Search Publications

Filter Publications

2023

2023 Publications

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
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. :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
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
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
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
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
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
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. :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
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
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
Nazim Bouatta, Mohammed AlQuraishi .  2023.   Structural biology at the scale of proteomes.. Nature structural & molecular biology. 30 (2) :129-130 ▶ 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, 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
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
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
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
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
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