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Eric Alm

Research Profile

Chemicals & Drugs

Physiology

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Oligonucleotide Array Sequence Analysis

Genes & Molecular Sequences

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Gene Expression Profiling

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TOP 3
Paramvir S Dehal; marcin joachimiak; Morgan N Price; John T Bates; Jason K Baumohl; Dylan Chivian; Greg D Friedland; Katherine H Huang; Keith Keller; Pavel Novichkov; Inna Dubchak; Eric J Alm; Adam P Arkin
MicrobesOnline: an integrated portal for comparative and functional genomics.
Dylan Chivian; Eoin L Brodie; Eric J Alm; David E Culley; Paramvir S Dehal; Todd Z DeSantis; Thomas M Gihring; Alla Lapidus; Li-Hung Lin; Stephen R Lowry; Duane P Moser; Paul M Richardson; Gordon Southam; Greg Wanger; Lisa M Pratt; Gary L Andersen; Terry C Hazen; Fred J Brockman; Adam P Arkin; Tullis C Onstott
Environmental genomics reveals a single-species ecosystem deep within Earth.
Sergey Stolyar; Qiang He; marcin joachimiak; Zhili He; Zamin Koo Yang; Sharon E Borglin; Dominique C Joyner; Katherine Huang; Eric J Alm; Terry C Hazen; Jizhong Zhou; Judy D Wall; Adam P Arkin; David A Stahl
Response of Desulfovibrio vulgaris to alkaline stress.

