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Items: 1 to 20 of 21

1.

Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage.

Xia J, Chiu LY, Nehring RB, Bravo Núñez MA, Mei Q, Perez M, Zhai Y, Fitzgerald DM, Pribis JP, Wang Y, Hu CW, Powell RT, LaBonte SA, Jalali A, Matadamas Guzmán ML, Lentzsch AM, Szafran AT, Joshi MC, Richters M, Gibson JL, Frisch RL, Hastings PJ, Bates D, Queitsch C, Hilsenbeck SG, Coarfa C, Hu JC, Siegele DA, Scott KL, Liang H, Mancini MA, Herman C, Miller KM, Rosenberg SM.

Cell. 2019 Jan 10;176(1-2):127-143.e24. doi: 10.1016/j.cell.2018.12.008.

PMID:
30633903
2.

ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, Erill I, Siegele DA, Hu JC, Mungall C, Chibucos MC.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1186-D1194. doi: 10.1093/nar/gky1036.

3.

The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.

Chibucos MC, Siegele DA, Hu JC, Giglio M.

Methods Mol Biol. 2017;1446:245-259.

PMID:
27812948
4.

Primer on the Gene Ontology.

Gaudet P, Škunca N, Hu JC, Dessimoz C.

Methods Mol Biol. 2017;1446:25-37.

PMID:
27812933
5.

An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli.

Nehring RB, Gu F, Lin HY, Gibson JL, Blythe MJ, Wilson R, Bravo Núñez MA, Hastings PJ, Louis EJ, Frisch RL, Hu JC, Rosenberg SM.

Nucleic Acids Res. 2016 Mar 18;44(5):e41. doi: 10.1093/nar/gkv1131. Epub 2015 Nov 17.

6.

An ontology for microbial phenotypes.

Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, Siegele DA, Hu JC, Giglio MG.

BMC Microbiol. 2014 Nov 30;14:294. doi: 10.1186/s12866-014-0294-3.

7.

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

Hu JC, Sherlock G, Siegele DA, Aleksander SA, Ball CA, Demeter J, Gouni S, Holland TA, Karp PD, Lewis JE, Liles NM, McIntosh BK, Mi H, Muruganujan A, Wymore F, Thomas PD, Altman T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D677-84. doi: 10.1093/nar/gkt1203. Epub 2013 Nov 26. Erratum in: Nucleic Acids Res. 2014 Oct 29;42(19):12330.

8.

Microbial virus genome annotation-mustering the troops to fight the sequence onslaught.

Brister JR, Le Mercier P, Hu JC.

Virology. 2012 Dec 20;434(2):175-80. doi: 10.1016/j.virol.2012.09.027. Epub 2012 Oct 18. Review.

9.

GONUTS: the Gene Ontology Normal Usage Tracking System.

Renfro DP, McIntosh BK, Venkatraman A, Siegele DA, Hu JC.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1262-9. doi: 10.1093/nar/gkr907. Epub 2011 Nov 22.

10.

EcoliWiki: a wiki-based community resource for Escherichia coli.

McIntosh BK, Renfro DP, Knapp GS, Lairikyengbam CR, Liles NM, Niu L, Supak AM, Venkatraman A, Zweifel AE, Siegele DA, Hu JC.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1270-7. doi: 10.1093/nar/gkr880. Epub 2011 Nov 7.

11.

Specificity of the E. coli LysR-type transcriptional regulators.

Knapp GS, Hu JC.

PLoS One. 2010 Dec 20;5(12):e15189. doi: 10.1371/journal.pone.0015189.

12.

The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology.

Rajagopala SV, Yamamoto N, Zweifel AE, Nakamichi T, Huang HK, Mendez-Rios JD, Franca-Koh J, Boorgula MP, Fujita K, Suzuki K, Hu JC, Wanner BL, Mori H, Uetz P.

BMC Genomics. 2010 Aug 11;11:470. doi: 10.1186/1471-2164-11-470.

13.

The oligomerization of CynR in Escherichia coli.

Knapp GS, Hu JC.

Protein Sci. 2009 Nov;18(11):2307-15. doi: 10.1002/pro.241.

14.

What we can learn about Escherichia coli through application of Gene Ontology.

Hu JC, Karp PD, Keseler IM, Krummenacker M, Siegele DA.

Trends Microbiol. 2009 Jul;17(7):269-78. doi: 10.1016/j.tim.2009.04.004. Epub 2009 Jul 1. Review.

15.

The oligomerization of OxyR in Escherichia coli.

Knapp GS, Tsai JW, Hu JC.

Protein Sci. 2009 Jan;18(1):101-7. doi: 10.1002/pro.5.

16.

The emerging world of wikis.

Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Kihara D, Knight TF Jr, Pico AR, Siegele DA, Wanner BL, Welch RD.

Science. 2008 Jun 6;320(5881):1289-90. doi: 10.1126/science.320.5881.1289b. No abstract available.

PMID:
18535227
17.

Assessing methods for identifying pair-wise atomic contacts across binding interfaces.

Fischer TB, Holmes JB, Miller IR, Parsons JR, Tung L, Hu JC, Tsai J.

J Struct Biol. 2006 Feb;153(2):103-12. Epub 2005 Dec 7.

PMID:
16377205
18.
19.

Proteome analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI-MS.

Champion MM, Campbell CS, Siegele DA, Russell DH, Hu JC.

Mol Microbiol. 2003 Jan;47(2):383-96.

20.

Screening peptide/protein libraries fused to the lambda repressor DNA-binding domain in E. coli cells.

Mariño-Ramírez L, Campbell L, Hu JC.

Methods Mol Biol. 2003;205:235-50. No abstract available.

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