Gerber Lab

Recent (last five years)

• Chen RJ, Ding T, Ming YH, Chen B, Williamson DFK, Jaume G, Chen B, Zhang A, Shao D, Song AH, Shaban M, Williams M, Vaidya A, Sahai S, Oldenburg L, Weishaupt LL, Wang JJ, Williams W, Le LP, Gerber GK, Mahmood F. A General-Purpose Self-Supervised Model for Computational Pathology. arXiv:2308.15474.
• Ming YH, Chen B, Williamson DFK, Chen RJ, Liang I, Ding T, Jaume G, Odintsov I, Zhang A, Le LP, Gerber GK, Parwani AV, Mahmood F. Towards a Visual-Language Foundation Model for Computational Pathology. arXiv:2307.12914.
• Gerber GK, Bhattarai SK, Du M, Glickman MS, Bucci V. Discovery of Host-Microbiome Interactions Using Multi-Modal, Sparse, Time-Aware, Bayesian Network-Structured Neural Topic Models. International Conference on Machine Learning Workshop on Computational Biology, 2023.
• Uppal G, Urtecho G, Richardson M, Moody T, Wang HH, Gerber GK. MC-SPACE: Microbial communities from spatially associated counts engine. International Conference on Machine Learning Workshop on Computational Biology, 2023.
• Kim Y, Worby CJ, Acharya S, van Dijk LR, Alfonsetti D, Gromko Z, Azimzadeh P, Dodson K, Gerber GK, Hultgren S, Earl AM, Berger B, Gibson TE. Strain Tracking with Uncertainty Quantification. bioRxiv: https://doi.org/10.1101/2023.01.25.525531.
• Maringanti VS, Bucci V, Gerber GK. MDITRE: scalable and interpretable machine learning for predicting host status from temporal microbiome dynamics. mSystems. 2022 Sep 7:e0013222. doi: 10.1128/msystems.00132-22. Epub ahead of print. PMID: 36069455.
• Gibson TE, Kim Y, Acharya S, Kaplan DE, DiBenedetto N, Lavin R, Berger, Allegretti JR, Bry L, Gerber GK. Microbial dynamics inference at ecosystem-scale. bioRxiv 2021.12.14.469105.
• Dawkins JJ, Allegretti JR, Gibson TE, McClure E, Delaney M, Bry L, Gerber GK. Gut metabolites predict Clostridioides difficile recurrence. Microbiome. 2022 Jun 9;10(1):87. doi: 10.1186/s40168-022-01284-1. PMID: 35681218; PMCID: PMC9178838.
• Girinathan BP, DiBenedetto N, Worley JN, Peltier J, Arrieta-Ortiz ML, Immanuel SRC, Lavin R, Delaney ML, Cummins CK, Hoffman M, Luo Y, Gonzalez-Escalona N, Allard M, Onderdonk AB, Gerber GK, Sonenshein AL, Baliga NS, Dupuy B, Bry L. In vivo commensal control of Clostridioides difficile virulence. Cell Host Microbe. 2021;29(11):1693-708 e7. Epub 2021/10/13. doi: 10.1016/j.chom.2021.09.007. PubMed PMID: 34637781; PMCID: PMC8651146.
• Maringanti VS, Bucci V, Gerber GK. Scalable learning of interpretable rules for the dynamic microbiome domain. bioRxiv 2020.06.25.172270.
• Creswell R*, Tan J*, Leff JW, Brooks B, Mahowald MA, Thieroff-Ekerdt R, Gerber GK. High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans. Genome Med 12, 59 (2020).
• Girinathan BP, DiBenedetto N*, Worley J*, Peltier J, Lavin R, Delaney ML, Cummins C, Onderdonk AB, Gerber GK, Dupuy B, Sonenshein AL, Bry L. The mechanisms of in vivo commensal control of Clostridioides difficile virulence. bioRxiv 2020.01.04.894915.
• Bogart E, Creswell R, Gerber GK. MITRE: inferring features from microbiota time-series data linked to host status. Genome Biol. 2019 09 02; 20(1):186.
• Kashani A, Brejnrod AD, Jin C, Kern T, Madsen AN, Holm LA, Gerber GK, Holm JC, Hansen T, Holst B, Arumugam M. Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice. Animal Microbiome 2019; 1:11.
• Abdel-Gadir A*, Stephen-Victor E*, Gerber GK*, Rivas MN, Sen W, Harb H, Wang L, Li N, Crestani E, Spielman S, Secor W, Biehl H, Dibendetto N, Dong X, Umetsu D, Bry L, Rashid, R, Chatila T. Microbiota Therapy Acts Via a Regulatory T Cell MyD88/RORγt Pathway to Suppress Food Allergy. Nat Med. 2019 Jul; 25(7):1164-1174.
• Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver P, Gerber GK. Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model. Cell Host Microbe. 2019 Jun 12; 25(6):803-814.e5.
• Ziesack M*, Gibson TE, Oliver J, Shumaker A, Hsu B, Riglar DT, Giessen T, DiBenedetto NV, Hsu B, Bry L, Way J, Silver P*, Gerber GK*. Engineered inter-species amino acid cross-feeding increases population evenness in a synthetic bacterial consortium. mSystems. 2019 Aug 13; 4(4).
• Kim S, Kerns SJ, Ziesack M, Bry L, Gerber GK, Way JC, Silver PA. Quorum sensing can be repurposed to promote information transfer between bacteria in the mammalian gut. ACS Synthetic Biology. 2018 7(9):2270-2281.
• Gibson TE, Gerber GK. Robust and Scalable Models of Microbiome Dynamics. ICML 36 Proceedings of Machine Learning Research PMLR. 2018 80: 1758-1767.
• Stein RR, Tanoue T, Szabady RL, Bhattarai SK, Olle B, Norman JM, Suda W, Oshima K, Hattori M, Gerber GK, Sander C, Honda K, Bucci V. Computer-guided design of optimal microbial consortia for immune system modulation. Elife. 2018 Apr 17;7. pii: e30916.
• Redhu NS, Bakthavatchalu V, Conaway EA, Shouval DS, Tsou AM, Goettel JA, Biswas A, Wang C, Field M, Muller W, Bleich A, Li N, Gerber GK, Bry L, Fox JG, Snapper SB, Horwitz BH. Macrophage dysfunction initiates colitis during weaning of infant mice lacking the interleukin-10 receptor. Elife. 2017 Jul 5;6. pii: e27652.
• Riglar DT, Giessen TW, Baym M, Kerns SJ, Niederhuber MJ, Bronson RT, Kotula JW, Gerber GK, Way JC, Silver PA. Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nat Biotechnol. 2017 Jul;35(7):653-658.
• Ussar S, Haering MF, Fujisaka S, Lutter D, Lee KY, Li N, Gerber GK, Bry L, Kahn CR. Regulation of Glucose Uptake and Enteroendocrine Function by the Intestinal Epithelial Insulin Receptor. Diabetes. 2017 Apr; 66(4):886-896.

