James Broach

Distinguished Professor and Chair of Biochemistry and Molecular Biology

James Broach

Huck Affiliations

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Publication Tags

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Genome Yeasts Degradation Oxidative Stress Yeast Nucleotides Neoplasms Amyotrophic Lateral Sclerosis Ribose Genes Mutation Type 1 Diabetes Mellitus Salvaging Genomics Pancreatitis Dna Binding Proteins Neuroglia Mutagenesis Carbon Retroelements Phosphates Cells Transcription Factors Nutrients Chromosomes

Most Recent Publications

mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis

Mercedeh Movassagh, Sarah U. Morton, Christine Hehnly, Jasmine Smith, Trang T. Doan, Rafael Irizarry, James R. Broach, Steven J. Schiff, Jeffrey A. Bailey, Joseph N. Paulson, 2022, BMC Genomics

Differential richness inference for 16S rRNA marker gene surveys

M. Senthil Kumar, Eric V. Slud, Christine Hehnly, Lijun Zhang, James Broach, Rafael A. Irizarry, Steven Schiff, Joseph N. Paulson, 2022, Genome Biology

Cell environment shapes TDP-43 function with implications in neuronal and muscle disease

Urša Šušnjar, Neva Škrabar, Anna Leigh Brown, Yasmine Abbassi, Hemali Phatnani, H. Phatnani, P. Fratta, J. Kwan, D. Sareen, J. R. Broach, Z. Simmons, X. Arcila-Londono, E. B. Lee, V. M. Van Deerlin, N. A. Shneider, E. Fraenkel, L. W. Ostrow, F. Baas, J. D. Berry, O. Butovsky, R. H. Baloh, Ophir Shalem, T. Heiman-Patterson, L. Stefanis, S. Chandran, S. Pal, C. Smith, A. Malaspina, M. G. Hammell, N. A. Patsopoulos, J. Dubnau, M. Poss, B. Zhang, N. Zaitlen, E. Hornstein, T. M. Miller, E. Dardiotis, R. Bowser, V. Menon, M. Harms, N. Atassi, D. J. Lange, D. J. MacGowan, C. McMillan, E. Aronica, B. Harris, J. Ravits, J. Crary, L. M. Thompson, T. Raj, 2022, Communications Biology

Rare MYC-N11S germline mutation indicative of inherited breast cancer in a multigeneration family

Laura Budurlean, Maria Baker, James Broach, 2022, BMJ Case Reports

Subtype-specific 3D genome alteration in acute myeloid leukaemia

Jie Xu, Fan Song, Huijue Lyu, Mikoto Kobayashi, Baozhen Zhang, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Josiah Hiu yuen Wong, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Hongbo Yang, Ross C. Hardison, Sinisa Dovat, Leonidas C. Platanias, Yarui Diao, Yue Yang, Tomoko Yamada, Aaron D. Viny, Ross L. Levine, David Claxton, James R. Broach, Hong Zheng, Feng Yue, 2022, Nature on p. 387-398

Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer

Brandon Labarge, Max Hennessy, Lijun Zhang, David Goldrich, Scott Chartrand, Carson Purnell, Sage Wright, David Goldenberg, James R. Broach, 2022, Cell Growth and Differentiation on p. 1420-1428

NASHFit: A randomized controlled trial of an exercise training program to reduce clotting risk in patients with NASH

Jonathan G. Stine, Ian R. Schreibman, Alison J. Faust, Jessica Dahmus, Benjamin Stern, Christopher Soriano, Gloriany Rivas, Breianna Hummer, Scot R. Kimball, Nate R. Geyer, Vernon M. Chinchilli, Rohit Loomba, Kathryn Schmitz, Christopher Sciamanna, Cindy Strine, Rachel Wentzel, Sara Marlin, Chris Sica, Jeff Vesek, Elaine Eyster, Lawrence Sinoway, Kathy Bentz, Nancy Handley, Brenda Hershey Fell, Shirlynn Mottilla, Christine Christ, Susan George, Terry Novchich, Megan Beyer, Kofi Clarke, Tiffany Myers, Martha Glading-Steinruck, Karen Krok, Thomas Ma, Thomas Riley, Elizabeth Thompson, Heather Tressler, James Broach, Trang Doan, Sue Patrick, Syndi Reed, Chris Hamilton, Kristin Slavoski, Deborah Tregea, 2022, Hepatology on p. 172-185

Standard Operating Procedures for Biospecimen Collection, Processing, and Storage: From the Type 1 Diabetes in Acute Pancreatitis Consortium

