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2022

2022 Publications

Kenneth Smith, Daniel Chawla, Bhavjinder Dhillon, Zhou Ji, Randi Vita, Eva van der Leest, Jing Weng, Ernest Tang, Amani Abid, Human Consortium, Bjoern Peters, Robert Hancock, Aris Floratos, Steven Kleinstein .  2022.   A curated collection of human vaccination response signatures.. Scientific data. 9 (1) :678 ▶ Go to Pubmed
Joann Diray-Arce, Helen Miller, Evan Henrich, Bram Gerritsen, Matthew Mulè, Slim Fourati, Jeremy Gygi, Thomas Hagan, Lewis Tomalin, Dmitry Rychkov, Dmitri Kazmin, Daniel Chawla, Hailong Meng, Patrick Dunn, John Campbell, Human Consortium, Minnie Sarwal, John Tsang, Ofer Levy, Bali Pulendran, Rafick Sekaly, Aris Floratos, Raphael Gottardo, Steven Kleinstein, Mayte Suárez-Fariñas .  2022.   The Immune Signatures data resource, a compendium of systems vaccinology datasets.. Scientific data. 9 (1) :635 ▶ Go to Pubmed
Ratul Chowdhury, Nazim Bouatta, Surojit Biswas, Christina Floristean, Anant Kharkar, Koushik Roy, Charlotte Rochereau, Gustaf Ahdritz, Joanna Zhang, George Church, Peter Sorger, Mohammed AlQuraishi .  2022.   Publisher Correction: Single-sequence protein structure prediction using a language model and deep learning.. Nature biotechnology. 40 (11) :1692 ▶ Go to Pubmed
Diego Coutinho, Prabhjot Mundi, Lianna Marks, Chelsey Burke, Michael Ortiz V, Daniel Diolaiti, Lauren Bird, Kelly Vallance, Glorymar Ibáñez, Daoqi You, Matthew Long, Nestor Rosales, Adina Grunn, Andoyo Ndengu, Armaan Siddiquee, Ervin Gaviria, Allison Rainey, Ladan Fazlollahi, Hajime Hosoi, Andrea Califano, Andrew Kung, Filemon Cruz .  2022.   Validation of a non-oncogene encoded vulnerability to exportin 1 inhibition in pediatric renal tumors.. Med (New York, N.Y.). 3 (11) :774-791.e7 ▶ Go to Pubmed
Ratul Chowdhury, Nazim Bouatta, Surojit Biswas, Christina Floristean, Anant Kharkar, Koushik Roy, Charlotte Rochereau, Gustaf Ahdritz, Joanna Zhang, George Church, Peter Sorger, Mohammed AlQuraishi .  2022.   Single-sequence protein structure prediction using a language model and deep learning.. Nat Biotechnol. 40 (11) :1617-1623 ▶ Go to Pubmed
Wei Zhong, Liping Chen, Xiaopan Li, Yichen Chen, Yao Zhang, Canjie Guo, Yufeng Shen, Huimin Chen .  2022.   Disability-adjusted life years and the trends of the burden of colorectal cancer: a population-based study in Shanghai, China during 2002 to 2016.. Chinese medical journal. 135 (24) :2950-2955 ▶ Go to Pubmed
Yizhuo Zhou, Ying Yang, Lihao Guo, Jun Qian, Jian Ge, Debora Sinner, Hongxu Ding, Andrea Califano, Wellington Cardoso V .  2022.   Airway basal cells show regionally distinct potential to undergo metaplastic differentiation.. eLife. 11 ▶ Go to Pubmed
Christina Guo, Ines Figueiredo, Bora Gurel, Antje Neeb, George Seed, Mateus Crespo, Suzanne Carreira, Jan Rekowski, Lorenzo Buroni, Jon Welti, Denisa Bogdan, Lewis Gallagher, Adam Sharp, Maria de la Maza, Pasquale Rescigno, Daniel Westaby, Khobe Chandran, Ruth Riisnaes, Ana Ferreira, Susana Miranda, Bianca Calì, Andrea Alimonti, Silvia Bressan, Alana Nguyen, Michael Shen, Jessica Hawley, Aleksandar Obradovic, Charles Drake, Claudia Bertan, Chloe Baker, Nina Tunariu, Wei Yuan, Johann de Bono .  2022.   B7-H3 as a Therapeutic Target in Advanced Prostate Cancer.. European urology. ▶ Go to Pubmed
