Svetlana Gerdes
Svetlana Gerdes
DuPont Danisco Research Center
Verified email at
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The RAST Server: rapid annotations using subsystems technology
RK Aziz, D Bartels, AA Best, M DeJongh, T Disz, RA Edwards, K Formsma, ...
BMC genomics 9, 1-15, 2008
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
R Overbeek, R Olson, GD Pusch, GJ Olsen, JJ Davis, T Disz, RA Edwards, ...
Nucleic acids research 42 (D1), D206-D214, 2014
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
T Brettin, JJ Davis, T Disz, RA Edwards, S Gerdes, GJ Olsen, R Olson, ...
Scientific reports 5 (1), 1-6, 2015
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
R Overbeek, T Begley, RM Butler, JV Choudhuri, HY Chuang, M Cohoon, ...
Nucleic acids research 33 (17), 5691-5702, 2005
Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center
AR Wattam, JJ Davis, R Assaf, S Boisvert, T Brettin, C Bun, N Conrad, ...
Nucleic acids research 45 (D1), D535-D542, 2017
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655
SY Gerdes, MD Scholle, JW Campbell, G Balazsi, E Ravasz, ...
Journal of bacteriology 185 (19), 5673-5684, 2003
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
JJ Davis, AR Wattam, RK Aziz, T Brettin, R Butler, RM Butler, P Chlenski, ...
Nucleic acids research 48 (D1), D606-D612, 2020
From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways
SY Gerdes, MD Scholle, M D'Souza, A Bernal, MV Baev, M Farrell, ...
Journal of Bacteriology 184 (16), 4555-4572, 2002
Whole-genome analysis of photosynthetic prokaryotes
J Raymond, O Zhaxybayeva, JP Gogarten, SY Gerdes, RE Blankenship
Prokaryotic heme biosynthesis: multiple pathways to a common essential product
HA Dailey, TA Dailey, S Gerdes, D Jahn, M Jahn, MR O'Brian, MJ Warren
Microbiology and Molecular Biology Reviews 81 (1), 10.1128/mmbr. 00048-16, 2017
NAD biosynthesis: identification of the tryptophan to quinolinate pathway in bacteria
O Kurnasov, V Goral, K Colabroy, S Gerdes, S Anantha, A Osterman, ...
Chemistry & biology 10 (12), 1195-1204, 2003
Red death in Caenorhabditis elegans caused by Pseudomonas aeruginosa PAO1
A Zaborin, K Romanowski, S Gerdes, C Holbrook, F Lepine, J Long, ...
Proceedings of the National Academy of Sciences 106 (15), 6327-6332, 2009
Evolution of proline biosynthesis: enzymology, bioinformatics, genetics, and transcriptional regulation
Y Fichman, SY Gerdes, H Kovács, L Szabados, A Zilberstein, LN Csonka
Biological Reviews 90 (4), 1065-1099, 2015
PATtyFams: protein families for the microbial genomes in the PATRIC database
JJ Davis, S Gerdes, GJ Olsen, R Olson, GD Pusch, M Shukla, V Vonstein, ...
Frontiers in microbiology 7, 118, 2016
Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin
HA Dailey, S Gerdes, TA Dailey, JS Burch, JD Phillips
Proceedings of the National Academy of Sciences 112 (7), 2210-2215, 2015
Essential genes on metabolic maps
S Gerdes, R Edwards, M Kubal, M Fonstein, R Stevens, A Osterman
Current opinion in biotechnology 17 (5), 448-456, 2006
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
LK McNeil, C Reich, RK Aziz, D Bartels, M Cohoon, T Disz, RA Edwards, ...
Nucleic acids research 35 (suppl_1), D347-D353, 2007
PATRIC as a unique resource for studying antimicrobial resistance
DA Antonopoulos, R Assaf, RK Aziz, T Brettin, C Bun, N Conrad, JJ Davis, ...
Briefings in bioinformatics 20 (4), 1094-1102, 2019
Ribosylnicotinamide kinase domain of NadR protein: identification and implications in NAD biosynthesis
OV Kurnasov, BM Polanuyer, S Ananta, R Sloutsky, A Tam, SY Gerdes, ...
Journal of bacteriology 184 (24), 6906-6917, 2002
Plant B vitamin pathways and their compartmentation: a guide for the perplexed
S Gerdes, C Lerma-Ortiz, O Frelin, SMD Seaver, CS Henry, ...
Journal of experimental botany 63 (15), 5379-5395, 2012
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