi, Clarisse Kayembe, Giovanni Medico, Ruchi Patel, Marcello Gaudiano, Rodolfo Machiorlatti, Giuseppina Astone, Maria Cacciapuoti, Giorgia Zanetti, Claudia Pignataro, Ruiz Eric, Sanjay Patel, Francesca Zammarchi, Claudio Zanettini, Lucio Queiroz, Anastasia Nikitina, Olga Kudryashova, Anton Karelin, Daniil Nikitin, Dmitry Tychinin, Ekaterina Postovalova, Alexander Bagaev, Viktor Svekolkin, Ekaterina Belova, Katerina Tikhonova, Sandrine Degryse, Chengqi Xu, Domenico Novero, Maurilio Ponzoni, Enrico Tiacci, Brunangelo Falini, Joo Song, Inna Khodos, Elisa de Stanchina, Gabriele Macari, Luciana Cafforio, Simone Gardini, Roberto Piva, Enzo Medico, Samuel Ng, Allison Moskowitz, Zachary Epstein, Andrew Intlekofer, Dogan Ahmed, Wing Chan, Peter Martin, Jia Ruan, Francesco Bertoni, Robin Foá, Joshua Brody, David Weinstock, Jaspreet Osan, Laura Santambrogio, Oliver Elemento, Doron Betel, Wayne Tam, Marco Ruella, Leandro Cerchietti, Raul Rabadan, Steven Horwitz, Giorgio Inghirami .  2025.   A patient-derived T cell lymphoma biorepository uncovers pathogenetic mechanisms and host-related therapeutic vulnerabilities.. Cell reports. Medicine. 6 (4) :102029 ▶ Go to Pubmed
Theresa Baumeister, Andrea Proaño-Vasco, Amira Metwaly, Karin Kleigrewe, Alexander Kuznetsov, Linus Schömig, Martin Borgmann, Mohammed Khiat, Akanksha Anand, Julia Strangmann, Katrin Böttcher, Dirk Haller, Andreas Dunkel, Veronika Somoza, Sinah Reiter, Chen Meng, Robert Thimme, Roland Schmid, Deepa Patil, Elke Burgermeister, Yiming Huang, Yiwei Sun, Harris Wang, Timothy Wang, Julian Abrams, Michael Quante .  2025.   Loss of FXR or Bile Acid-dependent Inhibition Accelerate Carcinogenesis of Gastroesophageal Adenocarcinoma.. Cellular and molecular gastroenterology and hepatology. 19 (8) :101505 ▶ Go to Pubmed
Michael Sierant, Sheng Jin, Kaya Bilguvar, Sarah Morton, Weilai Dong, Wei Jiang, Ziyu Lu, Boyang Li, Francesc López-Giráldez, Irina Tikhonova, Xue Zeng, Qiongshi Lu, Jungmin Choi, Junhui Zhang, Carol Nelson-Williams, James Knight, Hongyu Zhao, Junyue Cao, Shrikant Mane, Stanley Sedore, Peter Gruber, Monkol Lek, Elizabeth Goldmuntz, John Deanfield, Alessandro Giardini, Seema Mital, Mark Russell, William Gaynor, Eileen King, Michael Wagner, Deepak Srivastava, Yufeng Shen, Daniel Bernstein, George Porter, Jane Newburger, Jonathan Seidman, Amy Roberts, Mark Yandell, Joseph Yost, Martin Tristani-Firouzi, Richard Kim, Wendy Chung, Bruce Gelb, Christine Seidman, Martina Brueckner, Richard Lifton .  2025.   Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes.. Proceedings of the National Academy of Sciences of the United States of America. 122 (13) :e2420343122 ▶ Go to Pubmed
Michael Sierant, Sheng Jin, Kaya Bilguvar, Sarah Morton, Weilai Dong, Wei Jiang, Ziyu Lu, Boyang Li, Francesc López-Giráldez, Irina Tikhonova, Xue Zeng, Qiongshi Lu, Jungmin Choi, Junhui Zhang, Carol Nelson-Williams, James Knight, Hongyu Zhao, Junyue Cao, Shrikant Mane, Stanley Sedore, Peter Gruber, Monkol Lek, Elizabeth Goldmuntz, John Deanfield, Alessandro Giardini, Seema Mital, Mark Russell, William Gaynor, Eileen King, Michael Wagner, Deepak Srivastava, Yufeng Shen, Daniel Bernstein, George Porter, Jane Newburger, Jonathan Seidman, Amy Roberts, Mark Yandell, Joseph Yost, Martin Tristani-Firouzi, Richard Kim, Wendy Chung, Bruce Gelb, Christine Seidman, Martina Brueckner, Richard Lifton .  2025.   Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes.. Proceedings of the National Academy of Sciences of the United States of America. 122 (13) :e2420343122 ▶ Go to Pubmed