Pasquale Laise, Gideon Bosker, Andrea Califano, Mariano Alvarez .  2022.   A Patient-to-Model-to-Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture.. Curr Protoc. 2 (9) :e544 ▶ Go to Pubmed
Nadir Boni, Lawrence Shapiro, Barry Honig, Yinghao Wu, Rotem Rubinstein .  2022.   On the formation of ordered protein assemblies in cell-cell interfaces.. Proc Natl Acad Sci U S A. 119 (34) :e2206175119 ▶ Go to Pubmed
Guojie Zhong, Yufeng Shen .  2022.   Statistical models of the genetic etiology of congenital heart disease.. Current opinion in genetics & development. 76 :101967 ▶ Go to Pubmed
Corinne Lutomski, Tarick El-Baba, Carol Robinson V, Roland Riek, Sjors Scheres, Nieng Yan, Mohammed AlQuraishi, Lu Gan .  2022.   The next decade of protein structure.. Cell. 185 (15) :2617-2620 ▶ Go to Pubmed
Pasquale Laise, Megan Stanifer, Gideon Bosker, Xiaoyun Sun, Sergio Triana, Patricio Doldan, Federico La Manna, Marta De Menna, Ronald Realubit, Sergey Pampou, Charles Karan, Theodore Alexandrov, Marianna de Julio, Andrea Califano, Steeve Boulant, Mariano Alvarez .  2022.   A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection.. Commun Biol. 5 (1) :714 ▶ Go to Pubmed
Siqian Feng, Chaitanya Rastogi, Ryan Loker, William Glassford, Tomas Rube, Harmen Bussemaker, Richard Mann .  2022.   Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors.. Nat Commun. 13 (1) :3808 ▶ Go to Pubmed
Amy Lipman, Xiao Fan, Yufeng Shen, Wendy Chung .  2022.   Clinical and genetic characterization of CACNA1A-related disease.. Clin Genet. 102 (4) :288-295 ▶ Go to Pubmed
Amy Lipman, Xiao Fan, Yufeng Shen, Wendy Chung .  2022.   Clinical and genetic characterization of CACNA1A-related disease.. Clinical genetics. 102 (4) :288-295 ▶ Go to Pubmed
Parvathi Myer, Hyunjin Kim, Anna Blümel, Ellen Finnegan, Alexander Kel, Taylor Thompson V, John Greally, Jochen Prehn, Darran O'Connor, Richard Friedman, Aris Floratos, Sudipto Das .  2022.   Master Transcription Regulators and Transcription Factors Regulate Immune-Associated Differences Between Patients of African and European Ancestry With Colorectal Cancer.. Gastro hep advances. 1 (3) :328-341 ▶ Go to Pubmed
Jiwei Sun, Fengyuan Guo, Qingming Tang, Guangjin Chen, Jinfeng Peng, Yufeng Shen, Junyuan Zhang, Jingqiong Hu, Cheng Yang .  2022.   Identification of a novel immune gene panel in tongue squamous cell carcinoma.. American journal of translational research. 14 (5) :2801-2824 ▶ Go to Pubmed
Mohammed AlQuraishi, Samah Chahed, Dina Alani, Dexter Puckett, Presley Dowker, Katelin Hubbard, Yi Zhao, Ji Kim, Laurentia Nodit, Huma Fatima, Dallas Donohoe, Brynn Voy, Winyoo Chowanadisai, Ahmed Bettaieb .  2022.   Podocyte specific deletion of PKM2 ameliorates LPS-induced podocyte injury through beta-catenin.. Cell Commun Signal. 20 (1) :76 ▶ Go to Pubmed
Tomas Rube, Chaitanya Rastogi, Siqian Feng, Judith Kribelbauer, Allyson Li, Basheer Becerra, Lucas Melo, Bach Do, Xiaoting Li, Hammaad Adam, Neel Shah, Richard Mann, Harmen Bussemaker .  2022.   Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning.. Nat Biotechnol. ▶ Go to Pubmed
