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2023

2023 Publications

Alexander Raufi, Ilenia Pellicciotta, Carmine Palermo, Steven Sastra, Andrew Chen, Emily Alouani, Carlo Maurer, Michael May, Alina Iuga, Raul Rabadan, Kenneth Olive, Gulam Manji .  2023.   Cytotoxic chemotherapy potentiates the immune response and efficacy of combination CXCR4/PD-1 inhibition in models of pancreatic ductal adenocarcinoma.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Xiaoting Li, Lucas Melo, Harmen Bussemaker .  2023.   Benchmarking DNA binding affinity models using allele-specific transcription factor binding data.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Yige Zhao, Guojie Zhong, Jake Hagen, Hongbing Pan, Wendy Chung, Yufeng Shen .  2023.   A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Yige Zhao, Guojie Zhong, Jake Hagen, Hongbing Pan, Wendy Chung, Yufeng Shen .  2023.   A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Zachary Walsh, Parin Shah, Neeharika Kothapalli, Gergo Nikolenyi, Shivem Shah, Giuseppe Leuzzi, Michael Mu, Patricia Ho, Sinan Abuzaid, Zack Brodtman, Neil Vasan, Mohammed AlQuraishi, Joshua Milner, Alberto Ciccia, Johannes Melms, Benjamin Izar .  2023.   Massively parallel base editing screens to map variant effects on anti-tumor hallmarks of primary human T cells.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Quinn Solfisburg, Federico Baldini, Brittany Baldwin-Hunter, George Austin, Harry Lee, Heekuk Park, Daniel Freedberg, Charles Lightdale, Tal Korem, Julian Abrams .  2023.   The Salivary Microbiome and Predicted Metabolite Production are Associated with Barrett's Esophagus and High Grade Dysplasia or Adenocarcinoma.. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. ▶ Go to Pubmed
Nailah Smith, Eduard Reznik, Brygida Bisikirska, Vasiliki Polychronidou, Qian Wang, Arie Zask, Farhad Forouhar, Andrea Califano, Brent Stockwell .  2023.   Kinases Controlling Stability of the Oncogenic MYCN Protein.. ACS medicinal chemistry letters. 14 (12) :1664-1672 ▶ Go to Pubmed
Berna Sozen, Richard Flavell, Dudley Lamming, Debra Silver, Simona Parrinello, Cory Abate-Shen, Franziska Michor, Vijay Sankaran .  2023.   What approaches are needed to understand human development and disease?. Developmental cell. 58 (24) :2822-2825 ▶ Go to Pubmed
Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David Knowles, Raul Rabadan .  2023.   Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.. Genome biology. 24 (1) :291 ▶ Go to Pubmed
Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David Knowles, Raul Rabadan .  2023.   Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.. Genome biology. 24 (1) :291 ▶ Go to Pubmed
Julia Rogers, Gergo Nikolenyi, Mohammed AlQuraishi .  2023.   Growing ecosystem of deep learning methods for modeling protein-protein interactions.. Protein engineering, design & selection : PEDS. 36 ▶ Go to Pubmed
Michael Stokes, Alessandro Vasciaveo, Jonnell Small, Arie Zask, Eduard Reznik, Nailah Smith, Qian Wang, Jacob Daniels, Farhad Forouhar, Presha Rajbhandari, Andrea Califano, Brent Stockwell .  2023.   Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers.. Cell chemical biology. ▶ Go to Pubmed
Leonie Brockmann, Alexander Tran, Yiming Huang, Madeline Edwards, Carlotta Ronda, Harris Wang, Ivaylo Ivanov .  2023.   Intestinal microbiota-specific Th17 cells possess regulatory properties and suppress effector T cells via c-MAF and IL-10.. Immunity. 56 (12) :2719-2735.e7 ▶ Go to Pubmed
