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Ying Zhang
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Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)
DW Waite, I Vanwonterghem, C Rinke, DH Parks, Y Zhang, K Takai, ...
Frontiers in Microbiology 8, 682, 2017
3582017
Three-dimensional structural view of the central metabolic network of Thermotoga maritima
Y Zhang, I Thiele, D Weekes, Z Li, L Jaroszewski, K Ginalski, AM Deacon, ...
Science 325 (5947), 1544-1549, 2009
2242009
CutDB: a proteolytic event database
Y Igarashi, A Eroshkin, S Gramatikova, K Gramatikoff, Y Zhang, JW Smith, ...
Nucleic acids research 35 (suppl_1), D546-D549, 2007
1542007
Between order and disorder in protein structures: analysis of “dual personality” fragments in proteins
Y Zhang, B Stec, A Godzik
Structure 15 (9), 1141-1147, 2007
952007
Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure
PV Burra, Y Zhang, A Godzik, B Stec
Proceedings of the National Academy of Sciences 106 (26), 10505-10510, 2009
862009
Pan-genome analyses identify lineage-and niche-specific markers of evolution and adaptation in Epsilonproteobacteria
Y Zhang, SM Sievert
Frontiers in microbiology 5, 2014
812014
Addendum: comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)
DW Waite, I Vanwonterghem, C Rinke, DH Parks, Y Zhang, K Takai, ...
Frontiers in Microbiology 9, 369739, 2018
752018
The FGGY carbohydrate kinase family: insights into the evolution of functional specificities
Y Zhang, O Zagnitko, I Rodionova, A Osterman, A Godzik
PLoS computational biology 7 (12), e1002318, 2011
672011
Structural determinants of limited proteolysis
MD Kazanov, Y Igarashi, AM Eroshkin, P Cieplak, B Ratnikov, Y Zhang, ...
Journal of proteome research 10 (8), 3642-3651, 2011
672011
From the raw bar to the bench: Bivalves as models for human health
JAF Robledo, R Yadavalli, B Allam, EP Espinosa, M Gerdol, S Greco, ...
Developmental & Comparative Immunology 92, 260-282, 2019
612019
PMAP: databases for analyzing proteolytic events and pathways
Y Igarashi, E Heureux, KS Doctor, P Talwar, S Gramatikova, K Gramatikoff, ...
Nucleic acids research 37 (suppl_1), D611-D618, 2009
602009
Evolution of the natural transformation protein, ComEC, in bacteria
ZT Pimentel, Y Zhang
Frontiers in Microbiology 9, 423037, 2018
462018
PSAMM: a portable system for the analysis of metabolic models
JL Steffensen, K Dufault-Thompson, Y Zhang
PLoS computational biology 12 (2), e1004732, 2016
452016
The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest
C Rispe, F Legeai, PD Nabity, R Fernández, AK Arora, P Baa-Puyoulet, ...
BMC biology 18, 1-25, 2020
402020
Microbiome Analysis Reveals Diversity and Function of Mollicutes Associated with the Eastern Oyster, Crassostrea virginica
ZT Pimentel, K Dufault-Thompson, KT Russo, AK Scro, RM Smolowitz, ...
Msphere 6 (3), 10.1128/msphere. 00227-21, 2021
292021
Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments
F Gomaa, DR Utter, C Powers, DJ Beaudoin, VP Edgcomb, HL Filipsson, ...
Science Advances 7 (22), eabf1586, 2021
222021
Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core
Y Hwang, D Schulze-Makuch, FL Arens, JS Saenz, PS Adam, C Sager, ...
Microbiome 9, 1-17, 2021
202021
Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100
LE Williams, N Cullen, JA DeGiorgis, KJ Martinez, J Mellone, M Oser, ...
MICROBIOLOGY 165, 1315-1330, 2019
152019
A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation
K Dufault-Thompson, H Jian, R Cheng, J Li, F Wang, Y Zhang
Msystems 2 (2), 10.1128/msystems. 00165-16, 2017
142017
Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production
K Zhang, W Zhao, DA Rodionov, GM Rubinstein, DN Nguyen, ...
Msystems 6 (3), 10.1128/msystems. 01351-20, 2021
122021
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