Koide T - Search Results

1

Integration and visualization of systems biology data in context of the genome.

Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS. Bare JC, et al. Among authors: koide t. BMC Bioinformatics. 2010 Jul 19;11:382. doi: 10.1186/1471-2105-11-382. BMC Bioinformatics. 2010. PMID: 20642854 Free PMC article.

2

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS. Van PT, et al. Among authors: koide t. J Proteome Res. 2008 Sep;7(9):3755-64. doi: 10.1021/pr800031f. Epub 2008 Jul 25. J Proteome Res. 2008. PMID: 18652504 Free PMC article.

3

The role of predictive modelling in rationally re-engineering biological systems.

Koide T, Pang WL, Baliga NS. Koide T, et al. Nat Rev Microbiol. 2009 Apr;7(4):297-305. doi: 10.1038/nrmicro2107. Epub 2009 Mar 2. Nat Rev Microbiol. 2009. PMID: 19252506 Free PMC article. Review.

4

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.

Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS. Schmid AK, et al. Among authors: koide t. Mol Syst Biol. 2009;5:282. doi: 10.1038/msb.2009.40. Epub 2009 Jun 16. Mol Syst Biol. 2009. PMID: 19536205 Free PMC article.

5

Prevalence of transcription promoters within archaeal operons and coding sequences.

Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS. Koide T, et al. Mol Syst Biol. 2009;5:285. doi: 10.1038/msb.2009.42. Epub 2009 Jun 16. Mol Syst Biol. 2009. PMID: 19536208 Free PMC article.

6

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis.

Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ, Hoang L, Kalisiak E, Northen T, Trauger SA, Siuzdak G, Baliga NS. Facciotti MT, et al. Among authors: koide t. BMC Syst Biol. 2010 May 14;4:64. doi: 10.1186/1752-0509-4-64. BMC Syst Biol. 2010. PMID: 20470417 Free PMC article.

7

Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.

Zaramela LS, Vêncio RZ, ten-Caten F, Baliga NS, Koide T. Zaramela LS, et al. Among authors: koide t. PLoS One. 2014 Sep 19;9(9):e107680. doi: 10.1371/journal.pone.0107680. eCollection 2014. PLoS One. 2014. PMID: 25238539 Free PMC article.

8

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea.

Gomes-Filho JV, Zaramela LS, Italiani VC, Baliga NS, Vêncio RZ, Koide T. Gomes-Filho JV, et al. Among authors: koide t. RNA Biol. 2015;12(5):490-500. doi: 10.1080/15476286.2015.1019998. RNA Biol. 2015. PMID: 25806405 Free PMC article.

9

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.

Lorenzetti APR, Kusebauch U, Zaramela LS, Wu WJ, de Almeida JPP, Turkarslan S, L G de Lomana A, Gomes-Filho JV, Vêncio RZN, Moritz RL, Koide T, Baliga NS. Lorenzetti APR, et al. Among authors: koide t. mSystems. 2023 Apr 27;8(2):e0081622. doi: 10.1128/msystems.00816-22. Epub 2023 Mar 13. mSystems. 2023. PMID: 36912639 Free PMC article.

10

BayGO: Bayesian analysis of ontology term enrichment in microarray data.

Vêncio RZ, Koide T, Gomes SL, Pereira CA. Vêncio RZ, et al. Among authors: koide t. BMC Bioinformatics. 2006 Feb 23;7:86. doi: 10.1186/1471-2105-7-86. BMC Bioinformatics. 2006. PMID: 16504085 Free PMC article.

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