Search 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
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
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
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
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
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
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. :e003924 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
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
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
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
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
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
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
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
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
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