Debarshi Banerjee, Shuobo Boboila, Shunpei Okochi, James Angelastro, Angela Kadenhe-Chiweshe V, Gonzalo Lopez, Andrea Califano, Eileen Connolly, Lloyd Greene, Darrell Yamashiro .  2023.   Activating Transcription Factor 5 Promotes Neuroblastoma Metastasis by Inducing Anoikis Resistance.. Cancer research communications. 3 (12) :2518-2530 ▶ Go to Pubmed
Anna Dickson, Tekle Pauzaite, Esther Arnaiz, Brian Ortmann, James West, Norbert Volkmar, Anthony Martinelli, Zhaoqi Li, Niek Wit, Dennis Vitkup, Arthur Kaser, Paul Lehner, James Nathan .  2023.   Author Correction: A HIF independent oxygen-sensitive pathway for controlling cholesterol synthesis.. Nature communications. 14 (1) :7751 ▶ Go to Pubmed
Marie Hasselluhn, Amanda Decker-Farrell, Lukas Vlahos, Dafydd Thomas, Alvaro Curiel-Garcia, Carlo Maurer, Urszula Wasko, Lorenzo Tomassoni, Stephen Sastra, Carmine Palermo, Tanner Dalton, Alice Ma, Fangda Li, Ezequiel Tolosa, Hanina Hibshoosh, Martin Fernandez-Zapico, Alexander Muir, Andrea Califano, Kenneth Olive .  2023.   Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression.. Cancer discovery. ▶ Go to Pubmed
Thomas Postler, Anqi Wang, Francesco Brundu, Pingzhang Wang, Zikai Wu, Kelly Butler, Yenkel Grinberg-Bleyer, Suneeta Krishnareddy, Stephen Lagana, Anjali Saqi, Andrea Oeckinghaus, Raul Rabadan, Sankar Ghosh .  2023.   A pan-cancer analysis implicates human as a tumor-suppressor gene.. Proceedings of the National Academy of Sciences of the United States of America. 120 (46) :e2312595120 ▶ Go to Pubmed
Yoli Meydan, Federico Baldini, Tal Korem .  2023.   pymgpipe: microbiome metabolic modeling in Python.. Journal of open source software. 8 (88) ▶ Go to Pubmed
Lucas Hu, Eugene Douglass, Mikko Turunen, Sergey Pampou, Adina Grunn, Ron Realubit, Albert Antolin, Alexander Wang, Hai Li, Prem Subramaniam, Charles Karan, Mariano Alvarez, Andrea Califano .  2023.   Elucidating Compound Mechanism of Action and Polypharmacology with a Large-scale Perturbational Profile Compendium.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Sneha Rao, Francesco Brundu, Yannan Chen, Yan Sun, Huixiang Zhu, Robert Shprintzen, Raju Tomer, Raul Rabadan, Kam Leong, Sander Markx, Bin Xu, Joseph Gogos .  2023.   Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome and schizophrenia.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Nicole Edwards, Adhish Kashyap, Alissa Warren, Zachary Agricola, Alan Kenny, Yufeng Shen, Wendy Chung, Aaron Zorn .  2023.   Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in trachea-esophageal morphogenesis.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Qian Wang, Yicheng Guo, Liyuan Liu, Logan Schwanz, Zhiteng Li, Manoj Nair, Jerren Ho, Richard Zhang, Sho Iketani, Jian Yu, Yiming Huang, Yiming Qu, Riccardo Valdez, Adam Lauring, Yaoxing Huang, Aubree Gordon, Harris Wang, Lihong Liu, David Ho .  2023.   Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike.. Nature. 624 (7992) :639-644 ▶ Go to Pubmed
Haiqing Zhao, Diana Murray, Donald Petrey, Barry Honig .  2023.   ZEPPI: proteome-scale sequence-based evaluation of protein-protein interaction models.. Research square. ▶ Go to Pubmed