Clive Wasserfall, Anne Marie Dyer, Cate Speake, Dana K. Andersen, Kendall Thomas Baab, Melena D. Bellin, James R. Broach, Martha Campbell-Thompson, Vernon M. Chinchilli, Peter J. Lee, Walter G. Park, Richard E. Pratley, Jami L. Saloman, Emily K. Sims, Gong Tang, Dhiraj Yadav, Cemal Yazici, Darwin L. Conwell, 2022, Pancreas on p. 593-597

Type 1 Diabetes in Acute Pancreatitis Consortium: From Concept to Reality

Jose Serrano, Maren R. Laughlin, Melena D. Bellin, Dhiraj Yadav, Vernon M. Chinchilli, Dana K. Andersen, Carla Greenbaum, Richard Kozarek, Cate Speake, Sandra Lord, Shayan Irani, Peter Linsley, William Kwok, Adam Lacy-Hulbert, Jessica Hamerman, Henry Bahnson, Brooke Grubb, Cassandra Williams, Sarah Ackermann, Kimberly Varner, Mark O. Goodarzi, Stephen J. Pandol, James Buxbaum, Marcio Diniz, Marc Goodman, O. Joe Hines, Christie Jeon, Murray Korc, Debiao Li, Maxim Petrov, Joseph Pisegna, Jennifer Van Eyk, Santhi Swaroop Vege, Evan Fogel, Carmella Evans-Molina, Temel Tirkes, Stuart Sherman, Jeffrey Easler, Zed Saeed, Emily Sims, Richard Oram, Michael Weedon, Vikesh Singh, Lan Kong, Dajiang Liu, Jennifer Maranki, Ariana Pichardo-Lowden, Nazia Raja-Khan, James Broach, David Bradley, 2022, Pancreas on p. 563-567

Cytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus

Christine Hehnly, Paddy Ssentongo, Lisa M. Bebell, Kathy Burgoine, Joel Bazira, Claudio Fronterre, Elias Kumbakumba, Ronald Mulondo, Edith Mbabazi-Kabachelor, Sarah U. Morton, Joseph Ngonzi, Moses Ochora, Peter Olupot-Olupot, John Mugamba, Justin Onen, Drucilla J. Roberts, Kathryn Sheldon, Shamim A. Sinnar, Jasmine Smith, Peter Ssenyonga, Julius Kiwanuka, Joseph N. Paulson, Frederick A. Meier, Jessica E. Ericson, James R. Broach, Steven J. Schiff, 2022, International Journal of Infectious Diseases on p. 24-33

Most-Cited Papers

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

Aude Nicolas, Kevin P. Kenna, Alan E. Renton, Nicola Ticozzi, Faraz Faghri, Ruth Chia, Janice A. Dominov, Brendan J. Kenna, Mike A. Nalls, Pamela Keagle, Alberto M. Rivera, Wouter van Rheenen, Natalie A. Murphy, Joke J.F.A. van Vugt, Joshua T. Geiger, Rick A. Van der Spek, Hannah A. Pliner, Shankaracharya, Bradley N. Smith, Giuseppe Marangi, Simon D. Topp, Yevgeniya Abramzon, Athina Soragia Gkazi, John D. Eicher, Aoife Kenna, Francesco O. Logullo, Isabella L. Simone, Giancarlo Logroscino, Fabrizio Salvi, Ilaria Bartolomei, Giuseppe Borghero, Maria Rita Murru, Emanuela Costantino, Carla Pani, Roberta Puddu, Carla Caredda, Valeria Piras, Stefania Tranquilli, Stefania Cuccu, Daniela Corongiu, Maurizio Melis, Antonio Milia, Francesco Marrosu, Maria Giovanna Marrosu, Gianluca Floris, Antonino Cannas, Margherita Capasso, Claudia Caponnetto, Zachary Simmons, James Broach, 2018, Neuron on p. 1268-1283.e6

Integrative detection and analysis of structural variation in cancer genomes

Jesse R. Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T. Le, Galip Gürkan Yardımcı, Abhijit Chakraborty, Darrin V. Bann, Yanli Wang, Royden Clark, Lijun Zhang, Hongbo Yang, Tingting Liu, Sriranga Iyyanki, Lin An, Christopher Pool, Takayo Sasaki, Juan Carlos Rivera-Mulia, Hakan Ozadam, Bryan R. Lajoie, Rajinder Kaul, Michael Buckley, Kristen Lee, Morgan Diegel, Dubravka Pezic, Christina Ernst, Suzana Hadjur, Duncan T. Odom, John A. Stamatoyannopoulos, James R. Broach, Ross C. Hardison, Ferhat Ay, William Stafford Noble, Job Dekker, David M. Gilbert, Feng Yue, 2018, Nature Genetics on p. 1388-1398

