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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
Jinsook Son, Hongxu Ding, Thomas Farb, Alexander Efanov, Jiajun Sun, Julie Gore, Samreen Syed, Zhigang Lei, Qidi Wang, Domenico Accili, Andrea Califano .  2021.   BACH2 inhibition reverses β cell failure in type 2 diabetes models.. J Clin Invest. 131 (24) ▶ 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
Heike Blockus, Sebi Rolotti V, Miklos Szoboszlay, Eugénie Peze-Heidsieck, Tiffany Ming, Anna Schroeder, Nuno Apostolo, Kristel Vennekens, Phinikoula Katsamba, Fabiana Bahna, Seetha Mannepalli, Goran Ahlsen, Barry Honig, Lawrence Shapiro, Joris de Wit, Attila Losonczy, Franck Polleux .  2021.   Synaptogenic activity of the axon guidance molecule Robo2 underlies hippocampal circuit function.. Cell Rep. 37 (3) :109828 ▶ Go to Pubmed
Mohammed AlQuraishi, Peter Sorger .  2021.   Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms.. Nat Methods. 18 (10) :1169-1180 ▶ Go to Pubmed
Soonbum Park, Lijie Rong, Tomasz Owczarek, Matteo Di Bernardo, Rivka Shoulson, Chee-Wai Chua, Jaime Kim, Amir Lankarani, Prithi Chakrapani, Talal Syed, James McKiernan, David Solit, Michael Shen, Hikmat Al-Ahmadie, Cory Abate-Shen .  2021.   Novel mouse models of bladder cancer identify a prognostic signature associated with risk of disease progression.. Cancer Res. ▶ Go to Pubmed
Camila Prieto, Diu Nguyen, Zhaoqi Liu, Justin Wheat, Alexendar Perez, Saroj Gourkanti, Timothy Chou, Ersilia Barin, Anthony Velleca, Thomas Rohwetter, Arthur Chow, James Taggart, Angela Savino, Katerina Hoskova, Meera Dhodapkar, Alexandra Schurer, Trevor Barlowe, Ly Vu, Christina Leslie, Ulrich Steidl, Raul Rabadan, Michael Kharas .  2021.   Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia.. Nat Cancer. 2 :741-757 ▶ Go to Pubmed
Edgar González-Buendia, Junfei Zhao, Lu Wang, Subhas Mukherjee, Daniel Zhang, Víctor Arrieta, Eric Feldstein, Robert Kane, Seong Kang, Catalina Lee-Chang, Aayushi Mahajan, Li Chen, Ronald Realubit, Charles Karan, Lisa Magnuson, Craig Horbinski, Stacy Marshall, Jann Sarkaria, Ahmed Mohyeldin, Ichiro Nakano, Mukesh Bansal, Charles James, Daniel Brat, Atique Ahmed, Peter Canoll, Raul Rabadan, Ali Shilatifard, Adam Sonabend .  2021.   TOP2B Enzymatic Activity on Promoters and Introns Modulates Multiple Oncogenes in Human Gliomas.. Clin Cancer Res. ▶ Go to Pubmed
Mohammed AlQuraishi .  2021.   Protein-structure prediction revolutionized.. Nature. 596 (7873) :487-488 ▶ Go to Pubmed
Karen Gomez, Raul Rabadan .  2021.   A persistent look at how tumours evade therapy.. Nature. 596 (7873) :491-493 ▶ Go to Pubmed
Juan Patiño-Galindo, Ioan Filip, Ratul Chowdhury, Costas Maranas, Peter Sorger, Mohammed AlQuraishi, Raul Rabadan .  2021.   Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2.. Genome Med. 13 (1) :124 ▶ Go to Pubmed
Nazim Bouatta, Peter Sorger, Mohammed AlQuraishi .  2021.   Protein structure prediction by AlphaFold2: are attention and symmetries all you need?. Acta Crystallogr D Struct Biol. 77 (Pt 8) :982-991 ▶ Go to Pubmed