Florence Petit, Mauro Longoni, Julie Wells, Richard Maser, Eric Bogenschutz, Matthew Dysart, Hannah Contreras, Frederic Frénois, Barbara Pober, Robin Clark, Philip Giampietro, Hilger Ropers, Hao Hu, Maria Loscertales, Richard Wagner, Xingbin Ai, Harrison Brand, Anne-Sophie Jourdain, Marie-Ange Delrue, Brigitte Gilbert-Dussardier, Louise Devisme, Boris Keren, David McCulley, Lu Qiao, Rebecca Hernan, Julia Wynn, Tiana Scott, Daniel Calame, Zeynep Coban-Akdemir, Patricia Hernandez, Andres Hernandez-Garcia, Hagith Yonath, James Lupski, Yufeng Shen, Wendy Chung, Daryl Scott, Carol Bult, Patricia Donahoe, Frances High .  2023.   PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects.. American journal of human genetics. 110 (10) :1787-1803 ▶ Go to Pubmed
Irene Tang, Daniel Mallia, Qi Yan, Itsik Pe'er, Anita Raja, Ansaf Salleb-Aouissi, Ronald Wapner .  2023.   A Scoping Review of Preterm Birth Risk Factors.. American journal of perinatology. ▶ Go to Pubmed
Yim Cheng, Matei Banu, Wenting Zhao, Steven Rosenfeld, Peter Canoll, Peter Sims .  2023.   Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Xiaoting Li, Tuuli Lappalainen, Harmen Bussemaker .  2023.   Identifying genetic regulatory variants that affect transcription factor activity.. Cell genomics. 3 (9) :100382 ▶ Go to Pubmed
Xiaoting Li, Tuuli Lappalainen, Harmen Bussemaker .  2023.   Identifying genetic regulatory variants that affect transcription factor activity.. Cell genomics. 3 (9) :100382 ▶ Go to Pubmed
Alexandros Papachristodoulou, Isabel Heidegger, Renu Virk, Matteo Di Bernardo, Jaime Kim, Caroline Laplaca, Florencia Picech, Georg Schäfer, Guarionex De Castro, Hanina Hibshoosh, Massimo Loda, Helmut Klocker, Mark Rubin, Tian Zheng, Mitchell Benson, James McKiernan, Aditya Dutta, Cory Abate-Shen .  2023.   Metformin Overcomes the Consequences of NKX3.1 Loss to Suppress Prostate Cancer Progression.. European urology. ▶ Go to Pubmed
Yufeng Shen, Xinru Zhang, Jiangpeng Su, Lin Lin, Zeyi Jiang, Lin Qiu, Sida Wang, BingJi Wu, Changyu Pu, Xinzhi Cai, Yuqiao Liu, Xinxin Zhang .  2023.   Significantly Enhancing Mechanical and Thermal Properties of Cellulose-Based Composites by Adding Small Amounts of Lysozyme-Modified Graphene Nanoplatelets via Forming Strong Double-Cross-Linked Interface Interactions.. ACS applied materials & interfaces. 15 (36) :43159-43168 ▶ Go to Pubmed
Max Trauernicht, Chaitanya Rastogi, Stefano Manzo, Harmen Bussemaker, Bas van Steensel .  2023.   Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements.. Nucleic acids research. 51 (18) :9690-9702 ▶ Go to Pubmed
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi .  2023.   OpenProteinSet: Training data for structural biology at scale.. ArXiv. ▶ Go to Pubmed
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi .  2023.   OpenProteinSet: Training data for structural biology at scale.. ArXiv. ▶ Go to Pubmed
Sara Zaccara, Ryan Ries, Samie Jaffrey .  2023.   Publisher Correction: Reading, writing and erasing mRNA methylation.. Nature reviews. Molecular cell biology. 24 (10) :770 ▶ Go to Pubmed
Qi Yan, Rafael Guerrero, Raiyan Khan, Andy Surujnarine, Ronald Wapner, Matthew Hahn, Anita Raja, Ansaf Salleb-Aouissi, William Grobman, Hyagriv Simhan, Nathan Blue, Robert Silver, Judith Chung, Uma Reddy, Predrag Radivojac, Itsik Pe'er, David Haas .  2023.   Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b.. Genetics. 225 (2) ▶ Go to Pubmed
Changchang Liu, Peter Kutchukian, Nhan Nguyen, Mohammed AlQuraishi, Peter Sorger .  2023.   A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.. Journal of chemical information and modeling. 63 (17) :5457-5472 ▶ Go to Pubmed
Jingqiu Liao, Liat Shenhav, Julia Urban, Myrna Serrano, Bin Zhu, Gregory Buck, Tal Korem .  2023.   Microdiversity of the vaginal microbiome is associated with preterm birth.. Nature communications. 14 (1) :4997 ▶ Go to Pubmed
