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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
Jimin Park, Harris Wang .  2021.   Systematic dissection of σ sequence diversity and function in bacteria.. Cell reports. 36 (8) :109590 ▶ Go to Pubmed
Claudia Capdevila, Maria Trifas, Jonathan Miller, Troy Anderson, Peter Sims, Kelley Yan .  2021.   Cellular origins and lineage relationships of the intestinal epithelium.. American journal of physiology. Gastrointestinal and liver physiology. 321 (4) :G413-G425 ▶ 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
Jimin Park, Sung Yim, Harris Wang .  2021.   High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters.. ACS synthetic biology. 10 (8) :1859-1873 ▶ 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.. Proceedings of the National Academy of Sciences of the United States of America. 118 (29) ▶ 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
Qing Meng, Qiuqiang Gao, Shebli Mehrazarin, Kamonchanok Tangwanichgapong, Yu Wang, Yiming Huang, Yutong Pan, Samuel Robinson, Ziwen Liu, Amirali Zangiabadi, Renate Lux, Panos Papapanou, Edward Guo, Harris Wang, Luke Berchowitz, Yiping Han .  2021.   Fusobacterium nucleatum secretes amyloid-like FadA to enhance pathogenicity.. EMBO reports. 22 (7) :e52891 ▶ 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
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.. Nature cancer. 1 (11) :1082-1096 ▶ 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 medicine. 13 (1) :88 ▶ 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
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
Sonakshi Bhattacharjee, Florian Hamberger, Aashreya Ravichandra, Maximilian Miller, Ajay Nair, Silvia Affo, Aveline Filliol, LiKang Chin, Thomas Savage, Deqi Yin, Naita Wirsik, Adam Mehal, Nicholas Arpaia, Ekihiro Seki, Matthias Mack, Di Zhu, Peter Sims, Raghu Kalluri, Ben Stanger, Kenneth Olive, Thomas Schmidt, Rebecca Wells, Ingmar Mederacke, Robert Schwabe .  2021.   Tumor restriction by type I collagen opposes tumor-promoting effects of cancer-associated fibroblasts.. The Journal of clinical investigation. 131 (11) ▶ 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
Peter Szabo, Pranay Dogra, Joshua Gray, Steven Wells, Thomas Connors, Stuart Weisberg, Izabela Krupska, Rei Matsumoto, Maya Poon, Emma Idzikowski, Sinead Morris, Chloé Pasin, Andrew Yates, Amy Ku, Michael Chait, Julia Davis-Porada, Xinzheng Guo V, Jing Zhou, Matthew Steinle, Sean Mackay, Anjali Saqi, Matthew Baldwin, Peter Sims, Donna Farber .  2021.   Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19.. Immunity. 54 (4) :797-814.e6 ▶ 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
Luciano Garofano, Simona Migliozzi, Young Oh, Fulvio D'Angelo, Ryan Najac, Aram Ko, Brulinda Frangaj, Francesca Caruso, Kai Yu, Jinzhou Yuan, Wenting Zhao, Anna Di Stefano, Franck Bielle, Tao Jiang, Peter Sims, Mario Suvà, Fuchou Tang, Xiao-Dong Su, Michele Ceccarelli, Marc Sanson, Anna Lasorella, Antonio Iavarone .  2021.   Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities.. Nature cancer. 2 (2) :141-156 ▶ 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
Mehdi Damaghi, Jeffrey West, Mark Robertson-Tessi, Liping Xu, Meghan Ferrall-Fairbanks, Paul Stewart, Erez Persi, Brooke Fridley, Philipp Altrock, Robert Gatenby, Peter Sims, Alexander Anderson, Robert Gillies .  2021.   The harsh microenvironment in early breast cancer selects for a Warburg phenotype.. Proceedings of the National Academy of Sciences of the United States of America. 118 (3) ▶ 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
Sung Yim, Ross McBee, Alan Song, Yiming Huang, Ravi Sheth, Harris Wang .  2021.   Robust direct digital-to-biological data storage in living cells.. Nature chemical biology. 17 (3) :246-253 ▶ 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
Phuc Vo, Carlotta Ronda, Sanne Klompe, Ethan Chen, Christopher Acree, Harris Wang, Samuel Sternberg .  2021.   CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering.. Nature biotechnology. 39 (4) :480-489 ▶ Go to Pubmed
Phuc Vo, Carlotta Ronda, Sanne Klompe, Ethan Chen, Christopher Acree, Harris Wang, Samuel Sternberg .  2021.   CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering.. Nature biotechnology. 39 (4) :480-489 ▶ 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
Zhouzerui Liu, Jinzhou Yuan, Anna Lasorella, Antonio Iavarone, Jeffrey Bruce, Peter Canoll, Peter Sims .  2020.   Integrating single-cell RNA-seq and imaging with SCOPE-seq2.. Scientific reports. 10 (1) :19482 ▶ 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
Francesca Caruso, Luciano Garofano, Fulvio D'Angelo, Kai Yu, Fuchou Tang, Jinzhou Yuan, Jing Zhang, Luigi Cerulo, Stefano Pagnotta, Davide Bedognetti, Peter Sims, Mario Suvà, Xiao-Dong Su, Anna Lasorella, Antonio Iavarone, Michele Ceccarelli .  2020.   A map of tumor-host interactions in glioma at single-cell resolution.. GigaScience. 9 (10) ▶ Go to Pubmed
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