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2025

2025 Publications

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
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
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
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
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. ▶ 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
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
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
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
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
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 suppresses RNA-mediated innate immune responses in human cells to accommodate primate-specific Alu expansion.. bioRxiv : the preprint server for biology. ▶ 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 suppresses RNA-mediated innate immune responses in human cells to accommodate primate-specific Alu expansion.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Etowah Adams, Liam Bai, Minji Lee, Yiyang Yu, Mohammed AlQuraishi .  2025.   From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Anindita Dutta, Antonio Rodriguez-Calero, Kacey Ronaldson-Bouchard, Anne Offermann, Daoud Rahman, Twinkle Vhatkar, Dan Hasson, Mohammed Alshalalfa, Elai Davicioni, Jeffrey Karnes, Mark Rubin, Gordana Vunjak-Novakovic, Cory Abate-Shen, Juan Arriaga .  2025.   ATAD2 Drives Prostate Cancer Progression to Metastasis.. Molecular cancer research : MCR. 23 (5) :379-390 ▶ Go to Pubmed
Jiwei Sun, Tiantian Chen, Baoying Zhao, Wenjie Fan, Yufeng Shen, Haojie Wei, Man Zhang, Wenhao Zheng, Jinfeng Peng, Jinyu Wang, Yifan Wang, Lihong Fan, Yingying Chu, Lili Chen, Cheng Yang .  2025.   Correction to "Acceleration of Oral Wound Healing under Diabetes Mellitus Conditions Using Bioadhesive Hydrogel".. ACS applied materials & interfaces. 17 (5) :8749 ▶ Go to Pubmed
George Austin, Tal Korem .  2025.   Compositional transformations can reasonably introduce phenotype-associated values into sparse features.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Elena Kandror, Anqi Wang, Mathieu Carriere, Alexis Peterson, Will Liao, Andreas Tjärnberg, Jun Fung, Krishnaa Mahbubani, Jackson Loper, William Pangburn, Yuchen Xu, Kourosh Saeb-Parsy, Raul Rabadan, Tom Maniatis, Abbas Rizvi .  2025.   Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Luis Aparicio, Laura Crowley, John Christin, Caroline Laplaca, Hanina Hibshoosh, Raul Rabadan, Michael Shen .  2025.   Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer.. Genome medicine. 17 (1) :5 ▶ Go to Pubmed
Xi Fu, Shentong Mo, Alejandro Buendia, Anouchka Laurent, Anqi Shao, Maria Alvarez-Torres, Tianji Yu, Jimin Tan, Jiayu Su, Romella Sagatelian, Adolfo Ferrando, Alberto Ciccia, Yanyan Lan, David Owens, Teresa Palomero, Eric Xing, Raul Rabadan .  2025.   A foundation model of transcription across human cell types.. Nature. 637 (8047) :965-973 ▶ Go to Pubmed
Dejan Gagoski, Tomas Rube, Chaitanya Rastogi, Lucas Melo, Xiaoting Li, Rashmi Voleti, Neel Shah, Harmen Bussemaker .  2025.   Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
C Ryan, D Corcoran, N Banskota, Eckstein Indik, A Floratos, R Friedman, M Kobor, V Kraus, W Kraus, J MacIsaac, M Orenduff, C Pieper, J White, L Ferrucci, S Horvath, K Huffman, D Belsky .  2025.   The CALERIE Genomic Data Resource.. Nature aging. 5 (2) :320-331 ▶ Go to Pubmed
Xiangyi Ke, Benjamin van Soldt, Lukas Vlahos, Yizhuo Zhou, Jun Qian, Joel George, Claudia Capdevila, Ian Glass, Kelley Yan, Andrea Califano, Wellington Cardoso V .  2025.   Morphogenesis and regeneration share a conserved core transition cell state program that controls lung epithelial cell fate.. Developmental cell. 60 (6) :819-836.e7 ▶ Go to Pubmed
Dario De Felice, Alessandro Alaimo, Davide Bressan, Sacha Genovesi, Elisa Marmocchi, Nicole Annesi, Giulia Beccaceci, Davide Dalfovo, Federico Cutrupi, Stefano Medaglia, Veronica Foletto, Marco Lorenzoni, Francesco Gandolfi, Srinivasaraghavan Kannan, Chandra Verma, Alessandro Vasciaveo, Michael Shen, Alessandro Romanel, Fulvio Chiacchiera, Francesco Cambuli, Andrea Lunardi .  2025.   Rarγ-Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer.. EMBO reports. 26 (2) :443-469 ▶ Go to Pubmed