Daniel Landsburg, Stefan Barta, Radhakrishnan Ramchandren, Connie Batlevi, Swaminathan Iyer, Kevin Kelly, Ivana Micallef, Sonali Smith, Don Stevens, Mariano Alvarez, Andrea Califano, Yao Shen, Gideon Bosker, Jefferson Parker, Raul Soikes, Elizabeth Martinez, Reinhard von Roemeling, Robert Martell, Yasuhiro Oki .  2021.   Fimepinostat (CUDC-907) in patients with relapsed/refractory diffuse large B cell and high-grade B-cell lymphoma: report of a phase 2 trial and exploratory biomarker analyses.. Br J Haematol. ▶ Go to Pubmed
Kendra Sweet, Bhavana Bhatnagar, Hartmut Döhner, Will Donnellan, Olga Frankfurt, Michael Heuser, Vamsi Kota, Hongtao Liu, Emmanuel Raffoux, Gail Roboz, Christoph Röllig, Margaret Showel, Stephen Strickland, Susana Vives, Shijie Tang, Thaddeus Unger, Anita Joshi, Yao Shen, Mariano Alvarez, Andrea Califano, Marsha Crochiere, Yosef Landesman, Michael Kauffman, Jatin Shah, Sharon Shacham, Michael Savona, Pau Montesinos .  2021.   A 2:1 randomized, open-label, phase II study of selinexor vs. physician's choice in older patients with relapsed or refractory acute myeloid leukemia.. Leuk Lymphoma. :1-12 ▶ Go to Pubmed
Gulam Manji, Brian Van Tine, Shing Lee, Alexander Raufi, Ilenia Pellicciotta, Angela Hirbe, Jaya Pradhan, Andrew Chen, Raul Rabadan, Gary Schwartz .  2021.   A Phase I Study of the Combination of Pexidartinib and Sirolimus to Target Tumor-Associated Macrophages in Unresectable Sarcoma and Malignant Peripheral Nerve Sheath Tumors.. Clin Cancer Res. ▶ Go to Pubmed
Arianna Giacobbe, Cory Abate-Shen .  2021.   Modeling metastasis in mice: a closer look.. Trends Cancer. 7 (10) :916-929 ▶ Go to Pubmed
Kaiyi Zhu, Lingyi Cai, Chenqian Cui, Juan Toyos, Dimitris Anastassiou .  2021.   Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts.. PLoS Comput Biol. 17 (7) :e1009228 ▶ Go to Pubmed
Regina Troyanovsky, Alina Sergeeva, Indrajyoti Indra, Chi-Shuo Chen, Rei Kato, Lawrence Shapiro, Barry Honig, Sergey Troyanovsky .  2021.   Sorting of cadherin-catenin-associated proteins into individual clusters.. Proc Natl Acad Sci U S A. 118 (29) ▶ Go to Pubmed
Seth Taylor, Gabriel Santpere, Alexis Weinreb, Alec Barrett, Molly Reilly, Chuan Xu, Erdem Varol, Panos Oikonomou, Lori Glenwinkel, Rebecca McWhirter, Abigail Poff, Manasa Basavaraju, Ibnul Rafi, Eviatar Yemini, Steven Cook, Alexander Abrams, Berta Vidal, Cyril Cros, Saeed Tavazoie, Nenad Sestan, Marc Hammarlund, Oliver Hobert, David Miller .  2021.   Molecular topography of an entire nervous system.. Cell. 184 (16) :4329-4347.e23 ▶ Go to Pubmed
Zoila Lopez-Bujanda, Aleksandar Obradovic, Thomas Nirschl, Laura Crowley, Rodney Macedo, Alexandros Papachristodoulou, Timothy O'Donnell, Uri Laserson, Jelani Zarif, Ran Reshef, Tiezheng Yuan, Mithil Soni, Emmanuel Antonarakis, Michael Haffner, Benjamin Larman, Michael Shen, Pawel Muranski, Charles Drake .  2021.   TGM4: an immunogenic prostate-restricted antigen.. J Immunother Cancer. 9 (6) ▶ Go to Pubmed
Peter Freddolino, Haley Amemiya, Thomas Goss, Saeed Tavazoie .  2021.   Dynamic landscape of protein occupancy across the Escherichia coli chromosome.. PLoS Biol. 19 (6) :e3001306 ▶ Go to Pubmed