Anna Dickson, Tekle Pauzaite, Esther Arnaiz, Brian Ortmann, James West, Norbert Volkmar, Anthony Martinelli, Zhaoqi Li, Niek Wit, Dennis Vitkup, Arthur Kaser, Paul Lehner, James Nathan .  2023.   A HIF independent oxygen-sensitive pathway for controlling cholesterol synthesis.. Nature communications. 14 (1) :4816 ▶ Go to Pubmed
Zhengyu Jiang, Feijing Wu, Pasquale Laise, Tanaka Takayuki, Fu Na, Woosook Kim, Hiroki Kobayashi, Wenju Chang, Ryota Takahashi, Giovanni Valenti, Masaki Sunagawa, Ruth White, Marina Macchini, Bernhard Renz, Moritz Middelhoff, Yoku Hayakawa, Zinaida Dubeykovskaya, Xiangtian Tan, Timothy Chu, Karan Nagar, Yagnesh Tailor, Bryana Belin, Akanksha Anand, Samuel Asfaha, Michael Finlayson, Alina Iuga, Andrea Califano, Timothy Wang .  2023.   Tff2 defines transit-amplifying pancreatic acinar progenitors that lack regenerative potential and are protective against Kras-driven carcinogenesis.. Cell stem cell. 30 (8) :1091-1109.e7 ▶ Go to Pubmed
Kartikeya Nagendra, Adrien Izzet, Nicolas Judd, Ruben Zakine, Leah Friedman, Oliver Harrison, Léa-Laetitia Pontani, Lawrence Shapiro, Barry Honig, Jasna Brujic .  2023.   Push-pull mechanics of E-cadherin ectodomains in biomimetic adhesions.. Biophysical journal. 122 (17) :3506-3515 ▶ Go to Pubmed
Jia Li, Alessandro Vasciaveo, Dimitrios Karagiannis, Zhen Sun, Xiao Chen, Fabio Socciarelli, Ziv Frankenstein, Min Zou, Tania Pannellini, Yu Chen, Kevin Gardner, Brian Robinson, Johann de Bono, Cory Abate-Shen, Mark Rubin, Massimo Loda, Charles Sawyers, Andrea Califano, Chao Lu, Michael Shen .  2023.   NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Mara De Martino, Camille Daviaud, Hanna Minns, Artur Lazarian, Anja Wacker, Ana Costa, Nabeel Attarwala, Qiuying Chen, Seung-Won Choi, Raul Rabadan, Laura McIntire, Robyn Gartrell, James Kelly, Evagelia Laiakis, Claire Vanpouille-Box .  2023.   Radiation therapy promotes unsaturated fatty acids to maintain survival of glioblastoma.. Cancer letters. 570 :216329 ▶ Go to Pubmed
Guojie Zhong, Yoolim Choi, Yufeng Shen .  2023.   VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants.. Communications biology. 6 (1) :774 ▶ Go to Pubmed
Zhengping Shao, Brian Lee, Hanwen Zhang, Xiaohui Lin, Chen Li, Wenxia Jiang, Napon Chirathivat, Steven Gershik, Michael Shen, Richard Baer, Shan Zha .  2023.   Inactive PARP1 causes embryonic lethality and genome instability in a dominant-negative manner.. Proceedings of the National Academy of Sciences of the United States of America. 120 (31) :e2301972120 ▶ Go to Pubmed
Rei Matsumoto, Joshua Gray, Ksenia Rybkina, Hanna Oppenheimer, Lior Levy, Lilach Friedman, Muhammad Khamaisi, Wenzhao Meng, Aaron Rosenfeld, Rebecca Guyer, Marissa Bradley, David Chen, Mark Atkinson, Todd Brusko, Maigan Brusko, Thomas Connors, Eline Prak, Uri Hershberg, Peter Sims, Tomer Hertz, Donna Farber .  2023.   Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity.. Nature immunology. 24 (8) :1370-1381 ▶ Go to Pubmed
Quinn Solfisburg, Federico Baldini, Brittany Baldwin-Hunter, Harry Lee, Heekuk Park, Daniel Freedberg, Charles Lightdale, Tal Korem, Julian Abrams .  2023.   The Salivary Microbiome and Predicted Metabolite Production are Associated with Progression from Barrett's Esophagus to Esophageal Adenocarcinoma.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Thomas Connors, Rei Matsumoto, Shivali Verma, Peter Szabo, Rebecca Guyer, Joshua Gray, Zicheng Wang, Puspa Thapa, Pranay Dogra, Maya Poon, Ksenia Rybkina, Marissa Bradley, Emma Idzikowski, James McNichols, Masaru Kubota, Kalpana Pethe, Yufeng Shen, Mark Atkinson, Maigan Brusko, Todd Brusko, Andrew Yates, Peter Sims, Donna Farber .  2023.   Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood.. Immunity. 56 (8) :1894-1909.e5 ▶ Go to Pubmed
