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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
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, 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
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
Natanael Zarco, Athanassios Dovas, Virginea Farias, Naveen Nagaiah, Ashley Haddock, Peter Sims, Dolores Hambardzumyan, Christian Meyer, Peter Canoll, Steven Rosenfeld, Rajappa Kenchappa .  2024.   Resistance to spindle inhibitors in glioblastoma depends on STAT3 and therapy induced senescence.. iScience. 27 (12) :111311 ▶ 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
John Tuddenham, Masashi Fujita, 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, Hemali Phatnani, Neil Shneider, David Bennett, Philip De Jager, Serge Przedborski, Vilas Menon, Marta Olah .  2024.   Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Chrystal Mavros, Mareike Bongers, Frederik Neergaard, Frank Cusimano, Yiwei Sun, Andrew Kaufman, Miles Richardson, Susanne Kammler, Mette Kristensen, Morten Sommer, Harris Wang .  2024.   Bacteria Engineered to Produce Serotonin Modulate Host Intestinal Physiology.. ACS synthetic biology. 13 (12) :4002-4014 ▶ Go to Pubmed
Chrystal Mavros, Mareike Bongers, Frederik Neergaard, Frank Cusimano, Yiwei Sun, Andrew Kaufman, Miles Richardson, Susanne Kammler, Mette Kristensen, Morten Sommer, Harris Wang .  2024.   Bacteria Engineered to Produce Serotonin Modulate Host Intestinal Physiology.. ACS synthetic biology. 13 (12) :4002-4014 ▶ Go to Pubmed
Guillaume Urtecho, Thomas Moody, Yiming Huang, Ravi Sheth, Miles Richardson, Hélène Descamps, Andrew Kaufman, Opeyemi Lekan, Zetian Zhang, Florencia Velez-Cortes, Yiming Qu, Lucas Cohen, Deirdre Ricaurte, Travis Gibson, Georg Gerber, Christoph Thaiss, Harris Wang .  2024.   Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.. Cell systems. 15 (11) :1002-1017.e4 ▶ Go to Pubmed
Guillaume Urtecho, Thomas Moody, Yiming Huang, Ravi Sheth, Miles Richardson, Hélène Descamps, Andrew Kaufman, Opeyemi Lekan, Zetian Zhang, Florencia Velez-Cortes, Yiming Qu, Lucas Cohen, Deirdre Ricaurte, Travis Gibson, Georg Gerber, Christoph Thaiss, Harris Wang .  2024.   Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.. Cell systems. 15 (11) :1002-1017.e4 ▶ Go to Pubmed
Julia Davis-Porada, Alex George, Nora Lam, Daniel Caron, Joshua Gray, Jenny Huang, Jennifer Hwu, Steven Wells, Rei Matsumoto, Masaru Kubota, YoonSeung Lee, Rory Morrison-Colvin, Isaac Jensen, Basak Ural, Namir Shaabani, Daniela Weiskopf, Alba Grifoni, Alessandro Sette, Peter Szabo, John Teijaro, Peter Sims, Donna Farber .  2024.   Maintenance and functional regulation of immune memory to COVID-19 vaccines in tissues.. Immunity. 57 (12) :2895-2913.e8 ▶ 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
Verena Haage .  2024.   HDAC Inhibitors recapitulate Human Disease-Associated Microglia Signatures .. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Miles Richardson, Shijie Zhao, Ravi Sheth, Liyuan Lin, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris Wang .  2024.   SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Miles Richardson, Shijie Zhao, Ravi Sheth, Liyuan Lin, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris Wang .  2024.   SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
John Tuddenham, Mariko Taga, Verena Haage, Victoria Marshe, Tina Roostaei, Charles White, Annie Lee, Masashi Fujita, Anthony Khairallah, Ya Zhang, Gilad Green, Bradley Hyman, Matthew Frosch, Sarah Hopp, Thomas Beach, Geidy Serrano, John Corboy, Naomi Habib, Hans-Ulrich Klein, Rajesh Soni, Andrew Teich, Richard Hickman, Roy Alcalay, Neil Shneider, Julie Schneider, Peter Sims, David Bennett, Marta Olah, Vilas Menon, Philip De Jager .  2024.   A cross-disease resource of living human microglia identifies disease-enriched subsets and tool compounds recapitulating microglial states.. Nature neuroscience. 27 (12) :2521-2537 ▶ 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