Matthew Kearney, Lauren Franks, Shing Lee, Amy Tiersten, Della Makower, Tessa Cigler, Prabhjot Mundi, Dow-Chung Chi, Anupama Goel, Pam Klein, Eleni Andreopoulou, Joseph Sparano, Meghna Trivedi, Melissa Accordino, Andrea Califano, Dawn Hershman, Jose Silva, Kevin Kalinsky .  2021.   Phase I/II trial of ruxolitinib in combination with trastuzumab in metastatic HER2 positive breast cancer.. Breast Cancer Res Treat. 189 (1) :177-185 ▶ Go to Pubmed
Hans Koss, Barry Honig, Lawrence Shapiro, Arthur Palmer .  2021.   Dimerization of Cadherin-11 involves multi-site coupled unfolding and strand swapping.. Structure. ▶ 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
Delin Chen, Bo Chu, Xin Yang, Zhaoqi Liu, Ying Jin, Ning Kon, Raul Rabadan, Xuejun Jiang, Brent Stockwell, Wei Gu .  2021.   iPLA2β-mediated lipid detoxification controls p53-driven ferroptosis independent of GPX4.. Nat Commun. 12 (1) :3644 ▶ Go to Pubmed
Silvia Affo, Ajay Nair, Francesco Brundu, Aashreya Ravichandra, Sonakshi Bhattacharjee, Michitaka Matsuda, LiKang Chin, Aveline Filliol, Wen Wen, Xinhua Song, Aubrianna Decker, Jeremy Worley, Jorge Caviglia, Lexing Yu, Deqi Yin, Yoshinobu Saito, Thomas Savage, Rebecca Wells, Matthias Mack, Lars Zender, Nicholas Arpaia, Helen Remotti, Raul Rabadan, Peter Sims, Anne-Laure Leblond, Achim Weber, Marc-Oliver Riener, Brent Stockwell, Jellert Gaublomme, Josep Llovet, Raghu Kalluri, George Michalopoulos, Ekihiro Seki, Daniela Sia, Xin Chen, Andrea Califano, Robert Schwabe .  2021.   Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations.. Cancer Cell. 39 (6) :883 ▶ Go to Pubmed
Luigi Scotto, Cristina Kinahan, Eugene Douglass, Changchun Deng, Maryam Safari, Beatrice Casadei, Enrica Marchi, Jennifer Lue, Francesca Montanari, Lorenzo Falchi, Changhong Qiao, Nandakumar Renu, Susan Bates, Andrea Califano, Owen O'Connor .  2021.   Targeting the T-Cell Lymphoma Epigenome Induces Cell Death, Cancer Testes Antigens, Immune-Modulatory Signaling Pathways.. Mol Cancer Ther. 20 (8) :1422-1430 ▶ Go to Pubmed
Juan Arriaga, Sukanya Panja, Mohammed Alshalalfa, Junfei Zhao, Min Zou, Arianna Giacobbe, Chioma Madubata, Jaime Kim, Antonio Rodriguez, Ilsa Coleman, Renu Virk, Hanina Hibshoosh, Onur Ertunc, Büşra Ozbek, Julia Fountain, Jeffrey Karnes, Jun Luo, Emmanuel Antonarakis, Peter Nelson, Felix Feng, Mark Rubin, Angelo De Marzo, Raul Rabadan, Peter Sims, Antonina Mitrofanova, Cory Abate-Shen .  2020.   A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance.. Nat Cancer. 1 (11) :1082-1096 ▶ Go to Pubmed
Marco Fangazio, Erik Ladewig, Karen Gomez, Laura Garcia-Ibanez, Rahul Kumar, Julie Teruya-Feldstein, Davide Rossi, Ioan Filip, Qiang Pan-Hammarström, Giorgio Inghirami, Renzo Boldorini, German Ott, Annette Staiger, Björn Chapuy, Gianluca Gaidano, Govind Bhagat, Katia Basso, Raul Rabadan, Laura Pasqualucci, Riccardo Dalla-Favera .  2021.   Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma.. Proc Natl Acad Sci U S A. 118 (22) ▶ Go to Pubmed
Aleksandar Obradovic, Nivedita Chowdhury, Scott Haake, Casey Ager, Vinson Wang, Lukas Vlahos, Xinzheng Guo V, David Aggen, Kimryn Rathmell, Eric Jonasch, Joyce Johnson, Marc Roth, Kathryn Beckermann, Brian Rini, James McKiernan, Andrea Califano, Charles Drake .  2021.   Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages.. Cell. 184 (11) :2988-3005.e16 ▶ Go to Pubmed