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All Publications

2010: Paramvir S Dehal; marcin joachimiak; Morgan N Price; John T Bates; Jason K Baumohl; Dylan Chivian; Greg D Friedland; Katherine H Huang; Keith Keller; Pavel Novichkov; Inna Dubchak; Eric J Alm; Adam P Arkin
MicrobesOnline: an integrated portal for comparative and functional genomics.
Nucleic acids research 2010;38(Database issue):D396-400.
2008: Dylan Chivian; Eoin L Brodie; Eric J Alm; David E Culley; Paramvir S Dehal; Todd Z DeSantis; Thomas M Gihring; Alla Lapidus; Li-Hung Lin; Stephen R Lowry; Duane P Moser; Paul M Richardson; Gordon Southam; Greg Wanger; Lisa M Pratt; Gary L Andersen; Terry C Hazen; Fred J Brockman; Adam P Arkin; Tullis C Onstott
Environmental genomics reveals a single-species ecosystem deep within Earth.
Science (New York, N.Y.) 2008;322(5899):275-8.
2007: Sergey Stolyar; Qiang He; marcin joachimiak; Zhili He; Zamin Koo Yang; Sharon E Borglin; Dominique C Joyner; Katherine Huang; Eric J Alm; Terry C Hazen; Jizhong Zhou; Judy D Wall; Adam P Arkin; David A Stahl
Response of Desulfovibrio vulgaris to alkaline stress.
Journal of bacteriology 2007;189(24):8944-52.
2007: Kelly S Bender; Huei-Che Bill Yen; Christopher L Hemme; Zamin Yang; Zhili He; Qiang He; Jizhong Zhou; Katherine H Huang; Eric J Alm; Terry C Hazen; Adam P Arkin; Judy D Wall
Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough.
Applied and environmental microbiology 2007;73(17):5389-400.
2006: Eric J Alm; Katherine Huang; Adam P Arkin
The evolution of two-component systems in bacteria reveals different strategies for niche adaptation.
PLoS computational biology 2006;2(11):e143.
2006: M E Clark; Qiang He; Zhili He; Katherine H Huang; Eric J Alm; Xiu-Feng Wan; Terry C Hazen; Adam P Arkin; Judy D Wall; JZ Zhou; matthew w fields
Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion.
Applied and environmental microbiology 2006;72(8):5578-88.
2006: Morgan N Price; Adam P Arkin; Eric J Alm
The life-cycle of operons.
PLoS genetics 2006;2(6):e96.
2006: Qiang He; Katherine H Huang; Zhili He; Eric J Alm; matthew w fields; Terry C Hazen; Adam P Arkin; Judy D Wall; Jizhong Zhou
Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis.
Applied and environmental microbiology 2006;72(6):4370-81.
2006: Aindrila Mukhopadhyay; Zhili He; Eric J Alm; Adam P Arkin; Edward E Baidoo; Sharon C Borglin; Wenqiong Chen; Terry C Hazen; Qiang He; Hoi-Ying Holman; Katherine Huang; Rick Huang; Dominique C Joyner; Natalie Katz; Martin Keller; Paul Oeller; Alyssa M Redding; Jun Sun; Judy Wall; Jing Wei; Zamin Yang; Huei-Che Yen; Jizhong Zhou; Jay D Keasling
Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach.
Journal of bacteriology 2006;188(11):4068-78.
2006: Morgan N Price; Eric J Alm; Adam P Arkin
The histidine operon is ancient.
Journal of molecular evolution 2006;62(6):807-8.
2006: S R Chhabra; Qiang He; Katherine H Huang; Sara P Gaucher; Eric J Alm; Zhili He; Masood Z Hadi; Terry C Hazen; Judy D Wall; Jizhong Zhou; Adam P Arkin; A K Singh
Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough.
Journal of bacteriology 2006;188(5):1817-28.
2006: Adam B Leaphart; Dorothea K Thompson; Katherine Huang; Eric J Alm; Xiu-Feng Wan; Adam P Arkin; Steven D Brown; Liyou Wu; Tingfen Yan; Xueduan Liu; Gene S Wickham; ali khawwam
Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH.
Journal of bacteriology 2006;188(4):1633-42.
2006: Morgan N Price; Adam P Arkin; Eric J Alm
OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments.
BMC bioinformatics 2006;7():19.
2006: Steven D Brown; Madhavi Martin; Sameer Deshpande; Sudipta Seal; Katherine Huang; Eric J Alm; Yunfeng Yang; Liyou Wu; Tingfen Yan; Xueduan Liu; Adam P Arkin; Karuna Chourey; ali khawwam; Dorothea K Thompson
Cellular response of Shewanella oneidensis to strontium stress.
Applied and environmental microbiology 2006;72(1):890-900.
2005: Dmitry A Rodionov; Inna Dubchak; Adam P Arkin; Eric J Alm; Mikhail S Gelfand
Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.
PLoS computational biology 2005;1(5):e55.
2005: Eric J Alm; Katherine H Huang; Morgan N Price; Richard P Koche; Keith Keller; Inna Dubchak; Adam P Arkin
The MicrobesOnline Web site for comparative genomics.
Genome research 2005;15(7):1015-22.
2005: Morgan N Price; Katherine H Huang; Adam P Arkin; Eric J Alm
Operon formation is driven by co-regulation and not by horizontal gene transfer.
Genome research 2005;15(6):809-19.
2005: Yongqing Liu; Weimin Gao; Yue Wang; Liyou Wu; Xueduan Liu; Tingfen Yan; Eric J Alm; Adam P Arkin; Dorothea K Thompson; matthew w fields; ali khawwam
Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions.
Journal of bacteriology 2005;187(7):2501-7.
2005: Morgan N Price; Eric J Alm; Adam P Arkin
Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication.
Nucleic acids research 2005;33(10):3224-34.
2005: Morgan N Price; Katherine H Huang; Eric J Alm; Adam P Arkin
A novel method for accurate operon predictions in all sequenced prokaryotes.
Nucleic acids research 2005;33(3):880-92.
2004: Haichun Gao; Yue Wang; Xueduan Liu; Tingfen Yan; Liyou Wu; Eric J Alm; Adam P Arkin; Dorothea K Thompson; ali khawwam
Global transcriptome analysis of the heat shock response of Shewanella oneidensis.
Journal of bacteriology 2004;186(22):7796-803.
2004: Dmitry A Rodionov; Inna Dubchak; Adam P Arkin; Eric J Alm; Mikhail S Gelfand
Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.
Genome biology 2004;5(11):R90.
2003: Eric J Alm; Adam P Arkin
Biological networks.
Current opinion in structural biology 2003;13(2):193-202.
2000: E L McCallister; Eric J Alm; David Baker
Critical role of beta-hairpin formation in protein G folding.
Nature structural biology 2000;7(8):669-73.
2000: Qian Yi; Michelle Scalley-Kim; Eric J Alm; David Baker
NMR characterization of residual structure in the denatured state of protein L.
Journal of molecular biology 2000;299(5):1341-51.
2000: Darwin O V Alonso; Eric J Alm; Valerie Daggett
Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping.
Structure (London, England : 1993) 2000;8(1):101-10.
1999: DS Riddle; VP Grantcharova; JV Santiago; Eric J Alm; Ingo Ruczinski; David Baker
Experiment and theory highlight role of native state topology in SH3 folding.
Nature structural biology 1999;6(11):1016-24.
1999: Eric J Alm; David Baker
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(20):11305-10.
1999: Eric J Alm; David Baker
Matching theory and experiment in protein folding.
Current opinion in structural biology 1999;9(2):189-96.