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George Austin, Heekuk Park, Yoli Meydan, Dwayne Seeram, Tanya Sezin, Yue Lou, Brian Firek, Michael Morowitz, Jillian Banfield, Angela Christiano, Itsik Pe'er, Anne-Catrin Uhlemann, Liat Shenhav, Tal Korem .  2023.   Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data.. Nature biotechnology. ▶ Go to Pubmed
Donald Petrey, Haiqing Zhao, Stephen Trudeau, Diana Murray, Barry Honig .  2023.   PrePPI: A structure informed proteome-wide database of protein-protein interactions.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Francisco Jurado-Rueda, Lola Alonso-Guirado, Tomin Perea-Cham-Blee, Oliver Elliott, Ioan Filip, Raul Rabadan, Núria Malats .  2023.   Benchmarking of microbiome detection tools on RNA-seq synthetic databases according to diverse conditions.. Bioinformatics advances. 3 (1) :vbad014 ▶ Go to Pubmed
Francisco Jurado-Rueda, Lola Alonso-Guirado, Tomin Perea-Cham-Blee, Oliver Elliott, Ioan Filip, Raul Rabadan, Núria Malats .  2023.   Benchmarking of microbiome detection tools on RNA-seq synthetic databases according to diverse conditions.. Bioinformatics advances. 3 (1) :vbad014 ▶ Go to Pubmed
Matthew Lewis, Alexander Hsieh, Lu Qiao, Renjie Tan, Brigitte Kazzi, Alexandra Channing, Emily Griffin, Vaidehi Jobanputra, Jennifer Su, Chowdhury Shahryar, Lazaros Kochilas, William Gaynor, Teresa Lee, Elizabeth Goldmuntz, Mark Russell, Seema Mital, Martin Tristani, Martina Brueckner, Jane Newburger, Yufeng Shen, Wendy Chung .  2023.   Association of Predicted Damaging De Novo Variants on Ventricular Function in Individuals With Congenital Heart Disease.. Circulation. Genomic and precision medicine. 16 (2) :e003900 ▶ Go to Pubmed
Matei Banu, Athanassios Dovas, Michael Argenziano, Wenting Zhao, Henar Grajal, Dominique Higgins, Colin Sperring, Brianna Pereira, Ling Ye, Aayushi Mahajan, Nelson Humala, Julia Furnari, Pavan Upadhyayula, Fereshteh Zandkarimi, Trang Nguyen, Peter Wu, Li Hai, Charles Karan, Aida Razavilar, Markus Siegelin, Jan Kitajewski, Jeffrey Bruce, Brent Stockwell, Peter Sims, Peter Canoll .  2023.   A cell state specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Na Zhu, Charles Leduc, Ilene Fennoy, Blandine Re, Claudia Doege, Yufeng Shen, Wendy Chung, Rudolph Leibel .  2023.   Predicted loss of function alleles in Bassoon (BSN) are associated with obesity.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Na Zhu, Charles Leduc, Ilene Fennoy, Blandine Re, Claudia Doege, Yufeng Shen, Wendy Chung, Rudolph Leibel .  2023.   Predicted loss of function alleles in Bassoon (BSN) are associated with obesity.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
George Rosenberger, Wenxue Li, Mikko Turunen, Jing He, Prem Subramaniam, Sergey Pampou, Aaron Griffin, Charles Karan, Patrick Kerwin, Diana Murray, Barry Honig, Yansheng Liu, Andrea Califano .  2023.   Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Karen Gomez, Gianluca Schiavoni, Yoonhee Nam, Jean-Baptiste Reynier, Cole Khamnei, Michael Aitken, Giuseppe Palmieri, Antonio Cossu, Arnold Levine, Carel van Noesel, Brunangelo Falini, Laura Pasqualucci, Enrico Tiacci, Raul Rabadan .  2023.   Genomic landscape of virus-associated cancers.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Karen Gomez, Gianluca Schiavoni, Yoonhee Nam, Jean-Baptiste Reynier, Cole Khamnei, Michael Aitken, Giuseppe Palmieri, Antonio Cossu, Arnold Levine, Carel van Noesel, Brunangelo Falini, Laura Pasqualucci, Enrico Tiacci, Raul Rabadan .  2023.   Genomic landscape of virus-associated cancers.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Mai Sato, Rowyn Liebau, Zhaoqi Liu, Lizhi Liu, Raul Rabadan, Jean Gautier .  2023.   Correction: The UVSSA complex alleviates MYC-driven transcription stress.. The Journal of cell biology. 222 (3) ▶ Go to Pubmed
Yiming Huang, Ravi Sheth, Shijie Zhao, Lucas Cohen, Kendall Dabaghi, Thomas Moody, Yiwei Sun, Deirdre Ricaurte, Miles Richardson, Florencia Velez-Cortes, Tomasz Blazejewski, Andrew Kaufman, Carlotta Ronda, Harris Wang .  2023.   High-throughput microbial culturomics using automation and machine learning.. Nature biotechnology. 41 (10) :1424-1433 ▶ Go to Pubmed
Yiming Huang, Ravi Sheth, Shijie Zhao, Lucas Cohen, Kendall Dabaghi, Thomas Moody, Yiwei Sun, Deirdre Ricaurte, Miles Richardson, Florencia Velez-Cortes, Tomasz Blazejewski, Andrew Kaufman, Carlotta Ronda, Harris Wang .  2023.   High-throughput microbial culturomics using automation and machine learning.. Nature biotechnology. 41 (10) :1424-1433 ▶ Go to Pubmed
Emily Griffin, Shannon Nees, Sarah Morton, Julia Wynn, Nihir Patel, Vaidehi Jobanputra, Scott Robinson, Stephanie Kochav, Alice Tao, Carli Andrews, Nancy Cross, Judith Geva, Kristen Lanzilotta, Alyssa Ritter, Eileen Taillie, Alexandra Thompson, Chris Meyer, Rachel Akers, Eileen King, James Cnota, Richard Kim, George Porter, Martina Brueckner, Christine Seidman, Yufeng Shen, Bruce Gelb, Elizabeth Goldmuntz, Jane Newburger, Amy Roberts, Wendy Chung .  2023.   Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study.. Circulation. Genomic and precision medicine. 16 (2) :e003791 ▶ Go to Pubmed
Emily Griffin, Shannon Nees, Sarah Morton, Julia Wynn, Nihir Patel, Vaidehi Jobanputra, Scott Robinson, Stephanie Kochav, Alice Tao, Carli Andrews, Nancy Cross, Judith Geva, Kristen Lanzilotta, Alyssa Ritter, Eileen Taillie, Alexandra Thompson, Chris Meyer, Rachel Akers, Eileen King, James Cnota, Richard Kim, George Porter, Martina Brueckner, Christine Seidman, Yufeng Shen, Bruce Gelb, Elizabeth Goldmuntz, Jane Newburger, Amy Roberts, Wendy Chung .  2023.   Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study.. Circulation. Genomic and precision medicine. 16 (2) :e003791 ▶ Go to Pubmed
Emily Griffin, Shannon Nees, Sarah Morton, Julia Wynn, Nihir Patel, Vaidehi Jobanputra, Scott Robinson, Stephanie Kochav, Alice Tao, Carli Andrews, Nancy Cross, Judith Geva, Kristen Lanzilotta, Alyssa Ritter, Eileen Taillie, Alexandra Thompson, Chris Meyer, Rachel Akers, Eileen King, James Cnota, Richard Kim, George Porter, Martina Brueckner, Christine Seidman, Yufeng Shen, Bruce Gelb, Elizabeth Goldmuntz, Jane Newburger, Amy Roberts, Wendy Chung .  2023.   Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study.. Circulation. Genomic and precision medicine. 16 (2) :e003791 ▶ Go to Pubmed
Timothy Olsen, Pranay Talla, Julia Furnari, Jeffrey Bruce, Peter Canoll, Shan Zha, Peter Sims .  2023.   Scalable co-sequencing of RNA and DNA from individual nuclei.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Nazim Bouatta, Mohammed AlQuraishi .  2023.   Structural biology at the scale of proteomes.. Nature structural & molecular biology. 30 (2) :129-130 ▶ Go to Pubmed
Ophelia Venturelli, Harris Wang, Sylvie Estrela, Kerwyn Huang, Rodrigo Ledesma-Amaro, Alex Fedorec, Bärbel Stecher, Christopher Lawson, Amir Zarrinpar, Chun-Jun Guo, Orkun Soyer .  2023.   What is the key challenge in engineering microbiomes?. Cell systems. 14 (2) :85-90 ▶ Go to Pubmed
Ophelia Venturelli, Harris Wang, Sylvie Estrela, Kerwyn Huang, Rodrigo Ledesma-Amaro, Alex Fedorec, Bärbel Stecher, Christopher Lawson, Amir Zarrinpar, Chun-Jun Guo, Orkun Soyer .  2023.   What is the key challenge in engineering microbiomes?. Cell systems. 14 (2) :85-90 ▶ Go to Pubmed
Ophelia Venturelli, Harris Wang, Sylvie Estrela, Kerwyn Huang, Rodrigo Ledesma-Amaro, Alex Fedorec, Bärbel Stecher, Christopher Lawson, Amir Zarrinpar, Chun-Jun Guo, Orkun Soyer .  2023.   What is the key challenge in engineering microbiomes?. Cell systems. 14 (2) :85-90 ▶ Go to Pubmed
Stephen Trudeau, Howook Hwang, Deepika Mathur, Kamrun Begum, Donald Petrey, Diana Murray, Barry Honig .  2023.   PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions.. Protein science : a publication of the Protein Society. 32 (4) :e4594 ▶ Go to Pubmed
Ioan Filip, Anqi Wang, Oleksandr Kravets, Rose Orenbuch, Junfei Zhao, Tomin Perea-Chamblee, Gulam Manji, Evangelina de Maturana, Núria Malats, Kenneth Olive, Raul Rabadan .  2023.   Pervasiveness of HLA allele-specific expression loss across tumor types.. Genome medicine. 15 (1) :8 ▶ Go to Pubmed
Ioan Filip, Anqi Wang, Oleksandr Kravets, Rose Orenbuch, Junfei Zhao, Tomin Perea-Chamblee, Gulam Manji, Evangelina de Maturana, Núria Malats, Kenneth Olive, Raul Rabadan .  2023.   Pervasiveness of HLA allele-specific expression loss across tumor types.. Genome medicine. 15 (1) :8 ▶ 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.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Jingqiu Liao, Liat Shenhav, Myrna Serrano, Bin Zhu, Gregory Buck, Tal Korem .  2023.   Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Dennis Hsu, Jenny Gao, Norihiro Yamaguchi, Alexandra Pinzaru, Nandan Mandayam, Maria Liberti, Søren Heissel, Hanan Alwaseem, Saeed Tavazoie, Sohail Tavazoie .  2023.   Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Maya Poon, Daniel Caron, Zicheng Wang, Steven Wells, David Chen, Wenzhao Meng, Peter Szabo, Nora Lam, Masaru Kubota, Rei Matsumoto, Adeeb Rahman, Eline Prak, Yufeng Shen, Peter Sims, Donna Farber .  2023.   Tissue adaptation and clonal segregation of human memory T cells in barrier sites.. Nature immunology. 24 (2) :309-319 ▶ Go to Pubmed
Maya Poon, Daniel Caron, Zicheng Wang, Steven Wells, David Chen, Wenzhao Meng, Peter Szabo, Nora Lam, Masaru Kubota, Rei Matsumoto, Adeeb Rahman, Eline Prak, Yufeng Shen, Peter Sims, Donna Farber .  2023.   Tissue adaptation and clonal segregation of human memory T cells in barrier sites.. Nature immunology. 24 (2) :309-319 ▶ Go to Pubmed
William Kindschuh, Federico Baldini, Martin Liu, Jingqiu Liao, Yoli Meydan, Harry Lee, Almut Heinken, Ines Thiele, Christoph Thaiss, Maayan Levy, Tal Korem .  2023.   Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome.. Nature microbiology. 8 (2) :246-259 ▶ Go to Pubmed
Gabriel Sturm, Kalpita Karan, Anna Monzel, Balaji Santhanam, Tanja Taivassalo, Céline Bris, Sarah Ware, Marissa Cross, Atif Towheed, Albert Higgins-Chen, Meagan McManus, Andres Cardenas, Jue Lin, Elissa Epel, Shamima Rahman, John Vissing, Bruno Grassi, Morgan Levine, Steve Horvath, Ronald Haller, Guy Lenaers, Douglas Wallace, Marie-Pierre St-Onge, Saeed Tavazoie, Vincent Procaccio, Brett Kaufman, Erin Seifert, Michio Hirano, Martin Picard .  2023.   OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases.. Communications biology. 6 (1) :22 ▶ Go to Pubmed
Dennis Hsu, Jenny Gao, Norihiro Yamaguchi, Alexandra Pinzaru, Qiushuang Wu, Nandan Mandayam, Maria Liberti, Søren Heissel, Hanan Alwaseem, Saeed Tavazoie, Sohail Tavazoie .  2023.   Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells.. Science advances. 9 (1) :eade9120 ▶ Go to Pubmed
Dennis Hsu, Jenny Gao, Norihiro Yamaguchi, Alexandra Pinzaru, Qiushuang Wu, Nandan Mandayam, Maria Liberti, Søren Heissel, Hanan Alwaseem, Saeed Tavazoie, Sohail Tavazoie .  2023.   Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells.. Science advances. 9 (1) :eade9120 ▶ Go to Pubmed
Yufeng Shen, Huiliang Geng, Feifang Zhang, Zongying Li, Bingcheng Yang .  2023.   A polyethyleneimine-functionalized polymer substrate polar stationary phase.. Journal of chromatography. A. 1689 :463711 ▶ Go to Pubmed
Tizita Zeleke, Qingfei Pan, Codruta Chiuzan, Maika Onishi, Yuxin Li, Haiyan Tan, Mariano Alvarez, Erin Honan, Min Yang, Pei Chia, Partha Mukhopadhyay, Sean Kelly, Ruby Wu, Kathleen Fenn, Meghna Trivedi, Melissa Accordino, Katherine Crew, Dawn Hershman, Matthew Maurer, Simon Jones, Anthony High, Junmin Peng, Andrea Califano, Kevin Kalinsky, Jiyang Yu, Jose Silva .  2023.   Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer.. Nature cancer. 4 (2) :257-275 ▶ Go to Pubmed
Tizita Zeleke, Qingfei Pan, Codruta Chiuzan, Maika Onishi, Yuxin Li, Haiyan Tan, Mariano Alvarez, Erin Honan, Min Yang, Pei Chia, Partha Mukhopadhyay, Sean Kelly, Ruby Wu, Kathleen Fenn, Meghna Trivedi, Melissa Accordino, Katherine Crew, Dawn Hershman, Matthew Maurer, Simon Jones, Anthony High, Junmin Peng, Andrea Califano, Kevin Kalinsky, Jiyang Yu, Jose Silva .  2023.   Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer.. Nature cancer. 4 (2) :257-275 ▶ Go to Pubmed
Qian Wang, Sho Iketani, Zhiteng Li, Liyuan Liu, Yicheng Guo, Yiming Huang, Anthony Bowen, Michael Liu, Maple Wang, Jian Yu, Riccardo Valdez, Adam Lauring, Zizhang Sheng, Harris Wang, Aubree Gordon, Lihong Liu, David Ho .  2023.   Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants.. Cell. 186 (2) :279-286.e8 ▶ Go to Pubmed
Qian Wang, Sho Iketani, Zhiteng Li, Liyuan Liu, Yicheng Guo, Yiming Huang, Anthony Bowen, Michael Liu, Maple Wang, Jian Yu, Riccardo Valdez, Adam Lauring, Zizhang Sheng, Harris Wang, Aubree Gordon, Lihong Liu, David Ho .  2023.   Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants.. Cell. 186 (2) :279-286.e8 ▶ Go to Pubmed
Qian Wang, Sho Iketani, Zhiteng Li, Liyuan Liu, Yicheng Guo, Yiming Huang, Anthony Bowen, Michael Liu, Maple Wang, Jian Yu, Riccardo Valdez, Adam Lauring, Zizhang Sheng, Harris Wang, Aubree Gordon, Lihong Liu, David Ho .  2023.   Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants.. Cell. 186 (2) :279-286.e8 ▶ Go to Pubmed
Qian Wang, Sho Iketani, Zhiteng Li, Liyuan Liu, Yicheng Guo, Yiming Huang, Anthony Bowen, Michael Liu, Maple Wang, Jian Yu, Riccardo Valdez, Adam Lauring, Zizhang Sheng, Harris Wang, Aubree Gordon, Lihong Liu, David Ho .  2023.   Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants.. Cell. 186 (2) :279-286.e8 ▶ Go to Pubmed
Qian Wang, Sho Iketani, Zhiteng Li, Liyuan Liu, Yicheng Guo, Yiming Huang, Anthony Bowen, Michael Liu, Maple Wang, Jian Yu, Riccardo Valdez, Adam Lauring, Zizhang Sheng, Harris Wang, Aubree Gordon, Lihong Liu, David Ho .  2023.   Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants.. Cell. 186 (2) :279-286.e8 ▶ Go to Pubmed
Xiao Fan, Hongbing Pan, Alan Tian, Wendy Chung, Yufeng Shen .  2023.   SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants.. Briefings in bioinformatics. 24 (1) ▶ Go to Pubmed
Xiao Fan, Hongbing Pan, Alan Tian, Wendy Chung, Yufeng Shen .  2023.   SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants.. Briefings in bioinformatics. 24 (1) ▶ Go to Pubmed
Jennifer Zagelbaum, Allana Schooley, Junfei Zhao, Benjamin Schrank, Elsa Callen, Shan Zha, Max Gottesman, André Nussenzweig, Raul Rabadan, Job Dekker, Jean Gautier .  2023.   Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.. Nature structural & molecular biology. 30 (1) :99-106 ▶ Go to Pubmed
Jiwei Sun, Tiantian Chen, Baoying Zhao, Wenjie Fan, Yufeng Shen, Haojie Wei, Man Zhang, Wenhao Zheng, Jinfeng Peng, Jinyu Wang, Yifan Wang, Lihong Fan, Yingying Chu, Lili Chen, Cheng Yang .  2023.   Acceleration of Oral Wound Healing under Diabetes Mellitus Conditions Using Bioadhesive Hydrogel.. ACS applied materials & interfaces. 15 (1) :416-431 ▶ Go to Pubmed
Florencia Velez-Cortes, Harris Wang .  2022.   Characterization and Spatial Mapping of the Human Gut Metasecretome.. mSystems. 7 (6) :e0071722 ▶ Go to Pubmed
Florencia Velez-Cortes, Harris Wang .  2022.   Characterization and Spatial Mapping of the Human Gut Metasecretome.. mSystems. 7 (6) :e0071722 ▶ Go to Pubmed
Alessandro Vasciaveo, Juan Arriaga, Francisca de Almeida, Min Zou, Eugene Douglass, Florencia Picech, Maho Shibata, Antonio Rodriguez-Calero, Simone de Brot, Antonina Mitrofanova, Chee Chua, Charles Karan, Ronald Realubit, Sergey Pampou, Jaime Kim, Stephanie Afari, Timur Mukhammadov, Luca Zanella, Eva Corey, Mariano Alvarez, Mark Rubin, Michael Shen, Andrea Califano, Cory Abate-Shen .  2023.   OncoLoop: A Network-Based Precision Cancer Medicine Framework.. Cancer discovery. 13 (2) :386-409 ▶ Go to Pubmed
Alessandro Vasciaveo, Juan Arriaga, Francisca de Almeida, Min Zou, Eugene Douglass, Florencia Picech, Maho Shibata, Antonio Rodriguez-Calero, Simone de Brot, Antonina Mitrofanova, Chee Chua, Charles Karan, Ronald Realubit, Sergey Pampou, Jaime Kim, Stephanie Afari, Timur Mukhammadov, Luca Zanella, Eva Corey, Mariano Alvarez, Mark Rubin, Michael Shen, Andrea Califano, Cory Abate-Shen .  2023.   OncoLoop: A Network-Based Precision Cancer Medicine Framework.. Cancer discovery. 13 (2) :386-409 ▶ Go to Pubmed
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
Miguel Verbitsky, Sarathbabu Krishnamurthy, Priya Krithivasan, Daniel Hughes, Atlas Khan, Maddalena Marasà, Natalie Vena, Pavan Khosla, Junying Zhang, Tze Lim, Joseph Glessner, Chunhua Weng, Ning Shang, Yufeng Shen, George Hripcsak, Hakon Hakonarson, Iuliana Ionita-Laza, Brynn Levy, Eimear Kenny, Ruth Loos, Krzysztof Kiryluk, Simone Sanna-Cherchi, David Crosslin, Susan Furth, Bradley Warady, Robert Igo, Sudha Iyengar, Craig Wong, Afshin Parsa, Harold Feldman, Ali Gharavi .  2023.   Genomic Disorders in CKD across the Lifespan.. Journal of the American Society of Nephrology : JASN. 34 (4) :607-618 ▶ 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
Eleonora Spinazzi, Michael Argenziano, Pavan Upadhyayula, Matei Banu, Justin Neira, Dominique Higgins, Peter Wu, Brianna Pereira, Aayushi Mahajan, Nelson Humala, Osama Al-Dalahmah, Wenting Zhao, Akshay Save V, Brian Gill, Deborah Boyett, Tamara Marie, Julia Furnari, Tejaswi Sudhakar, Sylwia Stopka, Michael Regan, Vanessa Catania, Laura Good, Stergios Zacharoulis, Meenu Behl, Petros Petridis, Sachin Jambawalikar, Akiva Mintz, Angela Lignelli, Nathalie Agar, Peter Sims, Mary Welch, Andrew Lassman, Fabio Iwamoto, Randy D'Amico, Jack Grinband, Peter Canoll, Jeffrey Bruce .  2022.   Chronic convection-enhanced delivery of topotecan for patients with recurrent glioblastoma: a first-in-patient, single-centre, single-arm, phase 1b trial.. The Lancet. Oncology. 23 (11) :1409-1418 ▶ 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
Julie Trolle, Ross McBee, Andrew Kaufman, Sudarshan Pinglay, Henri Berger, Sergei German, Liyuan Liu, Michael Shen, Xinyi Guo, Andrew Martin, Michael Pacold, Drew Jones, Jef Boeke, Harris Wang .  2022.   Resurrecting essential amino acid biosynthesis in mammalian cells.. 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
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 .  2023.   B7-H3 as a Therapeutic Target in Advanced Prostate Cancer.. European urology. 83 (3) :224-238 ▶ 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
John Blackett, Yiwei Sun, Lawrence Purpura, Kara Margolis, Mitchell Elkind V, Sheila O'Byrne, Milton Wainberg, Julian Abrams, Harris Wang, Lin Chang, Daniel Freedberg .  2022.   Decreased Gut Microbiome Tryptophan Metabolism and Serotonergic Signaling in Patients With Persistent Mental Health and Gastrointestinal Symptoms After COVID-19.. Clinical and translational gastroenterology. 13 (10) :e00524 ▶ Go to Pubmed
John Blackett, Yiwei Sun, Lawrence Purpura, Kara Margolis, Mitchell Elkind V, Sheila O'Byrne, Milton Wainberg, Julian Abrams, Harris Wang, Lin Chang, Daniel Freedberg .  2022.   Decreased Gut Microbiome Tryptophan Metabolism and Serotonergic Signaling in Patients With Persistent Mental Health and Gastrointestinal Symptoms After COVID-19.. Clinical and translational gastroenterology. 13 (10) :e00524 ▶ Go to Pubmed
Yoshinaga Kawano, Madeline Edwards, Yiming Huang, Angelina Bilate, Leandro Araujo, Takeshi Tanoue, Koji Atarashi, Mark Ladinsky, Steven Reiner, Harris Wang, Daniel Mucida, Kenya Honda, Ivaylo Ivanov .  2022.   Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome.. Cell. 185 (19) :3501-3519.e20 ▶ Go to Pubmed
Yoshinaga Kawano, Madeline Edwards, Yiming Huang, Angelina Bilate, Leandro Araujo, Takeshi Tanoue, Koji Atarashi, Mark Ladinsky, Steven Reiner, Harris Wang, Daniel Mucida, Kenya Honda, Ivaylo Ivanov .  2022.   Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome.. Cell. 185 (19) :3501-3519.e20 ▶ Go to Pubmed
Xueya Zhou, Pamela Feliciano, Chang Shu, Tianyun Wang, Irina Astrovskaya, Jacob Hall, Joseph Obiajulu, Jessica Wright, Shwetha Murali, Simon Xu, Leo Brueggeman, Taylor Thomas, Olena Marchenko, Christopher Fleisch, Sarah Barns, LeeAnne Snyder, Bing Han, Timothy Chang, Tychele Turner, William Harvey, Andrew Nishida, Brian O'Roak, Daniel Geschwind, SPARK Consortium, Jacob Michaelson, Natalia Volfovsky, Evan Eichler, Yufeng Shen, Wendy Chung .  2022.   Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes.. Nature genetics. 54 (9) :1305-1319 ▶ 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
K Adelman, G Wilson, C Orlando, M Boxer .  1987.   A retained foreign body in the foot. A case report.. Journal of the American Podiatric Medical Association. 77 (4) :190-3 ▶ 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
Guojie Zhong, Priyanka Ahimaz, Nicole Edwards, Jacob Hagen, Christophe Faure, Qiao Lu, Paul Kingma, William Middlesworth, Julie Khlevner, Mahmoud Fiky, David Schindel, Elizabeth Fialkowski, Adhish Kashyap, Sophia Forlenza, Alan Kenny, Aaron Zorn, Yufeng Shen, Wendy Chung .  2022.   Erratum: Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas.. HGG advances. 3 (3) :100126 ▶ 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
Rajappa Kenchappa, Athanassios Dovas, Michael Argenziano, Christian Meyer, Lauren Stopfer, Matei Banu, Brianna Pereira, Jessica Griffith, Afroz Mohammad, Surabhi Talele, Ashley Haddock, Natanael Zarco, William Elmquist, Forest White, Vito Quaranta, Peter Sims, Peter Canoll, Steven Rosenfeld .  2022.   Activation of STAT3 through combined SRC and EGFR signaling drives resistance to a mitotic kinesin inhibitor in glioblastoma.. Cell reports. 39 (12) :110991 ▶ 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
Peter Freddolino, Haley Amemiya, Thomas Goss, Saeed Tavazoie .  2022.   Correction: Dynamic landscape of protein occupancy across the Escherichia coli chromosome.. PLoS biology. 20 (4) :e3001557 ▶ Go to Pubmed
Michael Chait, Mine Yilmaz, Shanila Shakil, Amy Ku, Pranay Dogra, Thomas Connors, Peter Szabo, Joshua Gray, Steven Wells, Masaru Kubota, Rei Matsumoto, Maya Poon, Mark Snyder, Matthew Baldwin, Peter Sims, Anjali Saqi, Donna Farber, Stuart Weisberg .  2022.   Immune and epithelial determinants of age-related risk and alveolar injury in fatal COVID-19.. JCI insight. 7 (11) ▶ 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
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
Jordan Metz, Nicholas Hornstein, Sohani Sharma, Jeremy Worley, Christian Gonzalez, Peter Sims .  2022.   High-throughput translational profiling with riboPLATE-seq.. Scientific reports. 12 (1) :5718 ▶ 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.. American journal of physiology. Gastrointestinal and liver physiology. 322 (6) :G583-G597 ▶ 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
Mark Snyder, Kaveh Moghbeli, Anna Bondonese, Andrew Craig, Iulia Popescu, Li Fan, Tracy Tabib, Robert Lafyatis, Kong Chen, Humberto Bittar, Elizabeth Lendermon, Joseph Pilewski, Bruce Johnson, Silpa Kilaru, Yingze Zhang, Pablo Sanchez, Jonathan Alder, Peter Sims, John McDyer .  2022.   Modulation of tissue resident memory T cells by glucocorticoids after acute cellular rejection in lung transplantation.. The Journal of experimental medicine. 219 (4) ▶ 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