Himanshu Gupta, Anthony Azevedo, Yu-C-Hieh Chen, Kristi Xing, Peter Sims, Erdem Varol, Richard Mann .  2025.   Decoding neuronal wiring by joint inference of cell identity and synaptic connectivity.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Lu Rao, Wenxing Li, Yufeng Shen, Wendy Chung, Arne Gennerich .  2025.   Distinct Clinical Phenotypes in KIF1A-Associated Neurological Disorders Result from Different Amino Acid Substitutions at the Same Residue in KIF1A.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Lu Rao, Wenxing Li, Yufeng Shen, Wendy Chung, Arne Gennerich .  2025.   Distinct Clinical Phenotypes in KIF1A-Associated Neurological Disorders Result from Different Amino Acid Substitutions at the Same Residue in KIF1A.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Nicholas Morano, Davys Lopez, Hagar Meltzer, Alina Sergeeva, Phinikoula Katsamba, Kevin Rostam, Himanshu Gupta, Jordan Becker, Bavat Bornstein, Filip Cosmanescu, Oren Schuldiner, Barry Honig, Richard Mann, Lawrence Shapiro .  2025.   Members of the DIP and Dpr adhesion protein families use cis inhibition to shape neural development in Drosophila.. PLoS biology. 23 (3) :e3003030 ▶ Go to Pubmed
Nicholas Morano, Davys Lopez, Hagar Meltzer, Alina Sergeeva, Phinikoula Katsamba, Kevin Rostam, Himanshu Gupta, Jordan Becker, Bavat Bornstein, Filip Cosmanescu, Oren Schuldiner, Barry Honig, Richard Mann, Lawrence Shapiro .  2025.   Members of the DIP and Dpr adhesion protein families use cis inhibition to shape neural development in Drosophila.. PLoS biology. 23 (3) :e3003030 ▶ Go to Pubmed
Alisia Fadini, Minhuan Li, Airlie McCoy, Thomas Terwilliger, Randy Read, Doeke Hekstra, Mohammed AlQuraishi .  2025.   AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Alisia Fadini, Minhuan Li, Airlie McCoy, Thomas Terwilliger, Randy Read, Doeke Hekstra, Mohammed AlQuraishi .  2025.   AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Gidsela Luna, Jamie Verheyden, Chunting Tan, Estelle Kim, Michelle Hwa, Jugraj Sahi, Yufeng Shen, Wendy Chung, David McCulley, Xin Sun .  2025.   MYRF is Essential in Mesothelial Cells to Promote Lung Development and Maturation.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Gidsela Luna, Jamie Verheyden, Chunting Tan, Estelle Kim, Michelle Hwa, Jugraj Sahi, Yufeng Shen, Wendy Chung, David McCulley, Xin Sun .  2025.   MYRF is Essential in Mesothelial Cells to Promote Lung Development and Maturation.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Yufeng Shen, Xiaomei Zhu, Feifang Zhang, Bingcheng Yang .  2025.   A hyperbranched anion exchanger obtained by carboxylate surface modified polymer substrate for ion chromatography.. Journal of chromatography. A. 1746 :465792 ▶ Go to Pubmed
Meltem Kars, David Stein, Peter Stenson, David Cooper, Wendy Chung, Peter Gruber, Christine Seidman, Yufeng Shen, Martin Tristani-Firouzi, Bruce Gelb, Yuval Itan .  2025.   Deciphering the digenic architecture of congenital heart disease using trio exome sequencing data.. American journal of human genetics. 112 (3) :583-598 ▶ Go to Pubmed
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Chao Chen, Harris Wang .  2025.   Diary of a cell in DNA 'chyrons'.. Nature chemical biology. 21 (4) :466-467 ▶ Go to Pubmed
Yiming Song, Xiaoyi Wang, Yufeng Shen, Liping Chen, Liuyi Yang, Ruilan Wang, Junyu Lu, Zhifang Gao, Xiaolu Lin, Yan Song, Qingwei Zhang, Xiaobo Li .  2025.   Trends and cross-country inequality in the incidence of GI cancers among the working-age population from 1990 to 2021: a Global Burden of Disease 2021 analysis.. Gut. 74 (6) :948-959 ▶ Go to Pubmed
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Gurdip Uppal, Guillaume Urtecho, Miles Richardson, Isin Comba, Jeongchan Lee, Thomas Moody, Harris Wang, Georg Gerber .  2024.   MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed