| Prevalence of transcription promoters within archaeal operons and coding sequences T Koide, DJ Reiss, JC Bare, WL Pang, MT Facciotti, AK Schmid, M Pan, ... Molecular systems biology 5 (1), 285, 2009 | 154 | 2009 |
| DNA Microarray-Based Genome Comparison of a Pathogenic and a Nonpathogenic Strain of Xylella fastidiosa Delineates Genes Important for Bacterial Virulence T Koide, PA Zaini, LM Moreira, RZN Vêncio, AY Matsukuma, AM Durham, ... Journal of Bacteriology 186 (16), 5442-5449, 2004 | 100 | 2004 |
| BayGO: Bayesian analysis of ontology term enrichment in microarray data RZN Vêncio, T Koide, SL Gomes, CA de B Pereira BMC bioinformatics 7, 1-11, 2006 | 76 | 2006 |
| The role of predictive modelling in rationally re-engineering biological systems T Koide, W Lee Pang, NS Baliga Nature Reviews Microbiology 7 (4), 297-305, 2009 | 75 | 2009 |
| A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability AK Schmid, DJ Reiss, M Pan, T Koide, NS Baliga Molecular systems biology 5 (1), 282, 2009 | 72 | 2009 |
| HTself: self–self based statistical test for low replication microarray studies RZN Vêncio, T Koide DNA Research 12 (3), 211-214, 2005 | 67 | 2005 |
| Global Gene Expression Analysis of the Heat Shock Response in the Phytopathogen Xylella fastidiosa T Koide, RZN Vêncio, SL Gomes Journal of bacteriology 188 (16), 5821-5830, 2006 | 62 | 2006 |
| Integration and visualization of systems biology data in context of the genome JC Bare, T Koide, DJ Reiss, D Tenenbaum, NS Baliga BMC bioinformatics 11, 1-8, 2010 | 49 | 2010 |
| Halobacterium salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage PT Van, AK Schmid, NL King, A Kaur, M Pan, K Whitehead, T Koide, ... Journal of proteome research 7 (9), 3755-3764, 2008 | 48 | 2008 |
| Gsk3β and Tomm20 are substrates of the SCFFbxo7/PARK15 ubiquitin ligase associated with Parkinson's disease FR Teixeira, SJ Randle, SP Patel, TET Mevissen, G Zenkeviciute, T Koide, ... Biochemical Journal 473 (20), 3563-3580, 2016 | 46 | 2016 |
| Iron Deficiency Generates Oxidative Stress and Activation of the SOS Response in Caulobacter crescentus L Leaden, LG Silva, RA Ribeiro, NM Dos Santos, APR Lorenzetti, ... Frontiers in microbiology 9, 2014, 2018 | 38 | 2018 |
| Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis MT Facciotti, WL Pang, F Lo, K Whitehead, T Koide, K Masumura, M Pan, ... BMC systems biology 4, 1-19, 2010 | 38 | 2010 |
| The Single Extracytoplasmic-Function Sigma Factor of Xylella fastidiosa Is Involved in the Heat Shock Response and Presents an Unusual Regulatory Mechanism JF da Silva Neto, T Koide, SL Gomes, MV Marques Journal of bacteriology 189 (2), 551-560, 2007 | 35 | 2007 |
| Sense overlapping transcripts in IS 1341-type transposase genes are functional non-coding RNAs in archaea JV Gomes-Filho, LS Zaramela, VCS Italiani, NS Baliga, RZN Vêncio, ... RNA biology 12 (5), 490-500, 2015 | 34 | 2015 |
| Site-directed gene disruption in Xylella fastidiosa JF da Silva Neto, T Koide, SL Gomes, MV Marques FEMS Microbiology Letters 210 (1), 105-110, 2002 | 34 | 2002 |
| Role of σ54 in the regulation of genes involved in type I and type IV pili biogenesis in Xylella fastidiosa JF da Silva Neto, T Koide, CM Abe, SL Gomes, MV Marques Archives of microbiology 189, 249-261, 2008 | 30 | 2008 |
| SpotWhatR: a user-friendly microarray data analysis system T Koide, SM Salem-Izacc, SL Gomes, RZ Vencio Genet Mol Res 5 (1), 93-107, 2006 | 26 | 2006 |
| Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life LS Zaramela, RZN Vêncio, F Ten-Caten, NS Baliga, T Koide PloS one 9 (9), e107680, 2014 | 25 | 2014 |
| The F-box protein FBXO25 promotes the proteasome-dependent degradation of ELK-1 protein FR Teixeira, AO Manfiolli, CS Soares, MMA Baqui, T Koide, MD Gomes Journal of Biological Chemistry 288 (39), 28152-28162, 2013 | 18 | 2013 |
| Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon JF da Silva Neto, T Koide, SL Gomes, MV Marques BMC microbiology 10, 1-12, 2010 | 17 | 2010 |