Mohammed AlQuraishi .  2021.   Machine learning in protein structure prediction.. Curr Opin Chem Biol. 65 :1-8 ▶ Go to Pubmed
Andrew Chen, Robyn Gartrell, Junfei Zhao, Pavan Upadhyayula, Wenting Zhao, Jinzhou Yuan, Hanna Minns, Athanassios Dovas, Jeffrey Bruce, Anna Lasorella, Antonio Iavarone, Peter Canoll, Peter Sims, Raul Rabadan .  2021.   Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker.. Genome Med. 13 (1) :88 ▶ Go to Pubmed
Silvia Affo, Ajay Nair, Francesco Brundu, Aashreya Ravichandra, Sonakshi Bhattacharjee, Michitaka Matsuda, LiKang Chin, Aveline Filliol, Wen Wen, Xinhua Song, Aubrianna Decker, Jeremy Worley, Jorge Caviglia, Lexing Yu, Deqi Yin, Yoshinobu Saito, Thomas Savage, Rebecca Wells, Matthias Mack, Lars Zender, Nicholas Arpaia, Helen Remotti, Raul Rabadan, Peter Sims, Anne-Laure Leblond, Achim Weber, Marc-Oliver Riener, Brent Stockwell, Jellert Gaublomme, Josep Llovet, Raghu Kalluri, George Michalopoulos, Ekihiro Seki, Daniela Sia, Xin Chen, Andrea Califano, Robert Schwabe .  2021.   Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations.. Cancer Cell. 39 (6) :866-882.e11 ▶ Go to Pubmed
Christine Moon, Clara Reglero, Jose Cortes, Aidan Quinn, Silvia Alvarez, Junfei Zhao, Wen-Hsuan Lin, Anisha Cooke, Francesco Abate, Craig Soderquist, Claudia Fiñana, Giorgio Inghirami, Elias Campo, Govind Bhagat, Raul Rabadan, Teresa Palomero, Adolfo Ferrando .  2021.   induces NF-κB signaling-driven peripheral T cell lymphoma.. Nat Cancer. 2 (1) :98-113 ▶ Go to Pubmed
Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie Brown, Juan Patiño-Galindo, Timothy Chu, Aidan Quinn, Thomas Gunning, Laura Belver, Alberto Ambesi-Impiombato, Valeria Tosello, Zhengqiang Wang, Maria Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Milagros Balbin, Concepción Nicolas, Julie Gastier-Foster, Meenakshi Devidas, Mignon Loh, Elisabeth Paietta, Martin Tallman, Jacob Rowe, Mark Litzow, Mark Minden, Jules Meijerink, Raul Rabadan, Adolfo Ferrando .  2020.   Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia.. Nat Cancer. 1 (11) :1113-1127 ▶ Go to Pubmed
Hyunju Oh, Jingyao Zhao, Yenkel Grinberg-Bleyer, Thomas Postler, Pingzhang Wang, Sung-Gyoo Park, Raul Rabadan, Matthew Hayden, Sankar Ghosh .  2021.   PDK1 Is Required for Maintenance of CD4 Foxp3 Regulatory T Cell Function.. J Immunol. 206 (8) :1776-1783 ▶ Go to Pubmed
Todd Lencz, Jin Yu, Raiyan Khan, Erin Flaherty, Shai Carmi, Max Lam, Danny Ben-Avraham, Nir Barzilai, Susan Bressman, Ariel Darvasi, Judy Cho, Lorraine Clark, Zeynep Gümüş, Joseph Vijai, Robert Klein, Steven Lipkin, Kenneth Offit, Harry Ostrer, Laurie Ozelius, Inga Peter, Anil Malhotra, Tom Maniatis, Gil Atzmon, Itsik Pe'er .  2021.   Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia.. Neuron. 109 (9) :1465-1478.e4 ▶ Go to Pubmed
Diana Murray, Donald Petrey, Barry Honig .  2021.   Integrating 3D structural information into systems biology.. J Biol Chem. 296 :100562 ▶ Go to Pubmed