2017-2012

• Fujisaka S, Ussar S, Clish C, Devkota S, Dreyfuss J, Sakaguchi M, Soto M, Konishi M, Softic S, Altindis E, Li N, Gerber GK, Bry L, Kahn CK. Antibiotic effects on gut microbiota and metabolism are host dependent. Journal of Clinical Investigation 2016 Oct.
• Louis DK, Feldman M, Carter AB, Dighe A, Pfeiffer J, Bry L, Almeida J, Saltz J, Braun J, Tomaszevski J, Gilbertson J, Sinard J, Gerber GK, Galli SJ, Golden JA, Becich MJ. Computational Pathology: The Path Ahead. Archives of Lab Med And Pathol. 2016 140(1):41-50.
• Jangi S, Gandhi R, Cox L, Li N, Glehn FV, Yan R, Patel B, Mazolla MA, Shirong Liu, Glanz B, Cook S, Tankou S, Stewart F, Melo K, Nejad P, Smith K, Topcuoglu B, Holden J, Kivisakk P, Chitnis T, DeJager P, Quintana F, Gerber GK, Bry L, and Weiner HL. Alterations of the human gut microbiome in multiple sclerosis. Nature Communications 2016 Jun 28;7:12015.
• Bucci B, Tzen B, Li N, Simmons M, Tanoue T, Bogart E, Deng L, Yeliseyev V, Delaney ML, Liu Q, Olle B, Stein RR, Honda K, Bry L, Gerber GK. MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses. Genome Biology 2016 Jun 3;17(1):121.
• Allegretti JR, Kearney S, Li N, Bogart E, Bullock K, Gerber GK, Bry L, Clish CB, Alm E, Korzenik JR. Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles. Aliment Pharmacol Ther. 2016 43(11):1142-53.
• Wang S, Charbonnier LM, Noval Rivas M, 2, Georgiev P, Li N, Gerber GK, Bry L, Chatila TA. MyD88-Dependent Microbial Sensing by Regulatory T cells Promotes Mucosal Tolerance and Enforces Commensalism. Immunity. 2015 43(2):289-303.
• Yaung SJ, Deng L, Li N, Braff JL, Church GM, Bry L, Wang H*, Gerber GK*. Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. Molecular Systems Biology. 2015 11:788.
• Carmody RN*, Gerber GK*, Luevano JM, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ. Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota. Cell Host Microbe. 2014 Dec 18.
• Belzer C*, Gerber GK*, Roeseler G*, Delaney M, DuBois A, Liu Q, Belavusava V, Yeliseyev V, Houseman A, Onderdonk A, Cavanaugh C, Bry L. Dynamics of the microbiota in response to host infection. PLoS ONE. 2014 9(7): e95534.
• Louis DK, Gerber GK, Baron JM, Bry L, Dighe AS, Getz G, Higgins JM, Kuo FC, Lane WJ, Michaelson JS, Le LP, Mermel CH, Gilbertson JR, Golden JA. Computational Pathology: An emerging definition. Archives of Lab Med And Pathol. 2014 138(9):1133-8.
• Gerber GK. The dynamic microbiome. FEBS Lett. 2014, doi: 10.1016/j.febslet.2014.02.037.
• Gerber GK. Longitudinal microbiome data analysis. In Metagenomics for Microbiology (eds Izard J and Rivera M), Academic Press/Elsevier, Waltham, MA, 2014.
• Noval Rivas M, Burton OT, Wise P, Zhang YQ, Hobson SA, Garcia Lloret M, Chehoud C, Kuczynski J, Desantis T, Warrington J, Hyde ER, Petrosino JF, Gerber GK, Bry L, Oettgen HC, Mazmanian SK, Chatila T. A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis. J Allergy Clin Immunol. 2013 Jan;131(1):201-212.
• Gerber GK, Onderdonk A, Bry L. Inferring dynamic signatures of microbes in complex host ecosystems. PLoS Comput Biol. 2012 Aug;8(8):e1002624.
• Chen L, Chen Z, Baker K, Halvorsen EM, Magdalena M, Gerber GK, Huang YH, Arthur JC, Dery KJ, Nagaishi T, Holmes KV, Beauchemin N, Shively JE, Jobin C, Onderdonk AB, Bry L, Higgins DE, Blumberg RS. Secretory immunity and pathogen resistance are mediated by CEACAM1-short isoforms in intestinal T cells. Immunity. 2012 37:930–946.

