Publications

Julien Hédou, Ivana Marić, Grégoire Bellan, Jakob Einhaus, Dyani K. Gaudillière, Francois-Xavier Ladant, Franck Verdonk, Ina A. Stelzer, Dorien Feyaerts, Amy S. Tsai, Edward A. Ganio, Maximilian Sabayev, Joshua Gillard, Jonas Amar, Amelie Cambriel, Tomiko T. Oskotsky, Alennie Roldan, Jonathan L. Golob, Marina Sirota, Thomas A. Bonham, Masaki Sato, Maïgane Diop, Xavier Durand, Martin S. Angst, David K. Stevenson, Nima Aghaeepour, Andrea Montanari, Brice Gaudillière (2024). Discovery of sparse, reliable omic biomarkers with Stabl. Nature Biotechnology.

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Jonathan L. Golob, Tomiko T. Oskotsky, Alice S. Tang, Alennie Roldan, Verena Chung, Connie W. Y. Ha, Ronald J. Wong, Kaitlin J. Flynn, Antonio Parraga-Leo, Camilla Wibrand, Samuel S. Minot, Boris Oskotsky, Gaia Andreoletti, Idit Kosti, Julie Bletz, Amber Nelson, Jifan Gao, Zhoujingpeng Wei, Guanhua Chen, Zheng-Zheng Tang, Pierfrancesco Novielli, Donato Romano, Ester Pantaleo, Nicola Amoroso, Alfonso Monaco, Mirco Vacca, Maria De Angelis, Roberto Bellotti, Sabina Tangaro, Abigail Kuntzleman, Isaac Bigcraft, Stephen Techtmann, Daehun Bae, Eunyoung Kim, Jongbum Jeon, Soobok Joe, Preterm Birth DREAM Community, Kevin R. Theis, Sherrianne Ng, Yun S. Lee, Patricia Diaz-Gimeno, Phillip R. Bennett, David A. MacIntyre, Gustavo Stolovitzky, Susan V. Lynch, Jake Albrecht, Nardhy Gomez-Lopez, Roberto Romero, David K. Stevenson, Nima Aghaeepour, Adi L. Tarca, James C. Costello, Marina Sirota (2023). Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Reports. Medicine.

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Jonathan Golob, Krishna Rao, Jeffrey A. Berinstein, William D. Chey, Chung Owyang, Nobuhiko Kamada, Peter D.R. Higgins, Vincent Young, Shrinivas Bishu, Allen A. Lee (2023). The Microbiome in Quiescent Crohn’s Disease with Persistent Symptoms Show Disruptions in Microbial Sulfur and Tryptophan Pathways. Gastro Hep Advances.

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Samuel S. Minot, Bailey Garb, Alennie Roldan, Alice S. Tang, Tomiko T. Oskotsky, Christopher Rosenthal, Noah G. Hoffman, Marina Sirota, Jonathan L. Golob (2023). MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies. Cell Reports Methods.

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Mary M. Riwes, Jonathan L. Golob, John Magenau, Mengrou Shan, Gregory Dick, Thomas Braun, Thomas M. Schmidt, Attaphol Pawarode, Sarah Anand, Monalisa Ghosh, John Maciejewski, Darren King, Sung Choi, Gregory Yanik, Marcus Geer, Ethan Hillman, Costas A. Lyssiotis, Muneesh Tewari, Pavan Reddy (2023). Feasibility of a dietary intervention to modify gut microbial metabolism in patients with hematopoietic stem cell transplantation. Nature Medicine.

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Jonathan Golob, Krishna Rao, Jeffrey Berinstein, William Chey, Chung Owyang, Nobuhiko Kamada, Peter Higgins, Vincent Young, Shrinivas Bishu, Allen Lee (2023). The Fecal Microbiome in Quiescent Crohn's Disease with Persistent Gastrointestinal Symptoms Show Enrichment of Oral Microbes But Depletion of Butyrate and Indole Producers. medRxiv: The Preprint Server for Health Sciences.

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Jonathan L. Golob (2023). Human Microbiomes and Disease for the Biomedical Data Scientist. Annual Review of Biomedical Data Science.

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Emma Lauder, Jonathan L Golob (2022). 504. Latent HHV7 Infection Attenuates Beneficial Host-Microbe Interactions in the Human Gut. Open Forum Infectious Diseases.

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Michael E. Bowdish, Christina E. Barkauskas, Jessica R. Overbey, Robert L. Gottlieb, Keren Osman, Abhijit Duggal, Mary E. Marks, Jonathan Hupf, Eustace Fernandes, Bradley G. Leshnower, Jonathan L. Golob, Alexander Iribarne, Athos J. Rassias, Ellen G. Moquete, Karen O’Sullivan, Helena L. Chang, Judson B. Williams, Sam Parnia, Nirav C. Patel, Nimesh D. Desai, Andrew M. Vekstein, Beth A. Hollister, Tammie Possemato, Christian Romero, Peter C. Hou, Elizabeth Burke, Jack Hayes, Fred Grossman, Silviu Itescu, Marc Gillinov, Francis D. Pagani, Patrick T. O’Gara, Michael J. Mack, Peter K. Smith, Emilia Bagiella, Alan J. Moskowitz, Annetine C. Gelijns (2022). A Randomized Trial of Mesenchymal Stromal Cells for Moderate to Severe ARDS From COVID-19. American Journal of Respiratory and Critical Care Medicine.