William Hahn, Joel Bader, Theodore Braun, Andrea Califano, Paul Clemons, Brian Druker, Andrew Ewald, Haian Fu, Subhashini Jagu, Christopher Kemp, William Kim, Calvin Kuo, Michael McManus, Gordon Mills, Xiulei Mo, Nidhi Sahni, Stuart Schreiber, Jessica Talamas, Pablo Tamayo, Jeffrey Tyner, Bridget Wagner, William Weiss, Daniela Gerhard, Cancer Network .  2021.   An expanded universe of cancer targets.. Cell. 184 (5) :1142-1155 ▶ Go to Pubmed
Casey Ager, Aleksandar Obradovic, Juan Arriaga, Matthew Chaimowitz, Andrea Califano, Cory Abate-Shen, Charles Drake .  2021.   Longitudinal Immune Profiling Reveals Unique Myeloid and T-cell Phenotypes Associated with Spontaneous Immunoediting in a Prostate Tumor Model.. Cancer Immunol Res. 9 (5) :529-541 ▶ Go to Pubmed
Raquel Cuella-Martin, Samuel Hayward, Xiao Fan, Xiao Chen, Jen-Wei Huang, Angelo Taglialatela, Giuseppe Leuzzi, Junfei Zhao, Raul Rabadan, Chao Lu, Yufeng Shen, Alberto Ciccia .  2021.   Functional interrogation of DNA damage response variants with base editing screens.. Cell. 184 (4) :1081-1097.e19 ▶ Go to Pubmed
Tyler Joseph, Itsik Pe'er .  2021.   An Introduction to Whole-Metagenome Shotgun Sequencing Studies.. Methods Mol Biol. 2243 :107-122 ▶ Go to Pubmed
Juan Patiño-Galindo, Ioan Filip, Raul Rabadan .  2021.   Global Patterns of Recombination across Human Viruses.. Mol Biol Evol. 38 (6) :2520-2531 ▶ Go to Pubmed
Feixiong Cheng, Junfei Zhao, Yang Wang, Weiqiang Lu, Zehui Liu, Yadi Zhou, William Martin, Ruisheng Wang, Jin Huang, Tong Hao, Hong Yue, Jing Ma, Yuan Hou, Jessica Castrillon, Jiansong Fang, Justin Lathia, Ruth Keri, Felice Lightstone, Elliott Antman, Raul Rabadan, David Hill, Charis Eng, Marc Vidal, Joseph Loscalzo .  2021.   Comprehensive characterization of protein-protein interactions perturbed by disease mutations.. Nat Genet. 53 (3) :342-353 ▶ Go to Pubmed
Zhaoqi Liu, Raul Rabadan .  2021.   Computing the Role of Alternative Splicing in Cancer.. Trends Cancer. 7 (4) :347-358 ▶ Go to Pubmed
Hongxu Ding, Ying Yang, Yuanqing Xue, Lucas Seninge, Henry Gong, Rojin Safavi, Andrea Califano, Joshua Stuart .  2021.   Prioritizing transcriptional factors in gene regulatory networks with PageRank.. iScience. 24 (1) :102017 ▶ Go to Pubmed
Yuan-Hung Lo, Kevin Kolahi, Yuhong Du, Chiung-Ying Chang, Andrey Krokhotin, Ajay Nair, Walter Sobba, Kasper Karlsson, Sunny Jones, Teri Longacre, Amanda Mah, Bahar Tercan, Alexandra Sockell, Hang Xu, Jose Seoane, Jin Chen, Ilya Shmulevich, Jonathan Weissman, Christina Curtis, Andrea Califano, Haian Fu, Gerald Crabtree, Calvin Kuo .  2021.   A CRISPR/Cas9-Engineered -Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation.. Cancer Discov. 11 (6) :1562-1581 ▶ Go to Pubmed
Evan Paull, Alvaro Aytes, Sunny Jones, Prem Subramaniam, Federico Giorgi, Eugene Douglass, Somnath Tagore, Brennan Chu, Alessandro Vasciaveo, Siyuan Zheng, Roel Verhaak, Cory Abate-Shen, Mariano Alvarez, Andrea Califano .  2021.   A modular master regulator landscape controls cancer transcriptional identity.. Cell. 184 (2) :334-351.e20 ▶ Go to Pubmed
Dinara Usmanova, Germán Plata, Dennis Vitkup .  2021.   The Relationship between the Misfolding Avoidance Hypothesis and Protein Evolutionary Rates in the Light of Empirical Evidence.. Genome Biol Evol. 13 (2) ▶ Go to Pubmed