Matthew Gallitto, Xu Zhang, Genesis Santos, Hong-Jian Wei, Ester Fernández, Shoufu Duan, Geoffrey Sedor, Nina Yoh, Danae Kokossis, Carlos Angel, Yi-Fang Wang, Erin White, Connor Kinslow, Xander Berg, Lorenzo Tomassoni, Fereshteh Zandkarimi, Iok Chio, Peter Canoll, Jeffrey Bruce, Neil Feldstein, Robyn Gartrell, Simon Cheng, James Garvin, Stergios Zacharoulis, Robert Wechsler-Reya, Jovana Pavisic, Andrea Califano, Zhiguo Zhang, Cheng-Chia Wu .  2025.   Targeted delivery of napabucasin with radiotherapy improves outcomes in diffuse midline glioma.. Neuro-oncology. 27 (3) :795-810 ▶ Go to Pubmed
Casey Ager, Aleksandar Obradovic, Patrick McCann, Matthew Chaimowitz, Alexander Wang, Neha Shaikh, Parin Shah, Samuel Pan, Caroline Laplaca, Renu Virk, Jessica Hill, Collin Jugler, Grace DeFranco, Nilika Bhattacharya, Kade Copple, Howard Scher, Guarionex DeCastro, Christopher Anderson, James McKiernan, Catherine Spina, Mark Stein, Karie Runcie, Charles Drake, Andrea Califano, Matthew Dallos .  2025.   Fc-enhanced anti-CTLA-4 depletes tumor-infiltrating regulatory T cells to augment immune effects of androgen ablation in high-risk prostate cancer.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Khemika Sudnawa .  2025.   Clinical characteristics, longitudinal adaptive functioning, and association with electroencephalogram activity in PPP2R5D-related neurodevelopmental disorder.. Clinical genetics. 107 (1) :34-43 ▶ Go to Pubmed
Miquel Anglada-Girotto, Daniel Moakley, Chaolin Zhang, Samuel Miravet-Verde, Andrea Califano, Luis Serrano .  2025.   Exon inclusion signatures enable accurate estimation of splicing factor activity.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
George Austin, Itsik Pe'er, Tal Korem .  2025.   Distributional bias compromises leave-one-out cross-validation.. ArXiv. ▶ Go to Pubmed
Adriana Salcedo, Maxime Tarabichi, Alex Buchanan, Shadrielle Espiritu, Hongjiu Zhang, Kaiyi Zhu, Tai-Hsien Yang, Ignaty Leshchiner, Dimitris Anastassiou, Yuanfang Guan, Gun Jang, Mohammed Mootor, Kerstin Haase, Amit Deshwar, William Zou, Imaad Umar, Stefan Dentro, Jeff Wintersinger, Kami Chiotti, Jonas Demeulemeester, Clemency Jolly, Lesia Sycza, Minjeong Ko, PCAWG Group, SMC-Het Participants, David Wedge, Quaid Morris, Kyle Ellrott, Peter Van Loo, Paul Boutros .  2025.   Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.. Nature biotechnology. 43 (4) :581-592 ▶ Go to Pubmed
Jeremy Worley, Heeju Noh, Daoqi You, Mikko Turunen, Hongxu Ding, Evan Paull, Aaron Griffin, Adina Grunn, Mingxuan Zhang, Kristina Guillan, Erin Bush, Samantha Brosius, Hanina Hibshoosh, Prabhjot Mundi, Peter Sims, Piero Dalerba, Filemon Cruz, Andrew Kung, Andrea Califano .  2025.   Identification and Pharmacological Targeting of Treatment-Resistant, Stem-like Breast Cancer Cells for Combination Therapy.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Zachary Walsh, Parin Shah, Neeharika Kothapalli, Shivem Shah, Gergo Nikolenyi, Zack Brodtman, Giuseppe Leuzzi, Meri Rogava, Michael Mu, Patricia Ho, Sinan Abuzaid, Neil Vasan, Mohammed AlQuraishi, Joshua Milner, Alberto Ciccia, Johannes Melms, Benjamin Izar .  2025.   Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens.. Nature biotechnology. 43 (3) :384-395 ▶ Go to Pubmed
Cory Abate-Shen, Katerina Politi .  2025.   The Evolution of Mouse Models of Cancer: Past, Present, and Future.. Cold Spring Harbor perspectives in medicine. 15 (5) ▶ Go to Pubmed
Yaniv Kazansky, Helen Mueller, Daniel Cameron, Phillip Demarest, Nadia Zaffaroni, Noemi Arrighetti, Valentina Zuco, Prabhjot Mundi, Yasumichi Kuwahara, Romel Somwar, Rui Qu, Andrea Califano, Elisa de Stanchina, Filemon Cruz, Andrew Kung, Mrinal Gounder, Alex Kentsis .  2025.   Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Shaoxun Liu .  2025.   Predicting the DNA binding specificity of transcription factor mutants using family-level biophysically interpretable machine learning.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed