Publications

Jingqiu Liao, Liat Shenhav, Julia Urban, Myrna Serrano, Bin Zhu, Gregory Buck, Tal Korem . 2023. Microdiversity of the vaginal microbiome is associated with preterm birth.. Nature communications. 14 (1) :4997 ▶ Go to Pubmed

Anna Dickson, Tekle Pauzaite, Esther Arnaiz, Brian Ortmann, James West, Norbert Volkmar, Anthony Martinelli, Zhaoqi Li, Niek Wit, Dennis Vitkup, Arthur Kaser, Paul Lehner, James Nathan . 2023. A HIF independent oxygen-sensitive pathway for controlling cholesterol synthesis.. Nature communications. 14 (1) :4816 ▶ Go to Pubmed

Zhengyu Jiang, Feijing Wu, Pasquale Laise, Tanaka Takayuki, Fu Na, Woosook Kim, Hiroki Kobayashi, Wenju Chang, Ryota Takahashi, Giovanni Valenti, Masaki Sunagawa, Ruth White, Marina Macchini, Bernhard Renz, Moritz Middelhoff, Yoku Hayakawa, Zinaida Dubeykovskaya, Xiangtian Tan, Timothy Chu, Karan Nagar, Yagnesh Tailor, Bryana Belin, Akanksha Anand, Samuel Asfaha, Michael Finlayson, Alina Iuga, Andrea Califano, Timothy Wang . 2023. Tff2 defines transit-amplifying pancreatic acinar progenitors that lack regenerative potential and are protective against Kras-driven carcinogenesis.. Cell stem cell. 30 (8) :1091-1109.e7 ▶ Go to Pubmed

Kartikeya Nagendra, Adrien Izzet, Nicolas Judd, Ruben Zakine, Leah Friedman, Oliver Harrison, Léa-Laetitia Pontani, Lawrence Shapiro, Barry Honig, Jasna Brujic . 2023. Push-pull mechanics of E-cadherin ectodomains in biomimetic adhesions.. Biophysical journal. 122 (17) :3506-3515 ▶ Go to Pubmed

Jia Li, Alessandro Vasciaveo, Dimitrios Karagiannis, Zhen Sun, Xiao Chen, Fabio Socciarelli, Ziv Frankenstein, Min Zou, Tania Pannellini, Yu Chen, Kevin Gardner, Brian Robinson, Johann de Bono, Cory Abate-Shen, Mark Rubin, Massimo Loda, Charles Sawyers, Andrea Califano, Chao Lu, Michael Shen . 2023. NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Mara De Martino, Camille Daviaud, Hanna Minns, Artur Lazarian, Anja Wacker, Ana Costa, Nabeel Attarwala, Qiuying Chen, Seung-Won Choi, Raul Rabadan, Laura McIntire, Robyn Gartrell, James Kelly, Evagelia Laiakis, Claire Vanpouille-Box . 2023. Radiation therapy promotes unsaturated fatty acids to maintain survival of glioblastoma.. Cancer letters. 570 :216329 ▶ Go to Pubmed

Guojie Zhong, Yoolim Choi, Yufeng Shen . 2023. VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants.. Communications biology. 6 (1) :774 ▶ Go to Pubmed

Zhengping Shao, Brian Lee, Hanwen Zhang, Xiaohui Lin, Chen Li, Wenxia Jiang, Napon Chirathivat, Steven Gershik, Michael Shen, Richard Baer, Shan Zha . 2023. Inactive PARP1 causes embryonic lethality and genome instability in a dominant-negative manner.. Proceedings of the National Academy of Sciences of the United States of America. 120 (31) :e2301972120 ▶ Go to Pubmed

Rei Matsumoto, Joshua Gray, Ksenia Rybkina, Hanna Oppenheimer, Lior Levy, Lilach Friedman, Muhammad Khamaisi, Wenzhao Meng, Aaron Rosenfeld, Rebecca Guyer, Marissa Bradley, David Chen, Mark Atkinson, Todd Brusko, Maigan Brusko, Thomas Connors, Eline Prak, Uri Hershberg, Peter Sims, Tomer Hertz, Donna Farber . 2023. Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity.. Nature immunology. 24 (8) :1370-1381 ▶ Go to Pubmed

