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2025

2025 Publications

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
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
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
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
Peter Szabo, Hanna Levitin, Thomas Connors, David Chen, Jenny Jin, Puspa Thapa, Rebecca Guyer, Daniel Caron, Joshua Gray, Rei Matsumoto, Masaru Kubota, Maigan Brusko, Todd Brusko, Donna Farber, Peter Sims .  2025.   Transcriptional control of T cell tissue adaptation and effector function in infants and adults.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Timothy Olsen, Pranay Talla, Romella Sagatelian, Julia Furnari, Jeffrey Bruce, Peter Canoll, Shan Zha, Peter Sims .  2025.   Scalable co-sequencing of RNA and DNA from individual nuclei.. Nature methods. 22 (3) :477-487 ▶ Go to Pubmed
Miles Richardson, Shijie Zhao, Liyuan Lin, Ravi Sheth, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris Wang .  2025.   Publisher Correction: SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.. Nature microbiology. 10 (3) :810 ▶ 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
Miles Richardson, Shijie Zhao, Liyuan Lin, Ravi Sheth, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris Wang .  2025.   SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.. Nature microbiology. 10 (2) :527-540 ▶ 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
Alexander Goldberg, Athanassios Dovas, Daniela Torres, Brianna Pereira, Ashwin Viswanathan, Sohani Sharma, Angeliki Mela, Edward Merricks, Cristina Megino-Luque, Julie McInvale, Markel Olabarria, Leila Shokooh, Hanzhi Zhao, Cady Chen, Corina Kotidis, Peter Calvaresi, Matei Banu, Aida Razavilar, Tejaswi Sudhakar, Ankita Saxena, Cole Chokran, Nelson Humala, Aayushi Mahajan, Weihao Xu, Jordan Metz, Eric Bushong, Daniela Boassa, Mark Ellisman, Elizabeth Hillman, Gunnar Hargus, Jose Bravo-Cordero, Guy McKhann, Brian Gill, Steven Rosenfeld, Catherine Schevon, Jeffrey Bruce, Peter Sims, Darcy Peterka, Peter Canoll .  2025.   Glioma-induced alterations in excitatory neurons are reversed by mTOR inhibition.. Neuron. 113 (6) :858-875.e10 ▶ 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
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
Mostafa Elshobary, Walaa Abo-Shanab, Stephan Ende, Mohammed AlQuraishi, Rania El-Shenody .  2025.   Optimizing Phaeodactylum tricornutum cultivation: integrated strategies for enhancing biomass, lipid, and fucoxanthin production.. Biotechnology for biofuels and bioproducts. 18 (1) :7 ▶ 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
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
Daniel Caron, William Specht, David Chen, Steven Wells, Peter Szabo, Isaac Jensen, Donna Farber, Peter Sims .  2025.   Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues.. Cell reports methods. 5 (1) :100938 ▶ Go to Pubmed
Alice Shin, Kensuke Sugiura, Secunda Kariuki, David Cohen, Samuel Flashner, Andres Klein-Szanto, Noriyuki Nishiwaki, Dechokyab De, Neil Vasan, Joel Gabre, Christopher Lengner, Peter Sims, Anil Rustgi .  2025.   LIN28B-mediated PI3K/AKT pathway activation promotes metastasis in colorectal cancer models.. The Journal of clinical investigation. 135 (8) ▶ 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
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
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
Noriyuki Nishiwaki, Kensuke Sugiura, Kensuke Suzuki, Alina Li, Constanza Contreras, Gizem Efe, Alice Shin, Dorsay Sadeghian, Jun Zhao, Anirban Maitra, Jason Pitarresi, Peter Sims, Rohit Chandwani, Anil Rustgi .  2025.   PRRX1 Has Functional Roles in Pancreatic Acinar to Ductal Metaplasia and Carcinogenesis.. Cellular and molecular gastroenterology and hepatology. 19 (4) :101442 ▶ Go to Pubmed
Noriyuki Nishiwaki, Kensuke Sugiura, Kensuke Suzuki, Alina Li, Constanza Contreras, Gizem Efe, Alice Shin, Dorsay Sadeghian, Jun Zhao, Anirban Maitra, Jason Pitarresi, Peter Sims, Rohit Chandwani, Anil Rustgi .  2025.   PRRX1 Has Functional Roles in Pancreatic Acinar to Ductal Metaplasia and Carcinogenesis.. Cellular and molecular gastroenterology and hepatology. 19 (4) :101442 ▶ 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
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
Xiangyi Ke, Benjamin van Soldt, Lukas Vlahos, Yizhuo Zhou, Jun Qian, Pasquale Laise, 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
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
Duo Chen, Yufeng Shen, Yi Qian, Shiman Chen, Luoxin Li, Zheng Zhou .  2025.   Simultaneous Implantation of Maxillary Fibroskeletal Lesions: A Case Report and Literature Review.. The Journal of craniofacial surgery. 36 (2) :e115-e118 ▶ Go to Pubmed
Chao Hou, Haiqing Zhao, Yufeng Shen .  2025.   Learning Biophysical Dynamics with Protein Language Models.. bioRxiv : the preprint server for biology. ▶ 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
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
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, Carolina Segura-Morales, 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
Miquel Anglada-Girotto, Carolina Segura-Morales, 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
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
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
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
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
Zhenning Tang, Ling Li, Xiaoying Huang, Yinbing Zhao, Qingyuan Liu, Chaolin Zhang .  2025.   Identification of Breast Cancer Immune-related Prognostic Characteristics in Tumor Microenvironment.. Recent patents on anti-cancer drug discovery. 20 (3) :415-431 ▶ Go to Pubmed