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Kohei Sugihara, Sho Kitamoto, Prakaimuk Saraithong, Hiroko Nagao-Kitamoto, Matthew Hoostal, Caroline McCarthy, Alexandra Rosevelt, Chithra K. Muraleedharan, Merritt G. Gillilland, Jin Imai, Maiko Omi, Shrinivas Bishu, John Y. Kao, Christopher J. Alteri, Nicolas Barnich, Thomas M. Schmidt, Asma Nusrat, Naohiro Inohara, Jonathan L. Golob, Nobuhiko Kamada (2022). Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction. Cell Reports.

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Matthew J. Pianko, Jonathan L. Golob (2022). Host-microbe interactions and outcomes in multiple myeloma and hematopoietic stem cell transplantation. Cancer Metastasis Reviews.

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Jin Imai, Hitoshi Ichikawa, Sho Kitamoto, Jonathan L. Golob, Motoki Kaneko, Junko Nagata, Miho Takahashi, Merritt G. Gillilland, Rika Tanaka, Hiroko Nagao-Kitamoto, Atsushi Hayashi, Kohei Sugihara, Shrinivas Bishu, Shingo Tsuda, Hiroyuki Ito, Seiichiro Kojima, Kazunari Karakida, Masashi Matsushima, Takayoshi Suzuki, Katsuto Hozumi, Norihito Watanabe, William V. Giannobile, Takayuki Shirai, Hidekazu Suzuki, Nobuhiko Kamada (2021). A potential pathogenic association between periodontal disease and Crohn's disease. JCI insight.

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Roberto J. Cieza, Jonathan L. Golob, Justin A. Colacino, Christiane E. Wobus (2021). Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses. Viruses.

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Jonathan L. Golob, Njira Lugogo, Adam S. Lauring, Anna S. Lok (2021). SARS-CoV-2 vaccines: a triumph of science and collaboration. JCI insight.

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Samuel S. Minot, Kevin C. Barry, Caroline Kasman, Jonathan L. Golob, Amy D. Willis (2021). geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response. Genome Biology.

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Jonathan L. Golob, Krishna Rao (2021). Signal vs. noise: how to analyze the microbiome and make progress on antimicrobial resistance. The Journal of Infectious Diseases.

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Amy E. Chang, Jonathan L. Golob, Thomas M. Schmidt, Daniel C. Peltier, Christopher D. Lao, Muneesh Tewari (2021). Targeting the Gut Microbiome to Mitigate Immunotherapy-Induced Colitis in Cancer. Trends in Cancer.

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Cathy A. Goldstein, Muneer Rizvydeen, Deirdre A. Conroy, Louise M. O’Brien, Gita Gupta, Emily C. Somers, Pratima Sharma, Jonathan L. Golob, Jonathan P. Troost, Helen J. Burgess (2021). The prevalence and impact of pre-existing sleep disorder diagnoses and objective sleep parameters in patients hospitalized for COVID-19. Journal of clinical sleep medicine: JCSM: official publication of the American Academy of Sleep Medicine.

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Jonathan Louis Golob, Samuel Schwartz Minot (2020). In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision. BMC bioinformatics.

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Elizabeth R. Duke, Brian D. Williamson, Bhavesh Borate, Jonathan L. Golob, Chiara Wychera, Terry Stevens-Ayers, Meei-Li Huang, Nicole Cossrow, Hong Wan, T. Christopher Mast, Morgan A. Marks, Mary Flowers, Keith R. Jerome, Lawrence Corey, Peter B. Gilbert, Joshua T. Schiffer, Michael Boeckh (2020). Cytomegalovirus viral load kinetics as surrogate endpoints after allogeneic transplantation. The Journal of Clinical Investigation.

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Pratima Sharma, Vincent Chen, Christopher M. Fung, Jonathan P. Troost, Vaiibhav N. Patel, Michael Combs, Silas Norman, Puneet Garg, Monica Colvin, Keith Aaronson, Christopher J. Sonnenday, Jonathan L. Golob, Emily C. Somers, Mona M. Doshi (2020). COVID-19 Outcomes Among Solid Organ Transplant Recipients: A Case-Control Study. Transplantation.

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Emily C Somers, Gregory A Eschenauer, Jonathan P Troost, Jonathan L Golob, Tejal N Gandhi, Lu Wang, Nina Zhou, Lindsay A Petty, Ji Hoon Baang, Nicholas O Dillman, David Frame, Kevin S Gregg, Dan R Kaul, Jerod Nagel, Twisha S Patel, Shiwei Zhou, Adam S Lauring, David A Hanauer, Emily Martin, Pratima Sharma, Christopher M Fung, Jason M Pogue (2020). Tocilizumab for treatment of mechanically ventilated patients with COVID-19. Clinical Infectious Diseases.

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Jonathan L. Golob, Martha M. DeMeules, Tillie Loeffelholz, Z. Z. Quinn, Michael K. Dame, Sabrina S. Silvestri, Michael C. Wu, Thomas M. Schmidt, Tina L. Fiedler, Matthew J. Hoostal, Marco Mielcarek, Jason Spence, Steven A. Pergam, David N. Fredricks (2019). Butyrogenic bacteria after acute graft-versus-host disease (GVHD) are associated with the development of steroid-refractory GVHD. Blood Advances.

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