Quinn Solfisburg, Federico Baldini, Brittany Baldwin-Hunter, Harry Lee, Heekuk Park, Daniel Freedberg, Charles Lightdale, Tal Korem, Julian Abrams . 2023. The Salivary Microbiome and Predicted Metabolite Production are Associated with Progression from Barrett's Esophagus to Esophageal Adenocarcinoma.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Thomas Connors, Rei Matsumoto, Shivali Verma, Peter Szabo, Rebecca Guyer, Joshua Gray, Zicheng Wang, Puspa Thapa, Pranay Dogra, Maya Poon, Ksenia Rybkina, Marissa Bradley, Emma Idzikowski, James McNichols, Masaru Kubota, Kalpana Pethe, Yufeng Shen, Mark Atkinson, Maigan Brusko, Todd Brusko, Andrew Yates, Peter Sims, Donna Farber . 2023. Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood.. Immunity. 56 (8) :1894-1909.e5 ▶ Go to Pubmed

Kaja Kostyrko, Marta Román, Alex Lee, David Simpson, Phuong Dinh, Stanley Leung, Kieren Marini, Marcus Kelly, Joshua Broyde, Andrea Califano, Peter Jackson, Alejandro Sweet-Cordero . 2023. UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma.. Nature communications. 14 (1) :3966 ▶ Go to Pubmed

Jaewon Min, Junfei Zhao, Jennifer Zagelbaum, Jina Lee, Sho Takahashi, Portia Cummings, Allana Schooley, Job Dekker, Max Gottesman, Raul Rabadan, Jean Gautier . 2023. Mechanisms of insertions at a DNA double-strand break.. Molecular cell. 83 (14) :2434-2448.e7 ▶ Go to Pubmed

Alina Sergeeva, Phinikoula Katsamba, Junzhuo Liao, Jared Sampson, Fabiana Bahna, Seetha Mannepalli, Nicholas Morano, Lawrence Shapiro, Richard Friesner, Barry Honig . 2023. Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity.. Journal of molecular biology. 435 (15) :168187 ▶ Go to Pubmed

Demis Menolfi, Brian Lee, Hanwen Zhang, Wenxia Jiang, Nicole Bowen, Yunyue Wang, Junfei Zhao, Antony Holmes, Steven Gershik, Raul Rabadan, Baek Kim, Shan Zha . 2023. ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion.. Nature communications. 14 (1) :3618 ▶ Go to Pubmed

Qi Yan, Rafael Guerrero, Raiyan Khan, Andy Surujnarine, Ronald Wapner, Matthew Hahn, Anita Raja, Ansaf SallebAouissi, William Grobman, Hyagriv Simhan, Nathan Blue, Robert Silver, Judith Chung, Uma Reddy, Predrag Radivojac, Itsik Pe'er, David Haas . 2023. Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed

Kensuke Sugiura, Yasunori Masuike, Kensuke Suzuki, Alice Shin, Nozomu Sakai, Hisahiro Matsubara, Masayuki Otsuka, Peter Sims, Christopher Lengner, Anil Rustgi . 2023. LIN28B promotes cell invasion and colorectal cancer metastasis via CLDN1 and NOTCH3.. JCI insight. 8 (14) ▶ Go to Pubmed

Demis Menolfi, Brian Lee, Hanwen Zhang, Wenxia Jiang, Nicole Bowen, Yunyue Wang, Junfei Zhao, Antony Holmes, Steven Gershik, Raul Rabadan, Baek Kim, Shan Zha . 2023. ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Norio Miyamura, Kodai Suzuki, Richard Friedman, Aristidis Floratos, Yuki Kunisada, Kazuya Masuda, Andrew Lowy, Moriya Tsuji, Kazuki Sugahara . 2023. A pancreatic cancer mouse model with human immunity.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Jie Ding, Sung-Jin Lee, Lukas Vlahos, Kanako Yuki, Cara Rada, Vincent van Unen, Meghah Vuppalapaty, Hui Chen, Asmiti Sura, Aaron McCormick, Madeline Tomaske, Samira Alwahabi, Huy Nguyen, William Nowatzke, Lily Kim, Lisa Kelly, Douglas Vollrath, Andrea Califano, Wen-Chen Yeh, Yang Li, Calvin Kuo . 2023. Therapeutic blood-brain barrier modulation and stroke treatment by a bioengineered FZD-selective WNT surrogate in mice.. Nature communications. 14 (1) :2947 ▶ Go to Pubmed

Michael Honigberg, Buu Truong, Raiyan Khan, Brenda Xiao, Laxmi Bhatta, Ha Vy, Rafael Guerrero, Art Schuermans, Margaret Selvaraj, Aniruddh Patel, Satoshi Koyama, So Cho, Shamsudheen Vellarikkal, Mark Trinder, Sarah Urbut, Kathryn Gray, Ben Brumpton, Snehal Patil, Sebastian Zöllner, Mariah Antopia, Richa Saxena, Girish Nadkarni, Ron Do, Qi Yan, Itsik Pe'er, Shefali Verma, Rajat Gupta, David Haas, Hilary Martin, David van Heel, Triin Laisk, Pradeep Natarajan . 2023. Polygenic prediction of preeclampsia and gestational hypertension.. Nature medicine. ▶ Go to Pubmed

Celine Schreidah, George Reynolds, Lauren Fahmy, Richard Carvajal, Maarten Vermeer, Sean Whittaker, Itsik Pe'er, Larisa Geskin . 2023. Scoping review of genetic databases for rare dermatologic diseases: Opportunity for artificial intelligence and machine learning.. JAAD international. 12 :24-31 ▶ Go to Pubmed

Somnath Tagore, Samuel Tsang, Gordon Mills, Andrea Califano . 2023. Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Min Jang, Parth Patel, Alexandre Pereira, Jon Willcox, Alireza Haghighi, Angela Tai, Kaoru Ito, Sarah Morton, Joshua Gorham, David McKean, Steven DePalma, Daniel Bernstein, Martina Brueckner, Wendy Chung, Alessandro Giardini, Elizabeth Goldmuntz, Jonathan Kaltman, Richard Kim, Jane Newburger, Yufeng Shen, Deepak Srivastava, Martin Tristani-Firouzi, Bruce Gelb, George Porter, Christine Seidman, Jonathan Seidman . 2023. Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease.. Circulation. Genomic and precision medicine. 16 (3) :224-231 ▶ Go to Pubmed

Luz Zapater, Elias Rodriguez-Fos, Merce Planas-Felix, Sara Lewis, Daniel Cameron, Phillip Demarest, Anika Nabila, Junfei Zhao, Paul Bergin, Casie Reed, Makiko Yamada, Alex Pagnozzi, Caroline Nava, Emilie Bourel-Ponchel, Derek Neilson, Ali Dursun, Köksal Özgül, Halil Akar, Nicholas Socci, Matthew Hayes, Raul Rabadan, David Torrents, Michael Kruer, Miklos Toth, Alex Kentsis . 2023. A transposase-derived gene required for human brain development.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Alistair Dunham, Pedro Beltrao, Mohammed AlQuraishi . 2023. High-throughput deep learning variant effect prediction with Sequence UNET.. Genome biology. 24 (1) :110 ▶ Go to Pubmed

Lara Tshering, Fu Luo, Savanah Russ, Mariola Szenk, Diana Rubel, Karis Tutuska, James Rail, Gábor Balázsi, Michael Shen, Flaminia Talos . 2023. Immune mechanisms shape the clonal landscape during early progression of prostate cancer.. Developmental cell. ▶ Go to Pubmed

Osama Al-Dalahmah, Michael Argenziano, Adithya Kannan, Aayushi Mahajan, Julia Furnari, Fahad Paryani, Deborah Boyett, Akshay Save, Nelson Humala, Fatima Khan, Juncheng Li, Hong Lu, Yu Sun, John Tuddenham, Alexander Goldberg, Athanassios Dovas, Matei Banu, Tejaswi Sudhakar, Erin Bush, Andrew Lassman, Guy McKhann, Brian Gill, Brett Youngerman, Michael Sisti, Jeffrey Bruce, Peter Sims, Vilas Menon, Peter Canoll . 2023. Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states.. Nature communications. 14 (1) :2586 ▶ Go to Pubmed

