| The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo R Bonneau, DJ Reiss, P Shannon, M Facciotti, L Hood, NS Baliga, ... Genome biology 7, 1-16, 2006 | 685 | 2006 |
| An integrated pipeline for de novo assembly of microbial genomes A Tritt, JA Eisen, MT Facciotti, AE Darling Public Library of Science 7 (9), e42304, 2012 | 499 | 2012 |
| Evaluation of algorithm performance in ChIP-seq peak detection EG Wilbanks, MT Facciotti PloS one 5 (7), e11471, 2010 | 423 | 2010 |
| Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea NS Baliga, R Bonneau, MT Facciotti, M Pan, G Glusman, EW Deutsch, ... Genome research 14 (11), 2221-2234, 2004 | 386 | 2004 |
| A predictive model for transcriptional control of physiology in a free living cell R Bonneau, MT Facciotti, DJ Reiss, AK Schmid, M Pan, A Kaur, ... Cell 131 (7), 1354-1365, 2007 | 366 | 2007 |
| Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response EA Becker, PM Seitzer, A Tritt, D Larsen, M Krusor, AI Yao, D Wu, ... PLoS Genetics 10 (11), e1004784, 2014 | 155 | 2014 |
| 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 | 155 | 2009 |
| General transcription factor specified global gene regulation in archaea MT Facciotti, DJ Reiss, M Pan, A Kaur, M Vuthoori, R Bonneau, ... Proceedings of the National Academy of Sciences 104 (11), 4630-4635, 2007 | 145 | 2007 |
| Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate S Rouhani, JP Cartailler, MT Facciotti, P Walian, R Needleman, JK Lanyi, ... Journal of molecular biology 313 (3), 615-628, 2001 | 143 | 2001 |
| Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle MT Facciotti, S Rouhani, FT Burkard, FM Betancourt, KH Downing, ... Biophysical Journal 81 (6), 3442-3455, 2001 | 141 | 2001 |
| A systems view of haloarchaeal strategies to withstand stress from transition metals A Kaur, M Pan, M Meislin, MT Facciotti, R El-Gewely, NS Baliga Genome research 16 (7), 841-854, 2006 | 133 | 2006 |
| Mauve assembly metrics AE Darling, A Tritt, JA Eisen, MT Facciotti Bioinformatics 27 (19), 2756-2757, 2011 | 131 | 2011 |
| Improved stearate phenotype in transgenic canola expressing a modified acyl-acyl carrier protein thioesterase MT Facciotti, PB Bertain, L Yuan Nature Biotechnology 17 (6), 593-597, 1999 | 129 | 1999 |
| IRF-1 and miRNA126 modulate VCAM-1 expression in response to a high-fat meal C Sun, K Alkhoury, YI Wang, GA Foster, CE Radecke, K Tam, ... Circulation research 111 (8), 1054-1064, 2012 | 124 | 2012 |
| Ultrafast protein dynamics of bacteriorhodopsin probed by photon echo and transient absorption spectroscopy JTM Kennis, DS Larsen, K Ohta, MT Facciotti, RM Glaeser, GR Fleming The Journal of Physical Chemistry B 106 (23), 6067-6080, 2002 | 119 | 2002 |
| Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its … T Persson, K Battenberg, IV Demina, T Vigil-Stenman, B Vanden Heuvel, ... PloS one 10 (5), e0127630, 2015 | 106 | 2015 |
| Microscale sulfur cycling in the phototrophic pink berry consortia of the S ippewissett S alt M arsh EG Wilbanks, U Jaekel, V Salman, PT Humphrey, JA Eisen, MT Facciotti, ... Environmental microbiology 16 (11), 3398-3415, 2014 | 104 | 2014 |
| A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq EG Wilbanks, DJ Larsen, RY Neches, AI Yao, CY Wu, RAS Kjolby, ... Nucleic acids research 40 (10), e74-e74, 2012 | 62 | 2012 |
| Model-based deconvolution of genome-wide DNA binding DJ Reiss, MT Facciotti, NS Baliga Bioinformatics 24 (3), 396-403, 2008 | 60 | 2008 |
| The effects of practice-based training on graduate teaching assistants’ classroom practices EA Becker, EJ Easlon, SC Potter, A Guzman-Alvarez, JM Spear, ... CBE—Life Sciences Education 16 (4), ar58, 2017 | 56 | 2017 |