Kaja Kostyrko, Marta Román, Alex Lee, David Simpson, Phuong Dinh, Stanley Leung, Kieren Marini, Marcus Kelly, Joshua Broyde, Andrea Califano, Peter Jackson, Alejandro Sweet-Cordero .  2023.   UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma.. Nature communications. 14 (1) :3966 ▶ Go to Pubmed
Jaewon Min, Junfei Zhao, Jennifer Zagelbaum, Jina Lee, Sho Takahashi, Portia Cummings, Allana Schooley, Job Dekker, Max Gottesman, Raul Rabadan, Jean Gautier .  2023.   Mechanisms of insertions at a DNA double-strand break.. Molecular cell. 83 (14) :2434-2448.e7 ▶ Go to Pubmed
Alina Sergeeva, Phinikoula Katsamba, Junzhuo Liao, Jared Sampson, Fabiana Bahna, Seetha Mannepalli, Nicholas Morano, Lawrence Shapiro, Richard Friesner, Barry Honig .  2023.   Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity.. Journal of molecular biology. 435 (15) :168187 ▶ Go to Pubmed
Alina Sergeeva, Phinikoula Katsamba, Junzhuo Liao, Jared Sampson, Fabiana Bahna, Seetha Mannepalli, Nicholas Morano, Lawrence Shapiro, Richard Friesner, Barry Honig .  2023.   Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity.. Journal of molecular biology. 435 (15) :168187 ▶ Go to Pubmed
Demis Menolfi, Brian Lee, Hanwen Zhang, Wenxia Jiang, Nicole Bowen, Yunyue Wang, Junfei Zhao, Antony Holmes, Steven Gershik, Raul Rabadan, Baek Kim, Shan Zha .  2023.   ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion.. Nature communications. 14 (1) :3618 ▶ Go to Pubmed
Qi Yan, Rafael Guerrero, Raiyan Khan, Andy Surujnarine, Ronald Wapner, Matthew Hahn, Anita Raja, Ansaf SallebAouissi, William Grobman, Hyagriv Simhan, Nathan Blue, Robert Silver, Judith Chung, Uma Reddy, Predrag Radivojac, Itsik Pe'er, David Haas .  2023.   Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Kensuke Sugiura, Yasunori Masuike, Kensuke Suzuki, Alice Shin, Nozomu Sakai, Hisahiro Matsubara, Masayuki Otsuka, Peter Sims, Christopher Lengner, Anil Rustgi .  2023.   LIN28B promotes cell invasion and colorectal cancer metastasis via CLDN1 and NOTCH3.. JCI insight. 8 (14) ▶ Go to Pubmed
Demis Menolfi, Brian Lee, Hanwen Zhang, Wenxia Jiang, Nicole Bowen, Yunyue Wang, Junfei Zhao, Antony Holmes, Steven Gershik, Raul Rabadan, Baek Kim, Shan Zha .  2023.   ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Norio Miyamura, Kodai Suzuki, Richard Friedman, Aristidis Floratos, Yuki Kunisada, Kazuya Masuda, Andrew Lowy, Moriya Tsuji, Kazuki Sugahara .  2023.   A pancreatic cancer mouse model with human immunity.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Norio Miyamura, Kodai Suzuki, Richard Friedman, Aristidis Floratos, Yuki Kunisada, Kazuya Masuda, Andrew Lowy, Moriya Tsuji, Kazuki Sugahara .  2023.   A pancreatic cancer mouse model with human immunity.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Norio Miyamura, Kodai Suzuki, Richard Friedman, Aristidis Floratos, Yuki Kunisada, Kazuya Masuda, Andrew Lowy, Moriya Tsuji, Kazuki Sugahara .  2023.   A pancreatic cancer mouse model with human immunity.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Jie Ding, Sung-Jin Lee, Lukas Vlahos, Kanako Yuki, Cara Rada, Vincent van Unen, Meghah Vuppalapaty, Hui Chen, Asmiti Sura, Aaron McCormick, Madeline Tomaske, Samira Alwahabi, Huy Nguyen, William Nowatzke, Lily Kim, Lisa Kelly, Douglas Vollrath, Andrea Califano, Wen-Chen Yeh, Yang Li, Calvin Kuo .  2023.   Therapeutic blood-brain barrier modulation and stroke treatment by a bioengineered FZD-selective WNT surrogate in mice.. Nature communications. 14 (1) :2947 ▶ Go to Pubmed