Liyuan Liu, Yiming Huang, Harris Wang . 2023. Fast and efficient template-mediated synthesis of genetic variants.. Nature methods. 20 (6) :841-848 ▶ Go to Pubmed

Aleksandar Obradovic, Casey Ager, Mikko Turunen, Thomas Nirschl, Mohsen Khosravi-Maharlooei, Alina Iuga, Christopher Jackson, Srinivasan Yegnasubramanian, Lorenzo Tomassoni, Ester Fernandez, Patrick McCann, Meri Rogava, Angelo DeMarzo, Christina Kochel, Mohamad Allaf, Trinity Bivalacqua, Michael Lim, Ronald Realubit, Charles Karan, Charles Drake, Andrea Califano . 2023. Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators.. Cancer cell. 41 (5) :933-949.e11 ▶ Go to Pubmed

Benjamin Hobson, Adrien Stanley, Mark Santos, Bruce Culbertson, Eugene Mosharov V, Peter Sims, David Sulzer . 2023. Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain.. Brain, behavior, and immunity. 111 :277-291 ▶ Go to Pubmed

Yun Lin, Daniel Mallia, Andrea Clark-Sevilla, Adam Catto, Alisa Leshchenko, Qi Yan, David Haas, Ronald Wapner, Itsik Pe'er, Anita Raja, Ansaf Salleb-Aouissi . 2023. A Comprehensive and Bias-Free Machine Learning Approach for Risk Prediction of Preeclampsia with Severe Features in a Nulliparous Study Cohort.. Research square. ▶ Go to Pubmed

Elphège Nora, Stein Aerts, Patricia Wittkopp, Harmen Bussemaker, Martha Bulyk, Saurabh Sinha, Julia Zeitlinger, Justin Crocker, Juan Bass . 2023. Emerging questions in transcriptional regulation.. Cell systems. 14 (4) :247-251 ▶ Go to Pubmed

Prabhjot Mundi, Filemon Cruz, Adina Grunn, Daniel Diolaiti, Audrey Mauguen, Allison Rainey, Kristina Guillan, Armaan Siddiquee, Daoqi You, Ronald Realubit, Charles Karan, Michael Ortiz V, Eugene Douglass, Melissa Accordino, Suzanne Mistretta, Frances Brogan, Jeffrey Bruce, Cristina Caescu, Richard Carvajal, Katherine Crew, Guarionex Decastro, Mark Heaney, Brian Henick, Dawn Hershman, June Hou, Fabio Iwamoto, Joseph Jurcic, Ravi Kiran, Michael Kluger, Teri Kreisl, Nicole Lamanna, Andrew Lassman, Emerson Lim, Gulam Manji, Guy McKhann, James McKiernan, Alfred Neugut, Kenneth Olive, Todd Rosenblat, Gary Schwartz, Catherine Shu, Michael Sisti, Ana Tergas, Reena Vattakalam, Mary Welch, Sven Wenske, Jason Wright, Peter Canoll, Hanina Hibshoosh, Kevin Kalinsky, Mahalaxmi Aburi, Peter Sims, Mariano Alvarez, Andrew Kung, Andrea Califano . 2023. A Transcriptome-Based Precision Oncology Platform for Patient-Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies.. Cancer discovery. 13 (6) :1386-1407 ▶ 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. Author Correction: Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.. Nature structural & molecular biology. ▶ Go to Pubmed

Yufeng Shen, Qingming Tang, Jiajia Wang, Zheng Zhou, Ying Yin, Yifan Zhang, Wenhao Zheng, Xinyuan Wang, Guangjin Chen, Jiwei Sun, Lili Chen . 2023. Targeting RORα in macrophages to boost diabetic bone regeneration.. Cell proliferation. :e13474 ▶ Go to Pubmed

Sara Viragova, Luis Aparicio, Pierangela Palmerini, Junfei Zhao, Luis Salazar, Alexandra Schurer, Anika Dhuri, Debashis Sahoo, Christopher Moskaluk, Raul Rabadan, Piero Dalerba . 2023. Inverse agonists of RAR/RXR signaling as lineage-specific anti-tumor agents against human Adenoid Cystic Carcinoma.. Journal of the National Cancer Institute. ▶ Go to Pubmed