Wesley Tansey, Kathy Li, Haoran Zhang, Scott Linderman, Raul Rabadan, David Blei, Chris Wiggins .  2021.   Dose-response modeling in high-throughput cancer drug screenings: an end-to-end approach.. Biostatistics. ▶ Go to Pubmed
Mai Sato, Andrew Liebau, Zhaoqi Liu, Lizhi Liu, Raul Rabadan, Jean Gautier .  2021.   The UVSSA complex alleviates MYC-driven transcription stress.. J Cell Biol. 220 (2) ▶ Go to Pubmed
Matko Kalac, Michael Mangone, Alison Rinderspacher, Shi-Xian Deng, Luigi Scotto, Michael Markson, Mukesh Bansal, Andrea Califano, Donald Landry, Owen O'Connor .  2020.   -quinoline-benzenesulfonamide derivatives exert potent anti-lymphoma effect by targeting NF-κB.. iScience. 23 (12) :101884 ▶ Go to Pubmed
Doowon Huh, Maria Passarelli, Jenny Gao, Shahnoza Dusmatova, Clara Goin, Lisa Fish, Alexandra Pinzaru, Henrik Molina, Zhiji Ren, Elizabeth McMillan, Hosseinali Asgharian, Hani Goodarzi, Sohail Tavazoie .  2021.   A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression.. EMBO J. 40 (2) :e106696 ▶ Go to Pubmed
George Rosenberger, Moritz Heusel, Isabell Bludau, Ben Collins, Claudia Martelli, Evan Williams, Peng Xue, Yansheng Liu, Ruedi Aebersold, Andrea Califano .  2020.   SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles.. Cell Syst. 11 (6) :589-607.e8 ▶ Go to Pubmed
Karthik Arumugam, William Shin, Valentina Schiavone, Lukas Vlahos, Xiaochuan Tu, Davide Carnevali, Jordan Kesner, Evan Paull, Neus Romo, Prem Subramaniam, Jeremy Worley, Xiangtian Tan, Andrea Califano, Maria Cosma .  2020.   The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State.. Cell Rep. 33 (10) :108474 ▶ Go to Pubmed
Zhaoqi Liu, Ioan Filip, Karen Gomez, Dewaldt Engelbrecht, Shabnum Meer, Pooja Lalloo, Pareen Patel, Yvonne Perner, Junfei Zhao, Jiguang Wang, Laura Pasqualucci, Raul Rabadan, Pascale Willem .  2020.   Genomic characterization of HIV-associated plasmablastic lymphoma identifies pervasive mutations in the JAK-STAT pathway.. Blood Cancer Discov. 1 (1) :112-125 ▶ Go to Pubmed
Se-Jin Lee, Adam Lehar, Yewei Liu, Chi Ly, Quynh-Mai Pham, Michael Michaud, Renata Rydzik, Daniel Youngstrom, Michael Shen, Vesa Kaartinen, Emily Germain-Lee, Thomas Rando .  2020.   Functional redundancy of type I and type II receptors in the regulation of skeletal muscle growth by myostatin and activin A.. Proc Natl Acad Sci U S A. 117 (49) :30907-30917 ▶ Go to Pubmed
Luis Aparicio, Mykola Bordyuh, Andrew Blumberg, Raul Rabadan .  2020.   A Random Matrix Theory Approach to Denoise Single-Cell Data.. Patterns (N Y). 1 (3) :100035 ▶ Go to Pubmed
Maho Shibata, Nusrat Epsi, Shouhong Xuan, Antonina Mitrofanova, Michael Shen .  2020.   Bipotent Progenitors Do Not Require Androgen Receptor for Luminal Specification during Prostate Organogenesis.. Stem Cell Reports. 15 (5) :1026-1036 ▶ Go to Pubmed
Jamie Yang, Saeed Tavazoie .  2020.   Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.. PLoS One. 15 (11) :e0239528 ▶ Go to Pubmed
Suji Han, Hyemi Shin, Jin-Ku Lee, Zhaoqi Liu, Raul Rabadan, Jeongwu Lee, Jihye Shin, Cheolju Lee, Heekyoung Yang, Donggeon Kim, Sung Kim, Jooyeon Kim, Jeong-Woo Oh, Doo-Sik Kong, Jung-Il Lee, Ho Seol, Jung Choi, Hyun Kang, Do-Hyun Nam .  2020.   Correction: Secretome analysis of patient-derived GBM tumorspheres identifies midkine as a potent therapeutic target.. Exp Mol Med. 52 (11) :1869 ▶ Go to Pubmed