Jie Ding, Sung-Jin Lee, Lukas Vlahos, Kanako Yuki, Cara Rada, Vincent van Unen, Meghah Vuppalapaty, Hui Chen, Asmiti Sura, Aaron McCormick, Madeline Tomaske, Samira Alwahabi, Huy Nguyen, William Nowatzke, Lily Kim, Lisa Kelly, Douglas Vollrath, Andrea Califano, Wen-Chen Yeh, Yang Li, Calvin Kuo .  2023.   Therapeutic blood-brain barrier modulation and stroke treatment by a bioengineered FZD-selective WNT surrogate in mice.. Nature communications. 14 (1) :2947 ▶ Go to Pubmed
Michael Honigberg, Buu Truong, Raiyan Khan, Brenda Xiao, Laxmi Bhatta, Ha Vy, Rafael Guerrero, Art Schuermans, Margaret Selvaraj, Aniruddh Patel, Satoshi Koyama, So Cho, Shamsudheen Vellarikkal, Mark Trinder, Sarah Urbut, Kathryn Gray, Ben Brumpton, Snehal Patil, Sebastian Zöllner, Mariah Antopia, Richa Saxena, Girish Nadkarni, Ron Do, Qi Yan, Itsik Pe'er, Shefali Verma, Rajat Gupta, David Haas, Hilary Martin, David van Heel, Triin Laisk, Pradeep Natarajan .  2023.   Polygenic prediction of preeclampsia and gestational hypertension.. Nature medicine. ▶ Go to Pubmed
Celine Schreidah, George Reynolds, Lauren Fahmy, Richard Carvajal, Maarten Vermeer, Sean Whittaker, Itsik Pe'er, Larisa Geskin .  2023.   Scoping review of genetic databases for rare dermatologic diseases: Opportunity for artificial intelligence and machine learning.. JAAD international. 12 :24-31 ▶ Go to Pubmed
Somnath Tagore, Samuel Tsang, Gordon Mills, Andrea Califano .  2023.   Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Somnath Tagore, Samuel Tsang, Gordon Mills, Andrea Califano .  2023.   Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Min Jang, Parth Patel, Alexandre Pereira, Jon Willcox, Alireza Haghighi, Angela Tai, Kaoru Ito, Sarah Morton, Joshua Gorham, David McKean, Steven DePalma, Daniel Bernstein, Martina Brueckner, Wendy Chung, Alessandro Giardini, Elizabeth Goldmuntz, Jonathan Kaltman, Richard Kim, Jane Newburger, Yufeng Shen, Deepak Srivastava, Martin Tristani-Firouzi, Bruce Gelb, George Porter, Christine Seidman, Jonathan Seidman .  2023.   Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease.. Circulation. Genomic and precision medicine. 16 (3) :224-231 ▶ Go to Pubmed
Min Jang, Parth Patel, Alexandre Pereira, Jon Willcox, Alireza Haghighi, Angela Tai, Kaoru Ito, Sarah Morton, Joshua Gorham, David McKean, Steven DePalma, Daniel Bernstein, Martina Brueckner, Wendy Chung, Alessandro Giardini, Elizabeth Goldmuntz, Jonathan Kaltman, Richard Kim, Jane Newburger, Yufeng Shen, Deepak Srivastava, Martin Tristani-Firouzi, Bruce Gelb, George Porter, Christine Seidman, Jonathan Seidman .  2023.   Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease.. Circulation. Genomic and precision medicine. :e003924 ▶ Go to Pubmed