Hubert Pakula, Mohamed Omar, Ryan Carelli, Filippo Pederzoli, Giuseppe Fanelli, Tania Pannellini, Lucie Van Emmenis, Silvia Rodrigues, Caroline Fidalgo-Ribeiro, Pier Nuzzo V, Nicholas Brady, Madhavi Jere, Caitlin Unkenholz, Mohammad Alexanderani, Francesca Khani, Francisca de Almeida, Cory Abate-Shen, Matthew Greenblatt, David Rickman, Christopher Barbieri, Brian Robinson, Luigi Marchionni, Massimo Loda . 2023. Distinct mesenchymal cell states mediate prostate cancer progression.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Guangjin Chen, Qingming Tang, Shaoling Yu, Yufeng Shen, Jiwei Sun, Jinfeng Peng, Ying Yin, Guangxia Feng, Xiaofeng Lu, Gang Mei, Yifan Zhang, Qian Wan, Luoying Zhang, Lili Chen . 2023. Developmental growth plate cartilage formation suppressed by artificial light at night via inhibiting BMAL1-driven collagen hydroxylation.. Cell death and differentiation. 30 (6) :1503-1516 ▶ Go to Pubmed

Arvind Ravi, Matthew Hellmann, Monica Arniella, Mark Holton, Samuel Freeman, Vivek Naranbhai, Chip Stewart, Ignaty Leshchiner, Jaegil Kim, Yo Akiyama, Aaron Griffin, Natalie Vokes, Mustafa Sakhi, Vashine Kamesan, Hira Rizvi, Biagio Ricciuti, Patrick Forde, Valsamo Anagnostou, Jonathan Riess, Don Gibbons, Nathan Pennell, Vamsidhar Velcheti, Subba Digumarthy, Mari Mino-Kenudson, Andrea Califano, John Heymach V, Roy Herbst, Julie Brahmer, Kurt Schalper, Victor Velculescu, Brian Henick, Naiyer Rizvi, Pasi Jänne, Mark Awad, Andrew Chow, Benjamin Greenbaum, Marta Luksza, Alice Shaw, Jedd Wolchok, Nir Hacohen, Gad Getz, Justin Gainor . 2023. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer.. Nature genetics. 55 (5) :807-819 ▶ Go to Pubmed

Tomasz Owczarek, Takashi Kobayashi, Ricardo Ramirez, Lijie Rong, Anna Puzio-Kuter, Gopa Iyer, Min Teo, Francisco Sanchez-Vega, Jingqiang Wang, Nikolaus Schultz, Tian Zheng, David Solit, Hikmat Al-Ahmadie, Cory Abate-Shen . 2023. Correction: ARF Confers a Context-Dependent Response to Chemotherapy in Muscle-Invasive Bladder Cancer.. Cancer research. 83 (7) :1159 ▶ Go to Pubmed

Nicola Floc'h, Carolyn Kinkade, Takashi Kobayashi, Alvaro Aytes, Celine Lefebvre, Antonina Mitrofanova, Robert Cardiff, Andrea Califano, Michael Shen, Cory Abate-Shen . 2023. Editor's Note: Dual Targeting of the Akt/mTOR Signaling Pathway Inhibits Castration-Resistant Prostate Cancer in a Genetically Engineered Mouse Model.. Cancer research. 83 (7) :1160 ▶ Go to Pubmed

Xuesong Ouyang, Walter Jessen, Hikmat Al-Ahmadie, Angel Serio, Yong Lin, Weichung-Joseph Shih, Victor Reuter, Peter Scardino, Michael Shen, Bruce Aronow, Andrew Vickers, William Gerald, Cory Abate-Shen . 2023. Editor's Note: Activator Protein-1 Transcription Factors Are Associated with Progression and Recurrence of Prostate Cancer.. Cancer research. 83 (7) :1161 ▶ Go to Pubmed

Vincent FitzPatrick, Christ Leemans, Joris van Arensbergen, Bas van Steensel, Harmen Bussemaker . 2023. Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR.. Nucleic acids research. ▶ Go to Pubmed