Kwang-Soo Kim, Junyi Zhang, Víctor Arrieta, Crismita Dmello, Elena Grabis, Karl Habashy, Joseph Duffy, Junfei Zhao, Andrew Gould, Li Chen, Jian Hu, Irina Balyasnikova, Dhan Chand, Dan Levey, Peter Canoll, Wenting Zhao, Peter Sims, Raul Rabadan, Surya Pandey, Bin Zhang, Catalina Lee-Chang, Dieter Heiland, Adam Sonabend .  2024.   MAPK/ERK signaling in gliomas modulates interferon responses, T cell recruitment, microglia phenotype, and immune checkpoint blockade efficacy.. bioRxiv : the preprint server for biology. ▶ 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
J Beatson, B Marsh, D Talbot .  1985.   A clinical comparison of pivmecillinam plus pivampicillin (Miraxid) and a triple tetracycline combination (Deteclo) in respiratory infections treated in general practice.. The Journal of international medical research. 13 (4) :197-202 ▶ Go to Pubmed
Matei Banu, Athanassios Dovas, Michael Argenziano, Wenting Zhao, Colin Sperring, Henar Grajal, Zhouzerui Liu, Dominique Higgins, Misha Amini, Brianna Pereira, Ling Ye, Aayushi Mahajan, Nelson Humala, Julia Furnari, Pavan Upadhyayula, Fereshteh Zandkarimi, Trang Nguyen, Damian Teasley, Peter Wu, Li Hai, Charles Karan, Tyrone Dowdy, Aida Razavilar, Markus Siegelin, Jan Kitajewski, Mioara Larion, Jeffrey Bruce, Brent Stockwell, Peter Sims, Peter Canoll .  2024.   A cell state-specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma.. The EMBO journal. 43 (20) :4492-4521 ▶ Go to Pubmed
George Austin, Tal Korem .  2026.   Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective.. The Journal of infectious diseases. 233 (1) :76-86 ▶ Go to Pubmed
Peter Sims .  2024.   In praise of physician associates.. BMJ (Clinical research ed.). 386 :q1842 ▶ Go to Pubmed
Alina Li, Kensuke Sugiura, Noriyuki Nishiwaki, Kensuke Suzuki, Dorsay Sadeghian, Jun Zhao, Anirban Maitra, David Falvo, Rohit Chandwani, Jason Pitarresi, Peter Sims, Anil Rustgi .  2024.   FRA1 controls acinar cell plasticity during murine Kras-induced pancreatic acinar to ductal metaplasia.. Developmental cell. 59 (22) :3025-3042.e7 ▶ 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
Aarti Kumar, Pranav Gwalani, Prasad Iyer, Kenneth Wang, Gary Falk, Gregory Ginsberg, Charles Lightdale, Armando Del Portillo, Stephen Lagana, Yun Li, Hongzhe Li, Jeanine Genkinger, Zhezhen Jin, Anil Rustgi, Timothy Wang, Harris Wang, Michael Quante, Julian Abrams .  2024.   Shifts in Serum Bile Acid Profiles Associated With Barrett's Esophagus and Stages of Progression to Esophageal Adenocarcinoma.. Clinical and translational gastroenterology. 15 (10) :e1 ▶ Go to Pubmed
Aarti Kumar, Pranav Gwalani, Prasad Iyer, Kenneth Wang, Gary Falk, Gregory Ginsberg, Charles Lightdale, Armando Del Portillo, Stephen Lagana, Yun Li, Hongzhe Li, Jeanine Genkinger, Zhezhen Jin, Anil Rustgi, Timothy Wang, Harris Wang, Michael Quante, Julian Abrams .  2024.   Shifts in Serum Bile Acid Profiles Associated With Barrett's Esophagus and Stages of Progression to Esophageal Adenocarcinoma.. Clinical and translational gastroenterology. 15 (10) :e1 ▶ Go to Pubmed
Leandro Araujo, Madeline Edwards, Koichiro Irie, Yiming Huang, Yoshinaga Kawano, Alexander Tran, Simona De Michele, Govind Bhagat, Harris Wang, Ivaylo Ivanov .  2024.   Context-dependent role of group 3 innate lymphoid cells in mucosal protection.. Science immunology. 9 (98) :eade7530 ▶ Go to Pubmed
Leandro Araujo, Madeline Edwards, Koichiro Irie, Yiming Huang, Yoshinaga Kawano, Alexander Tran, Simona De Michele, Govind Bhagat, Harris Wang, Ivaylo Ivanov .  2024.   Context-dependent role of group 3 innate lymphoid cells in mucosal protection.. Science immunology. 9 (98) :eade7530 ▶ Go to Pubmed
Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang .  2024.   Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences.. Genome research. 34 (7) :1052-1065 ▶ Go to Pubmed
Ye Zheng, Daniel Caron, Ju Kim, Seong-Hwan Jun, Yuan Tian, Mair Florian, Kenneth Stuart, Peter Sims, Raphael Gottardo .  2024.   ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets.. Research square. ▶ Go to Pubmed
Daniel Moakley, Chaolin Zhang .  2024.   Oncogenic NOVA1 expression dysregulates alternative splicing in breast cancer.. 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, 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
Theresa Baumeister .  2024.   Microbiota metabolized Bile Acids accelerate Gastroesophageal Adenocarcinoma via FXR inhibition.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Daniel Moakley, Melissa Campbell, Miquel Anglada-Girotto, Huijuan Feng, Andrea Califano, Edmund Au, Chaolin Zhang .  2024.   Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Jose Martí, Chloe Hsu, Charlotte Rochereau, Chenling Xu, Tomasz Blazejewski, Hunter Nisonoff, Sean Leonard, Christina Kang-Yun, Jennifer Chlebek, Dante Ricci, Dan Park, Harris Wang, Jennifer Listgarten, Yongqin Jiao, Jonathan Allen .  2024.   GENTANGLE: integrated computational design of gene entanglements.. Bioinformatics (Oxford, England). 40 (7) ▶ Go to Pubmed
Jose Martí, Chloe Hsu, Charlotte Rochereau, Chenling Xu, Tomasz Blazejewski, Hunter Nisonoff, Sean Leonard, Christina Kang-Yun, Jennifer Chlebek, Dante Ricci, Dan Park, Harris Wang, Jennifer Listgarten, Yongqin Jiao, Jonathan Allen .  2024.   GENTANGLE: integrated computational design of gene entanglements.. Bioinformatics (Oxford, England). 40 (7) ▶ Go to Pubmed
Natanael Zarco, Athanassios Dovas, Virginea Farias, Naveen Nagaiah, Ashley Haddock, Peter Sims, Dolores Hambardzumyan, Christian Meyer, Peter Canoll, Steven Rosenfeld, Rajappa Kenchappa .  2024.   Resistance to Spindle Inhibitors in Glioblastoma Depends on STAT3 and Therapy Induced Senescence.. 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
Claudia Capdevila, Jonathan Miller, Liang Cheng, Adam Kornberg, Joel George, Hyeonjeong Lee, Theo Botella, Christine Moon, John Murray, Stephanie Lam, Ruben Calderon, Ermanno Malagola, Gary Whelan, Chyuan-Sheng Lin, Arnold Han, Timothy Wang, Peter Sims, Kelley Yan .  2024.   Time-resolved fate mapping identifies the intestinal upper crypt zone as an origin of Lgr5+ crypt base columnar cells.. Cell. 187 (12) :3039-3055.e14 ▶ Go to Pubmed
Joshua Gray, Daniel Caron, Steven Wells, Rebecca Guyer, Peter Szabo, Daniel Rainbow, Can Ergen, Ksenia Rybkina, Marissa Bradley, Rei Matsumoto, Kalpana Pethe, Masaru Kubota, Sarah Teichmann, Joanne Jones, Nir Yosef, Mark Atkinson, Maigan Brusko, Todd Brusko, Thomas Connors, Peter Sims, Donna Farber .  2024.   Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span.. Science immunology. 9 (96) :eadn3954 ▶ 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
Qian Wang, Yicheng Guo, Logan Schwanz, Ian Mellis, Yiwei Sun, Yiming Qu, Guillaume Urtecho, Riccardo Valdez, Emily Stoneman, Aubree Gordon, Harris Wang, David Ho, Lihong Liu .  2024.   SARS-CoV-2 omicron BA.2.87.1 exhibits higher susceptibility to serum neutralization than EG.5.1 and JN.1.. Emerging microbes & infections. 13 (1) :2359004 ▶ 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
Yocelyn Recinos, Suying Bao, Xiaojian Wang, Brittany Phillips, Yow-Tyng Yeh, Sebastien Weyn-Vanhentenryck, Maurice Swanson, Chaolin Zhang .  2024.   Lineage-specific splicing regulation of MAPT gene in the primate brain.. Cell genomics. 4 (6) :100563 ▶ Go to Pubmed