Robyn Gartrell, Thomas Enzler, Pan Kim, Benjamin Fullerton, Ladan Fazlollahi, Andrew Chen, Hanna Minns, Subha Perni, Stuart Weisberg, Emanuelle Rizk, Samuel Wang, Eun Oh, Xinzheng Guo V, Codruta Chiuzan, Gulam Manji, Susan Bates, John Chabot, Beth Schrope, Michael Kluger, Jean Emond, Raul Rabadan, Donna Farber, Helen Remotti, David Horowitz, Yvonne Saenger .  2022.   Neoadjuvant chemoradiation alters the immune microenvironment in pancreatic ductal adenocarcinoma.. Oncoimmunology. 11 (1) :2066767 ▶ Go to Pubmed
Cory Abate-Shen, Francisca de Almeida .  2022.   Establishment of the LNCaP Cell Line - The Dawn of an Era for Prostate Cancer Research.. Cancer Res. 82 (9) :1689-1691 ▶ Go to Pubmed
Alexandros Papachristodoulou, Cory Abate-Shen .  2022.   Precision intervention for prostate cancer: Re-evaluating who is at risk.. Cancer Lett. 538 :215709 ▶ Go to Pubmed
Kacey Ronaldson-Bouchard, Diogo Teles, Keith Yeager, Daniel Tavakol, Yimu Zhao, Alan Chramiec, Somnath Tagore, Max Summers, Sophia Stylianos, Manuel Tamargo, Busub Lee, Susan Halligan, Erbil Abaci, Zongyou Guo, Joanna Jacków, Alberto Pappalardo, Jerry Shih, Rajesh Soni, Shivam Sonar, Carrie German, Angela Christiano, Andrea Califano, Karen Hirschi, Christopher Chen, Andrzej Przekwas, Gordana Vunjak-Novakovic .  2022.   A multi-organ chip with matured tissue niches linked by vascular flow.. Nature biomedical engineering. 6 (4) :351-371 ▶ Go to Pubmed
Jose Cortes, Ioan Filip, Robert Albero, Juan Patiño-Galindo, Aidan Quinn, Wen-Hsuan Lin, Anouchka Laurent, Bobby Shih, Jessie Brown, Anisha Cooke, Adam Mackey, Jonah Einson, Sakellarios Zairis, Alfredo Rivas-Delgado, Maria Laginestra, Stefano Pileri, Elias Campo, Govind Bhagat, Adolfo Ferrando, Raul Rabadan, Teresa Palomero .  2022.   Oncogenic Vav1-Myo1f induces therapeutically targetable macrophage-rich tumor microenvironment in peripheral T cell lymphoma.. Cell reports. 39 (3) :110695 ▶ Go to Pubmed
David Schoenfeld, Royce Zhou, Sakellarios Zairis, William Su, Nicole Steinbach, Deepti Mathur, Ankita Bansal, Alexis Zachem, Bertilia Tavarez, Dan Hasson, Emily Bernstein, Raul Rabadan, Ramon Parsons .  2022.   Loss of PBRM1 Alters Promoter Histone Modifications and Activates ALDH1A1 to Drive Renal Cell Carcinoma.. Mol Cancer Res. 20 (8) :1193-1207 ▶ Go to Pubmed
Shuwa Xu, Alina Sergeeva, Phinikoula Katsamba, Seetha Mannepalli, Fabiana Bahna, Jude Bimela, Lawrence Zipursky, Lawrence Shapiro, Barry Honig, Kai Zinn .  2022.   Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules.. Cell reports. 39 (1) :110618 ▶ Go to Pubmed
Moritz Middelhoff, Giovanni Valenti, Lorenzo Tomassoni, Yosuke Ochiai, Bryana Belin, Ryota Takahashi, Ermanno Malagola, Henrik Nienhüser, Michael Finlayson, Yoku Hayakawa, Leah Zamechek, Bernhard Renz, Benedikt Westphalen, Michael Quante, Kara Margolis, Peter Sims, Pasquale Laise, Andrea Califano, Meenakshi Rao, Michael Gershon, Timothy Wang .  2022.   Adult enteric Dclk1-positive glial and neuronal cells reveal distinct responses to acute intestinal injury.. Am J Physiol Gastrointest Liver Physiol. 322 (6) :G583-G597 ▶ Go to Pubmed
Aleksandar Obradovic, Diana Graves, Michael Korrer, Yu Wang, Sohini Roy, Abdullah Naveed, Yaomin Xu, Adam Luginbuhl, Joseph Curry, Michael Gibson, Kamran Idrees, Paula Hurley, Peng Jiang, Shirley Liu, Ravindra Uppaluri, Charles Drake, Andrea Califano, Young Kim .  2022.   Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer.. Clinical cancer research : an official journal of the American Association for Cancer Research. 28 (10) :2094-2109 ▶ Go to Pubmed
