Jeremy Zucker
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Structure, function and diversity of the healthy human microbiome
nature 486 (7402), 207-214, 2012
A framework for human microbiome research
nature 486 (7402), 215-221, 2012
Metabolic reconstruction for metagenomic data and its application to the human microbiome
S Abubucker, N Segata, J Goll, AM Schubert, J Izard, BL Cantarel, ...
PLoS computational biology 8 (6), e1002358, 2012
The BioPAX community standard for pathway data sharing
E Demir, MP Cary, S Paley, K Fukuda, C Lemer, I Vastrik, G Wu, ...
Nature biotechnology 28 (9), 935-942, 2010
Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
GC Kettler, AC Martiny, K Huang, J Zucker, ML Coleman, S Rodrigue, ...
PLoS genetics 3 (12), e231, 2007
The Mycobacterium tuberculosis regulatory network and hypoxia
JE Galagan, K Minch, M Peterson, A Lyubetskaya, E Azizi, L Sweet, ...
Nature 499 (7457), 178-183, 2013
Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production
C Colijn, A Brandes, J Zucker, DS Lun, B Weiner, MR Farhat, TY Cheng, ...
PLoS computational biology 5 (8), e1000489, 2009
Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus
KL Palmer, P Godfrey, A Griggs, VN Kos, J Zucker, C Desjardins, ...
MBio 3 (1), 10.1128/mbio. 00318-11, 2012
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans
CA Desjardins, GC Cerqueira, JM Goldberg, JCD Hotopp, BJ Haas, ...
Nature genetics 45 (5), 495-500, 2013
Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis
CA Desjardins, MD Champion, JW Holder, A Muszewska, J Goldberg, ...
PLoS genetics 7 (10), e1002345, 2011
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development
JW Holder, JC Ulrich, AC DeBono, PA Godfrey, CA Desjardins, J Zucker, ...
PLoS Genetics 7 (9), e1002219, 2011
TB database 2010: overview and update
JE Galagan, P Sisk, C Stolte, B Weiner, M Koehrsen, F Wymore, ...
Tuberculosis 90 (4), 225-235, 2010
A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola
GH Thomas, J Zucker, SJ Macdonald, A Sorokin, I Goryanin, AE Douglas
BMC systems biology 3, 1-9, 2009
Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis
AM McGuire, B Weiner, ST Park, I Wapinski, S Raman, G Dolganov, ...
BMC genomics 13 (1), 1-27, 2012
Microbial community metabolic modeling: a community data‐driven network reconstruction
CS Henry, HC Bernstein, P Weisenhorn, RC Taylor, JY Lee, J Zucker, ...
Journal of cellular physiology 231 (11), 2339-2345, 2016
Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa
C Wu, F Yang, KM Smith, M Peterson, R Dekhang, Y Zhang, J Zucker, ...
G3: Genes, Genomes, Genetics 4 (9), 1731-1745, 2014
From annotated genomes to metabolic flux models and kinetic parameter fitting
D Segrè, J Zucker, J Katz, X Lin, P D'haeseleer, WP Rindone, ...
OMICS A Journal of Integrative Biology 7 (3), 301-316, 2003
Circadian proteomic analysis uncovers mechanisms of post-transcriptional regulation in metabolic pathways
JM Hurley, MS Jankowski, H De los Santos, AM Crowell, SB Fordyce, ...
Cell systems 7 (6), 613-626. e5, 2018
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
JM Dreyfuss, JD Zucker, HM Hood, LR Ocasio, MS Sachs, JE Galagan
PLoS computational biology 9 (7), e1003126, 2013
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