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

Oliver H. Tam, Nikolay V. Rozhkov, Regina Shaw, Duyang Kim, Isabel Hubbard, Samantha Fennessey, Nadia Propp, Hemali Phatnani, Justin Kwan, Dhruv Sareen, James R. Broach, Zachary Simmons, Ximena Arcila-Londono, Edward B. Lee, Vivianna M. Van Deerlin, Neil A. Shneider, Ernest Fraenkel, Lyle W. Ostrow, Frank Baas, Noah Zaitlen, James D. Berry, Andrea Malaspina, Pietro Fratta, Gregory A. Cox, Leslie M. Thompson, Steve Finkbeiner, Efthimios Dardiotis, Timothy M. Miller, Siddharthan Chandran, Suvankar Pal, Eran Hornstein, Daniel J. MacGowan, Terry Heiman-Patterson, Molly G. Hammell, Nikolaos A. Patsopoulos, Oleg Butovsky, Joshua Dubnau, Avindra Nath, Robert Bowser, Matt Harms, Eleonora Aronica, Mary Poss, Jennifer Phillips-Cremins, John Crary, Nazem Atassi, Dale J. Lange, Darius J. Adams, Leonidas Stefanis, Marc Gotkine, Robert Baloh, 2019, Cell Reports on p. 1164-1177.e5

Shared polygenic risk and causal inferences in amyotrophic lateral sclerosis

Sara Bandres-Ciga, Alastair J. Noyce, Gibran Hemani, Aude Nicolas, Andrea Calvo, Gabriele Mora, Alessandro Arosio, Marco Barberis, Ilaria Bartolomei, Stefania Battistini, Michele Benigni, Giuseppe Borghero, Maura Brunetti, Stefania Cammarosano, Antonino Cannas, Antonio Canosa, Margherita Capasso, Claudia Caponnetto, Carla Caredda, Paola Carrera, Federico Casale, Sebastiano Cavallaro, Adriano Chiò, Tiziana Colletti, Francesca L. Conforti, Amelia Conte, Lucia Corrado, Emanuela Costantino, Sandra D'Alfonso, Antonio Fasano, Cinzia Femiano, Carlo Ferrarese, Nicola Fini, Gianluca Floris, Giuseppe Fuda, Fabio Giannini, Maurizio Grassano, Antonio Ilardi, Vincenzo La Bella, Serena Lattante, Giancarlo Logroscino, Francesco O. Logullo, Daniela Loi, Christian Lunetta, Gianluigi Mancardi, Paola Mandich, Jessica Mandrioli, Umberto Manera, James Broach, Zachary Simmons, 2019, Annals of Neurology on p. 470-481

The Yeast Environmental Stress Response Regulates Mutagenesis Induced by Proteotoxic Stress

Erika Shor, Catherine A. Fox, James R. Broach, 2013, PLoS Genetics

Genetic heterogeneity of amyotrophic lateral sclerosis: Implications for clinical practice and research

Xiaowei W. Su, James Broach, James Connor, Glenn S. Gerhard, Zachary Simmons, 2014, Muscle and Nerve on p. 786-803

Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses

Natalia Petrenko, Razvan V. Chereji, Megan N. McClean, Alexandre V. Morozov, James R. Broach, 2013, Molecular Biology of the Cell on p. 2045-2057

The yeast genome undergoes significant topological reorganization in quiescence

Mark T. Rutledge, Mariano Russo, Jon Matthew Belton, Job Dekker, James R. Broach, 2015, Nucleic Acids Research on p. 8299-8313

Nucleotide degradation and ribose salvage in yeast

Yi Fan Xu, Fabien Létisse, Farnaz Absalan, Wenyun Lu, Ekaterina Kuznetsova, Greg Brown, Amy A. Caudy, Alexander F. Yakunin, James R. Broach, Joshua D. Rabinowitz, 2013, Molecular Systems Biology

An integrative ENCODE resource for cancer genomics

Jing Zhang, Donghoon Lee, Vineet Dhiman, Peng Jiang, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Shan Yu, Qin Cao, Arif Harmanci, Koon Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Rutenberg Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Yucheng T. Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessica Adrian, James R. Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert J. Klein, Michael Snyder, David M. Gilbert, Kevin Yip, Chao Cheng, Feng Yue, X. Shirley Liu, Kevin P. White, Mark Gerstein, 2020, Nature Communications