Aleksandar Obradovic, Diana Graves, Michael Korrer, Yu Wang, Sohini Roy, Abdullah Naveed, Yaomin Xu, Adam Luginbuhl, Joseph Curry, Michael Gibson, Kamran Idrees, Paula Hurley, Peng Jiang, Shirley Liu, Ravindra Uppaluri, Charles Drake, Andrea Califano, Young Kim .  2022.   Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer.. Clinical cancer research : an official journal of the American Association for Cancer Research. 28 (10) :2094-2109 ▶ Go to Pubmed
Aleksandar Obradovic, Diana Graves, Michael Korrer, Yu Wang, Sohini Roy, Abdullah Naveed, Yaomin Xu, Adam Luginbuhl, Joseph Curry, Michael Gibson, Kamran Idrees, Paula Hurley, Peng Jiang, Shirley Liu, Ravindra Uppaluri, Charles Drake, Andrea Califano, Young Kim .  2022.   Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer.. Clin Cancer Res. 28 (10) :2094-2109 ▶ Go to Pubmed
Francesco Cambuli, Veronica Foletto, Alessandro Alaimo, Dario De Felice, Francesco Gandolfi, Maria Palumbieri, Michela Zaffagni, Sacha Genovesi, Marco Lorenzoni, Martina Celotti, Emiliana Bertossio, Giosuè Mazzero, Arianna Bertossi, Alessandra Bisio, Francesco Berardinelli, Antonio Antoccia, Marco Gaspari, Mattia Barbareschi, Michelangelo Fiorentino, Michael Shen, Massimo Loda, Alessandro Romanel, Andrea Lunardi .  2022.   Intra-epithelial non-canonical Activin A signaling safeguards prostate progenitor quiescence.. EMBO Rep. 23 (5) :e54049 ▶ Go to Pubmed
Kerry Goodman, Phinikoula Katsamba, Rotem Rubinstein, Goran Ahlsen, Fabiana Bahna, Seetha Mannepalli, Hanbin Dan, Rosemary Sampogna V, Lawrence Shapiro, Barry Honig .  2022.   How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition.. eLife. 11 ▶ Go to Pubmed
Alberto Bartolomé, Nina Suda, Junjie Yu, Changyu Zhu, Jinsook Son, Hongxu Ding, Andrea Califano, Domenico Accili, Utpal Pajvani .  2022.   Notch-mediated Ephrin signaling disrupts islet architecture and β cell function.. JCI insight. 7 (6) ▶ Go to Pubmed
Víctor Arrieta, Andrew Chen, Robert Kane, Seong Kang, Cynthia Kassab, Crismita Dmello, Junfei Zhao, Kirsten Burdett, Pavan Upadhyayula, Catalina Lee-Chang, Joseph Shilati, Dinesh Jaishankar, Li Chen, Andrew Gould, Daniel Zhang, Jinzhou Yuan, Wenting Zhao, Xiaoyang Ling, Jared Burks, Brice Laffleur, Christina Amidei, Jeffrey Bruce, Rimas Lukas V, Jonathan Yamaguchi, David Cieremans, Gerson Rothschild, Uttiya Basu, Matthew McCord, Daniel Brat, Hui Zhang, Lee Cooper, Bin Zhang, Peter Sims, Tim Cloughesy, Robert Prins, Peter Canoll, Roger Stupp, Amy Heimberger, Craig Horbinski, Fabio Iwamoto, Raul Rabadan, Adam Sonabend .  2022.   Publisher Correction: ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma.. Nature cancer. 3 (3) :373 ▶ Go to Pubmed
Pasquale Laise, Megan Stanifer, Gideon Bosker, Xiaoyun Sun, Sergio Triana, Patricio Doldan, Federico La Manna, Marta De Menna, Ronald Realubit, Sergey Pampou, Charles Karan, Theodore Alexandrov, Marianna de Julio, Andrea Califano, Steeve Boulant, Mariano Alvarez .  2022.   A Model for Network-Based Identification and Pharmacological Targeting of Aberrant, Replication-Permissive Transcriptional Programs Induced by Viral Infection.. Research square. ▶ Go to Pubmed