Vartika Mishra, Diane Ré, Virginia Le Verche, Mariano Alvarez, Alessandro Vasciaveo, Arnaud Jacquier, Paschalis-Tomas Doulias, Todd Greco, Monica Nizzardo, Dimitra Papadimitriou, Tetsuya Nagata, Paola Rinchetti, Eduardo Perez-Torres, Kristin Politi, Burcin Ikiz, Kevin Clare, Manuel Than, Stefania Corti, Harry Ischiropoulos, Francesco Lotti, Andrea Califano, Serge Przedborski .  2020.   Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow.. Nat Commun. 11 (1) :5579 ▶ Go to Pubmed
Elena Anghileri, Natalia Di Ianni, Rosina Paterra, Tiziana Langella, Junfei Zhao, Marica Eoli, Monica Patanè, Bianca Pollo, Valeria Cuccarini, Antonio Iavarone, Raul Rabadan, Gaetano Finocchiaro, Serena Pellegatta .  2021.   High tumor mutational burden and T-cell activation are associated with long-term response to anti-PD1 therapy in Lynch syndrome recurrent glioblastoma patient.. Cancer Immunol Immunother. 70 (3) :831-842 ▶ Go to Pubmed
Andrew Chiang, Jonathan Chang, Jiayao Wang, Dennis Vitkup .  2021.   Exons as units of phenotypic impact for truncating mutations in autism.. Mol Psychiatry. 26 (5) :1685-1695 ▶ Go to Pubmed
Daniela Cerezo-Wallis, Marta Contreras-Alcalde, Kevin Troulé, Xavier Catena, Cynthia Mucientes, Tonantzin Calvo, Estela Cañón, Cristina Tejedo, Paula Pennacchi, Sabrina Hogan, Peter Kölblinger, Héctor Tejero, Andrew Chen, Nuria Ibarz, Osvaldo Graña-Castro, Lola Martinez, Javier Muñoz, Pablo Ortiz-Romero, José Rodriguez-Peralto, Gonzalo Gómez-López, Fátima Al-Shahrour, Raul Rabadan, Mitchell Levesque, David Olmeda, María Soengas .  2020.   Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state.. Nat Med. 26 (12) :1865-1877 ▶ Go to Pubmed
Paola Nicoletti, Daniel Carr, Sarah Barrett, Laurence McEvoy, Peter Friedmann, Neil Shear, Matthew Nelson, Anca Chiriac, Natalia Blanca-López, José Cornejo-García, Francesco Gaeta, Alla Nakonechna, Maria Torres, Cristiano Caruso, Rocco Valluzzi, Aris Floratos, Yufeng Shen, Rebecca Pavlos, Elizabeth Phillips, Pascal Demoly, Antonino Romano, Miguel Blanca, Munir Pirmohamed .  2021.   Beta-lactam-induced immediate hypersensitivity reactions: A genome-wide association study of a deeply phenotyped cohort.. The Journal of allergy and clinical immunology. 147 (5) :1830-1837.e15 ▶ Go to Pubmed
Gaojianyong Wang, Dimitris Anastassiou .  2020.   Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis.. Sci Rep. 10 (1) :17199 ▶ Go to Pubmed
Gorka Lasso, Barry Honig, Sagi Shapira .  2021.   A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease.. Cell Syst. 12 (1) :82-91.e3 ▶ Go to Pubmed
Bo Liu, Zhaoqi Liu, Sisi Chen, Michelle Ki, Caroline Erickson, Jorge Reis-Filho, Benjamin Durham, Qing Chang, Elisa de Stanchina, Yiwei Sun, Raul Rabadan, Omar Abdel-Wahab, Sarat Chandarlapaty .  2021.   Mutant SF3B1 promotes AKT- and NF-κB-driven mammary tumorigenesis.. J Clin Invest. 131 (1) ▶ Go to Pubmed
Md Bhuyan, Itsik Pe'er, Sohel Rahman .  2021.   SICaRiO: short indel call filtering with boosting.. Brief Bioinform. 22 (4) ▶ Go to Pubmed
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