Luz Zapater, Elias Rodriguez-Fos, Merce Planas-Felix, Sara Lewis, Daniel Cameron, Phillip Demarest, Anika Nabila, Junfei Zhao, Paul Bergin, Casie Reed, Makiko Yamada, Alex Pagnozzi, Caroline Nava, Emilie Bourel-Ponchel, Derek Neilson, Ali Dursun, Köksal Özgül, Halil Akar, Nicholas Socci, Matthew Hayes, Raul Rabadan, David Torrents, Michael Kruer, Miklos Toth, Alex Kentsis .  2023.   A transposase-derived gene required for human brain development.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Luz Zapater, Elias Rodriguez-Fos, Merce Planas-Felix, Sara Lewis, Daniel Cameron, Phillip Demarest, Anika Nabila, Junfei Zhao, Paul Bergin, Casie Reed, Makiko Yamada, Alex Pagnozzi, Caroline Nava, Emilie Bourel-Ponchel, Derek Neilson, Ali Dursun, Köksal Özgül, Halil Akar, Nicholas Socci, Matthew Hayes, Raul Rabadan, David Torrents, Michael Kruer, Miklos Toth, Alex Kentsis .  2023.   A transposase-derived gene required for human brain development.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Alistair Dunham, Pedro Beltrao, Mohammed AlQuraishi .  2023.   High-throughput deep learning variant effect prediction with Sequence UNET.. Genome biology. 24 (1) :110 ▶ Go to Pubmed
Lara Tshering, Fu Luo, Savanah Russ, Mariola Szenk, Diana Rubel, Karis Tutuska, James Rail, Gábor Balázsi, Michael Shen, Flaminia Talos .  2023.   Immune mechanisms shape the clonal landscape during early progression of prostate cancer.. Developmental cell. ▶ Go to Pubmed
Osama Al-Dalahmah, Michael Argenziano, Adithya Kannan, Aayushi Mahajan, Julia Furnari, Fahad Paryani, Deborah Boyett, Akshay Save, Nelson Humala, Fatima Khan, Juncheng Li, Hong Lu, Yu Sun, John Tuddenham, Alexander Goldberg, Athanassios Dovas, Matei Banu, Tejaswi Sudhakar, Erin Bush, Andrew Lassman, Guy McKhann, Brian Gill, Brett Youngerman, Michael Sisti, Jeffrey Bruce, Peter Sims, Vilas Menon, Peter Canoll .  2023.   Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states.. Nature communications. 14 (1) :2586 ▶ Go to Pubmed
Liyuan Liu, Yiming Huang, Harris Wang .  2023.   Fast and efficient template-mediated synthesis of genetic variants.. Nature methods. 20 (6) :841-848 ▶ Go to Pubmed
Aleksandar Obradovic, Casey Ager, Mikko Turunen, Thomas Nirschl, Mohsen Khosravi-Maharlooei, Alina Iuga, Christopher Jackson, Srinivasan Yegnasubramanian, Lorenzo Tomassoni, Ester Fernandez, Patrick McCann, Meri Rogava, Angelo DeMarzo, Christina Kochel, Mohamad Allaf, Trinity Bivalacqua, Michael Lim, Ronald Realubit, Charles Karan, Charles Drake, Andrea Califano .  2023.   Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators.. Cancer cell. 41 (5) :933-949.e11 ▶ Go to Pubmed
Benjamin Hobson, Adrien Stanley, Mark Santos, Bruce Culbertson, Eugene Mosharov V, Peter Sims, David Sulzer .  2023.   Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain.. Brain, behavior, and immunity. 111 :277-291 ▶ Go to Pubmed
Yun Lin, Daniel Mallia, Andrea Clark-Sevilla, Adam Catto, Alisa Leshchenko, Qi Yan, David Haas, Ronald Wapner, Itsik Pe'er, Anita Raja, Ansaf Salleb-Aouissi .  2023.   A Comprehensive and Bias-Free Machine Learning Approach for Risk Prediction of Preeclampsia with Severe Features in a Nulliparous Study Cohort.. Research square. ▶ Go to Pubmed
Yun Lin, Daniel Mallia, Andrea Clark-Sevilla, Adam Catto, Alisa Leshchenko, Qi Yan, David Haas, Ronald Wapner, Itsik Pe'er, Anita Raja, Ansaf Salleb-Aouissi .  2023.   A Comprehensive and Bias-Free Machine Learning Approach for Risk Prediction of Preeclampsia with Severe Features in a Nulliparous Study Cohort.. Research square. ▶ Go to Pubmed
Elphège Nora, Stein Aerts, Patricia Wittkopp, Harmen Bussemaker, Martha Bulyk, Saurabh Sinha, Julia Zeitlinger, Justin Crocker, Juan Bass .  2023.   Emerging questions in transcriptional regulation.. Cell systems. 14 (4) :247-251 ▶ Go to Pubmed
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