Eugene Douglass, Robert Allaway, Bence Szalai, Wenyu Wang, Tingzhong Tian, Adrià Fernández-Torras, Ron Realubit, Charles Karan, Shuyu Zheng, Alberto Pessia, Ziaurrehman Tanoli, Mohieddin Jafari, Fangping Wan, Shuya Li, Yuanpeng Xiong, Miquel Duran-Frigola, Martino Bertoni, Pau Badia-I-Mompel, Lídia Mateo, Oriol Guitart-Pla, Verena Chung, DREAM Consortium, Jing Tang, Jianyang Zeng, Patrick Aloy, Julio Saez-Rodriguez, Justin Guinney, Daniela Gerhard, Andrea Califano .  2022.   A community challenge for a pancancer drug mechanism of action inference from perturbational profile data.. Cell reports. Medicine. 3 (1) :100492 ▶ Go to Pubmed
Elise Flynn, Athena Tsu, Silva Kasela, Sarah Kim-Hellmuth, François Aguet, Kristin Ardlie, Harmen Bussemaker, Pejman Mohammadi, Tuuli Lappalainen .  2022.   Transcription factor regulation of eQTL activity across individuals and tissues.. PLoS genetics. 18 (1) :e1009719 ▶ Go to Pubmed
Marta Galán-Díez, Florence Borot, Abdullah Ali, Junfei Zhao, Eva Gil-Iturbe, Xiaochuan Shan, Na Luo, Yongfeng Liu, Xi-Ping Huang, Brygida Bisikirska, Rossella Labella, Irwin Kurland, Bryan Roth, Matthias Quick, Siddhartha Mukherjee, Raul Rabadan, Martin Carroll, Azra Raza, Stavroula Kousteni .  2022.   Subversion of Serotonin Receptor Signaling in Osteoblasts by Kynurenine Drives Acute Myeloid Leukemia.. Cancer discovery. 12 (4) :1106-1127 ▶ Go to Pubmed
Smadar Shilo, Anastasia Godneva, Marianna Rachmiel, Tal Korem, Yuval Bussi, Dmitry Kolobkov, Tal Karady, Noam Bar, Bat Wolf, Yitav Glantz-Gashai, Michal Cohen, Nehama Zuckerman-Levin, Naim Shehadeh, Noah Gruber, Neriya Levran, Shlomit Koren, Adina Weinberger, Orit Pinhas-Hamiel, Eran Segal .  2022.   The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control.. Diabetes care. 45 (3) :555-563 ▶ Go to Pubmed
John Christin, Michael Shen .  2022.   Modeling tumor plasticity in organoid models of human cancer.. Trends in cancer. 8 (3) :161-163 ▶ Go to Pubmed
Tyler Joseph, Philippe Chlenski, Aviya Litman, Tal Korem, Itsik Pe'er .  2022.   Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.. Genome research. 32 (3) :558-568 ▶ Go to Pubmed
Andrew Lassman, Patrick Wen, Martin van den Bent, Scott Plotkin, Annemiek Walenkamp, Adam Green, Kai Li, Christopher Walker, Hua Chang, Sharon Tamir, Leah Henegar, Yao Shen, Mariano Alvarez, Andrea Califano, Yosef Landesman, Michael Kauffman, Sharon Shacham, Morten Mau-Sørensen .  2022.   A Phase II Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma.. Clin Cancer Res. 28 (3) :452-460 ▶ Go to Pubmed
Laura Crowley, Michael Shen .  2022.   Heterogeneity and complexity of the prostate epithelium: New findings from single-cell RNA sequencing studies.. Cancer Lett. 525 :108-114 ▶ Go to Pubmed
Smadar Shilo, Anastasia Godneva, Marianna Rachmiel, Tal Korem, Dmitry Kolobkov, Tal Karady, Noam Bar, Bat Wolf, Yitav Glantz-Gashai, Michal Cohen, Nehama Levin, Naim Shehadeh, Noah Gruber, Neriya Levran, Shlomit Koren, Adina Weinberger, Orit Pinhas-Hamiel, Eran Segal .  2022.   Prediction of Personal Glycemic Responses to Food for Individuals With Type 1 Diabetes Through Integration of Clinical and Microbial Data.. Diabetes care. 45 (3) :502-511 ▶ Go to Pubmed
Weiping Li, Michael Shen .  2022.   Prostate cancer cell heterogeneity and plasticity: Insights from studies of genetically-engineered mouse models.. Semin Cancer Biol. 82 :60-67 ▶ Go to Pubmed