L Khoo, D McComas, J Rankin, M Shen, T Sharma, C Shi . 2023. Compensating for gyroradius effects in beamlines with small Helmholtz coils.. The Review of scientific instruments. 94 (3) :035102 ▶ Go to Pubmed

Carlo Maurer, Alvaro Curiel-Garcia, Sam Holmstrom, Pasquale Laise, Carmine Palermo, Steven Sastra, Anthony Andren, Zhang Li, Tessa LeLarge, Irina Sagalovskiy, Daniel Ross, Vilma Rosario, Kate Lu, Ethan Ferraiuolo, Nicholas Spinosa, Winston Wong, Kaitlin Shaw, John Chabot, Jeanine Genkinger, Hanina Hibshoosh, Gulam Manji, Alina Iuga, Roland Schmid, Michael Badgley, Kristen Johnson, Andrea Califano, Costas Lyssiotis, Kenneth Olive . 2023. Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Diego Gelsinger, Phuc Vo, Sanne Klompe, Carlotta Ronda, Harris Wang, Samuel Sternberg . 2023. Bacterial genome engineering using CRISPR RNA-guided transposases.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed

Aaron Griffin, Lukas Vlahos, Codruta Chiuzan, Andrea Califano . 2023. NaRnEA: An Information Theoretic Framework for Gene Set Analysis.. Entropy (Basel, Switzerland). 25 (3) ▶ Go to Pubmed

Sitara Persad, Zi-Ning Choo, Christine Dien, Noor Sohail, Ignas Masilionis, Ronan Chaligne, Tal Nawy, Chrysothemis Brown, Roshan Sharma, Itsik Pe'er, Manu Setty, Dana Pe'er . 2023. SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data.. Nature biotechnology. ▶ Go to Pubmed

Zhenyi Su, Ning Kon, Jingjie Yi, Haiqing Zhao, Wanwei Zhang, Qiaosi Tang, Huan Li, Hiroki Kobayashi, Zhiming Li, Shoufu Duan, Yanqing Liu, Kenneth Olive, Zhiguo Zhang, Barry Honig, James Manfredi, Anil Rustgi, Wei Gu . 2023. Specific regulation of BACH1 by the hotspot mutant p53 reveals a distinct gain-of-function mechanism.. Nature cancer. 4 (4) :564-581 ▶ 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. Erratum to "B7-H3 as a Therapeutic Target in Advanced Prostate Cancer" [Eur Urol 2023;83(3):224-38].. European urology. 83 (6) :e168-e169 ▶ Go to Pubmed

Balaji Santhanam, Panos Oikonomou, Saeed Tavazoie . 2023. Systematic assessment of prognostic molecular features across cancers.. Cell genomics. 3 (3) :100262 ▶ Go to Pubmed

Crismita Dmello, Junfei Zhao, Li Chen, Andrew Gould, Brandyn Castro, Víctor Arrieta, Daniel Zhang, Kwang-Soo Kim, Deepak Kanojia, Peng Zhang, Jason Miska, Ragini Yeeravalli, Karl Habashy, Ruth Saganty, Seong Kang, Jawad Fares, Connor Liu, Gavin Dunn, Elizabeth Bartom, Matthew Schipma, Patrick Hsu, Mahmoud Alghamri, Maciej Lesniak, Amy Heimberger, Raul Rabadan, Catalina Lee-Chang, Adam Sonabend . 2023. Checkpoint kinase 1/2 inhibition potentiates anti-tumoral immune response and sensitizes gliomas to immune checkpoint blockade.. Nature communications. 14 (1) :1566 ▶ Go to Pubmed

Jason Kirk, Jie Wang, Amanda Tracz, Mark Long, Spencer Rosario, Yibing Ji, Rahul Kumar, Xiaozhuo Liu, Prashant Singh, Igor Puzanov, Gurkamal Chatta, Qing Cheng, Jiaoti Huang, Jeffrey Wrana, Jonathan Lovell, Han Yu, Song Liu, Michael Shen, Tao Liu, Dean Tang . 2023. Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells.. bioRxiv : the preprint server for biology. ▶ 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.. Journal of molecular biology. 435 (14) :168052 ▶ Go to Pubmed

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

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

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

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

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

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

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

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

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