2011 and earlier

• Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S. Discovering homotypic binding events at high spatial resolution. Bioinformatics. 2010 Dec 15;26(24):3028-3034.
• Gerber GK, Dowell RD, Jaakkola TS, Gifford DK. Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol. 2007 Aug;3(8):e148.
• Gerber GK, Dowell RD, Jaakkola TS, Gifford DK. Hierarchical Dirichlet process-based models for discovery of cross-species mammalian gene expression programs. MIT-CSAIL Technical Report. 2007;MIT-CSAIL-TR-2007-037. 
• Qi Y*, Rolfe A*, MacIsaac KD*, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. High-resolution computational models of genome binding events.  Nat Biotechnol. 2006 Aug;24(8):963-970.
• Schreiber J, Jenner RG, Murray HL, Gerber GK, Gifford DK, Young RA. Coordinated binding of NF-κB family members in the response of human cells to lipopolysaccharide. Proc Natl Acad Sci U.S.A. 2006 Apr 11;103(15):5899-5904.
• Bar-Joseph Z*, Gerber GK*, Lee T*, Rinaldi N, Yoo J, Robert F, Gordon B, Fraenkel E, Jaakkola T, Young R, Gifford D.  Computational discovery of gene modules and regulatory networks.  Nat Biotechnol. 2003 Nov;21(11):1337-1342.
• Bar-Joseph Z, Gerber GK, Simon I, Gifford D, Jaakkola T. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes.  Proc Natl Acad Sci U.S.A. 2003 Sep 2;100(18):10146-10151.
• Bar-Joseph Z, Gerber GK, Gifford D, Jaakkola T, Simon I. Continuous representations of time-series gene expression data.  J Comput Biol. 2003;10(3-4):341-356. 
• Lee TI, Rinaldi, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25;298(5594):799-804.
• Bar-Joseph Z, Gerber GK, Gifford D, Jaakkola T, Simon I. A new approach to analyzing gene expression time series data. In Proceedings of The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB). 2002;39-48.
• Gerber GK. Action!: A System For Creating and Delivering Multi-participant Interactive Cinematic Dramas. In International Conference on Application and Development of Computer Games in the 21st Century (ADCOG21) 2001.

Theses

• Gerber GK. Computational Discovery of Gene Modules, Regulatory Networks and Expression Programs. Harvard-MIT HST Ph.D. Thesis, July 2007.
• Gerber GK. Do the Time-Warp: Continuous Alignment of Gene Expression Time-Series Data. MIT Masters’ thesis, February 2003.