Yocelyn Recinos, Suying Bao, Xiaojian Wang, Brittany Phillips, Yow-Tyng Yeh, Sebastien Weyn-Vanhentenryck, Maurice Swanson, Chaolin Zhang .  2024.   Lineage-specific splicing regulation of MAPT gene in the primate brain.. Cell genomics. 4 (6) :100563 ▶ 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
Yocelyn Recinos, Dmytro Ustianenko, Yow-Tyng Yeh, Xiaojian Wang, Martin Jacko, Lekha Yesantharao V, Qiyang Wu, Chaolin Zhang .  2024.   CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements.. Nature communications. 15 (1) :3839 ▶ Go to Pubmed
Yocelyn Recinos, Dmytro Ustianenko, Yow-Tyng Yeh, Xiaojian Wang, Martin Jacko, Lekha Yesantharao V, Qiyang Wu, Chaolin Zhang .  2024.   CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements.. Nature communications. 15 (1) :3839 ▶ Go to Pubmed
Chi-Lee Ho, Michael Gilbert, Guillaume Urtecho, Hyoungjoo Lee, David Drew, Samuel Klempner, Jin Cho, Thomas Ryan, Naryan Rustgi, Hyuk Lee, Jeeyun Lee, Alexander Caraballo, Marina Magicheva-Gupta V, Carmen Rios, Alice Shin, Yuen-Yi Tseng, Jeremy Davis, Daniel Chung, Andrew Chan, Harris Wang, Sandra Ryeom .  2024.   Stool Protein Mass Spectrometry Identifies Biomarkers for Early Detection of Diffuse-type Gastric Cancer.. Cancer prevention research (Philadelphia, Pa.). 17 (8) :361-376 ▶ Go to Pubmed
Yim Cheng, Matei Banu, Wenting Zhao, Steven Rosenfeld, Peter Canoll, Peter Sims .  2024.   Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma.. Cell reports. 43 (5) :114139 ▶ Go to Pubmed
Chencheng Xu, Suying Bao, Hao Chen, Tao Jiang, Chaolin Zhang .  2024.   Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Huijuan Feng, Xiang-Jun Lu, Suvrajit Maji, Linxi Liu, Dmytro Ustianenko, Noam Rudnick, Chaolin Zhang .  2024.   Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes.. Nature communications. 15 (1) :2279 ▶ Go to Pubmed
Huijuan Feng, Xiang-Jun Lu, Suvrajit Maji, Linxi Liu, Dmytro Ustianenko, Noam Rudnick, Chaolin Zhang .  2024.   Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes.. Nature communications. 15 (1) :2279 ▶ Go to Pubmed
Verena Haage, John Tuddenham, Natacha Comandante-Lou, Alex Bautista, Anna Monzel, Rebecca Chiu, Masashi Fujita, Frankie Garcia, Prabesh Bhattarai, Ronak Patel, Alice Buonfiglioli, Juan Idiarte, Mathieu Herman, Alison Rinderspacher, Angeliki Mela, Wenting Zhao, Michael Argenziano, Julia Furnari, Matei Banu, Donald Landry, Jeffrey Bruce, Peter Canoll, Ya Zhang, Tal Nuriel, Caghan Kizil, Andrew Sproul, Lotje de Witte, Peter Sims, Vilas Menon, Martin Picard, Philip De Jager .  2024.   A pharmacological toolkit for human microglia identifies Topoisomerase I inhibitors as immunomodulators for Alzheimer's disease.. 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
Giuseppe Leuzzi, Alessandro Vasciaveo, Angelo Taglialatela, Xiao Chen, Tessa Firestone, Allison Hickman, Wendy Mao, Tanay Thakar, Alina Vaitsiankova, Jen-Wei Huang, Raquel Cuella-Martin, Samuel Hayward, Jordan Kesner, Ali Ghasemzadeh, Tarun Nambiar, Patricia Ho, Alexander Rialdi, Maxime Hebrard, Yinglu Li, Jinmei Gao, Saarang Gopinath, Oluwatobi Adeleke, Bryan Venters, Charles Drake, Richard Baer, Benjamin Izar, Ernesto Guccione, Michael-Christopher Keogh, Raphael Guerois, Lu Sun, Chao Lu, Andrea Califano, Alberto Ciccia .  2024.   SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion.. Cell. ▶ Go to Pubmed
Giangela Stokes, Zhuowei Li, Nicole Talaba, William Genthe, Maria Brix, Betty Pham, Mark Wienhold, Gracia Sandok, Rebecca Hernan, Julia Wynn, Haiyang Tang, Diana Tabima, Allison Rodgers, Timothy Hacker, Naomi Chesler, Pan Zhang, Rabi Murad, Jason Yuan, Yufeng Shen, Wendy Chung, David McCulley .  2024.   Rescuing lung development through embryonic inhibition of histone acetylation.. Science translational medicine. 16 (732) :eadc8930 ▶ Go to Pubmed
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