MLpronto: A tool for democratizing machine learning. Jacob Tjaden and Brian Tjaden. PLoS ONE, 18(11):e0294924, 2023.
MLpronto webserver: a tool for rapid, robust, and reproducible machine learning. No ML background needed whatsoever.
TargetRNA3: predicting prokaryotic RNA regulatory targets with machine learning. Brian Tjaden. Genome Biology, 24:276, 2023.
TargetRNA3 webserver: a tool for predicting targets of small regulatory RNAs in prokaryotes.
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA. Jonathan Jagodnik, Brian Tjaden, Wilma Ross, and Richard L. Gourse. Nucleic Acids Research, 51(2):852-869, 2023.
Escherichia coli transcriptome assembly from a compendium of RNA-seq data sets. Brian Tjaden. RNA Biology, 20(1):77-84, 2023.
A computational system for identifying operons based on RNA-seq data. Brian Tjaden. Methods, 176:62-70, 2020.
Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response. Elias R. Gerrick, Thibault Barbier, Michael R. Chase, Raylin Xu, Josie François, Vincent H. Lin, Matthew J. Szucs, Jeremy M. Rock, Rushdy Ahmad, Brian Tjaden, Jonathan Livny, and Sarah M. Fortune. Proceedings of the National Academy of the Sciences, 115(25):6464-6469, 2018.
Transcriptome analysis of Neisseria gonorrhoeae during natural infection reveals differential expression of antibiotic resistance determinants between men and women. Kathleen Nudel, Ryan McClure, Matthew Moreau, Emma Briars, A. Jeanine Abrams, Brian Tjaden, Xiao-Hong Su, David Trees, Peter A. Rice, Paola Massari, and Caroline A. Genco. mSphere, 3(3):e00312-18, 2018.
Identification and characterization of serotype-specific variation in group A Streptococcus pilus expression. Gregory Calfee, Jessica L. Danger, Ira Jain, Eric W. Miller, Poulomee Sarkar, Brian Tjaden, Bernd Kreikemeyer, and Paul Sumby. Infection and Immunity, 86(2):e00792-17, 2018.
Probing the sRNA regulatory landscape of P. aeruginosa: post-transcriptional control of determinants of pathogenicity and antibiotic susceptibility. Yi-Fan Zhang, Kook Han, Courtney E. Chandler, Brian Tjaden, Robert K. Ernst, and Stephen Lory. Molecular Microbiology, 106(6):919-937, 2017.
GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation. Kook Han, Brian Tjaden, and Stephen Lory. Nature Microbiology, 2(3):16239, 2017.
De novo assembly of bacterial transcriptomes from RNA-seq data. Brian Tjaden. Genome Biology, 16:1, 2015.
Rockhopper 2 software for de novo transcript assembly from bacterial RNA-seq data.
The gonococcal transcriptome during infection of the lower genital tract in women. Ryan McClure, Kathleen Nudel, Paola Massari, Brian Tjaden, Xiaohong Su, Peter A. Rice, and Caroline A. Genco. PLoS One, 10(8):e0133982, 2015.
TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Mary Beth Kery, Monica Feldman, Jonathan Livny, and Brian Tjaden. Nucleic Acids Research, 42(W1): W124-W129, 2014.
TargetRNA2 web server for identifying targets of sRNAs in bacteria.
Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions. Ryan McClure, Brian Tjaden, and Caroline Genco. Frontiers in Microbiology, 5:546, 2014.
Computational analysis of bacterial RNA-seq data. Ryan McClure, Divya Balasubramanian, Yan Sun, Maksym Bobrovskyy, Paul Sumby, Caroline A. Genco, Carin K. Vanderpool, and Brian Tjaden. Nucleic Acids Research, 41(14):e140, 2013.
Rockhopper software for analyzing bacterial RNA-seq data.
Mutations in interaction surfaces differentially impact E. coli Hfq association with small RNAs and their mRNA targets. Aixia Zhang, Daniel J. Schu, Brian C. Tjaden, Gisela Storz, and Susan Gottesman. Journal of Molecular Biology, 425(19):3678-3697, 2013.
tRNA-like elements in Haloferax volcanii. Annette Hölzle, Britta Stoll, Thomas Schnattinger, Uwe Schöning, Brian Tjaden, and Anita Marchfelder. Biochimie, 94(4):940-946, 2012.
Biocomputational identification of bacterial small RNAs and their target binding sites. Brian Tjaden. Regulatory RNAs, 2:273-293, 2012.
Computational identification of sRNA targets. Brian Tjaden. Bacterial Regulatory RNA: Methods and Protocols in Methods in Molecular Biology, 905:227-234, 2012.
Assessing computational tools for the discovery of small RNA genes in bacteria. Xiaojun Lu, Heidi Goodrich-Blair, and Brian Tjaden. RNA, 17:1635-1647, 2011.
Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeon Haloferax volcanii. Julia Babski, Brian Tjaden, Björn Voss, Angelika Jellen-Ritter, Anita Marchfelder, Wolfgang Hess, and Jörg Soppa. RNA Biology, 8(5):806-816, 2011.
The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. John M. Chaston, Garret Suen, Sarah L. Tucker, Aaron W. Andersen, Archna Bhasin, Edna Bode, Helge B. Bode, Alexander O. Brachmann, Charles E. Cowles, Kimberley N. Cowles, Creg Darby, Limaris de Leon, Kevin Drace, Zijin Du, Alain Givaudan, Erin E. Herbert Tran, Kelsea A. Jewell, Jennifer J. Knack, Karina C. Krasomil-Osterfeld, Ryan Kukor, Anne Lanois, Phil Latreille, Nancy K. Leimgruber, Carolyn M. Lipke, Renyi Liu, Xiaojun Lu, Eric C. Martens, Pradeep R. Marri, Claudine Medigue, Megan L. Menard, Nancy M. Miller, Nydia Morales-Soto, Stacie Norton, Jean-Claude Ogier, Samantha S. Orchard, Dongjin Park, Youngjin Park, Barbara A. Qurollo, Darby Renneckar Sugar, Gregory R. Richards, Zoe Rouy, Brad Slominski, Kathryn Slominski, Holly Snyder, Brian C. Tjaden, Ransome van der Hoeven, Roy D. Welch, Cathy Wheeler, Bosong Xiang, Brad Barbazuk, Sophie Gaudriault, Brad Goodner, Steven C. Slater, Steven Forst, Barry S. Goldman, Heidi Goodrich-Blair. PLoS ONE, 6(11):e27909, 2011.
Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea. Barbara O. Gvakharia, Brian Tjaden, Neeraja Vajrala, Luis A. Sayavedra-Soto, and Daniel Arp. FEMS Microbiology Letters, 312(1):46-54, 2010.
Small RNAs in the halophilic archaeon Haloferax volcanii. Jörg Soppa, Julia Straub, Mariam Brenneis, Angelika Jellen-Ritter, Ruth Heyer, Susan Fischer, Michaela Granzow, Björn Voss, Wolfgang R. Hess, Brian Tjaden, and Anita Marchfelder. Biochemical Society Transactions, 37(1):133-136, 2009.
Small non-coding RNAs in Streptomyces coelicolor. Julia P. Swiercz, Hindra, Jan Bobek, Henry J. Haiser, Christina Di Berardo, Brian Tjaden, and Marie A. Elliot. Nucleic Acids Research, 36(22):7240-7251, 2008.
TargetRNA: a tool for predicting targets of small RNA action in bacteria. Brian Tjaden. Nucleic Acids Research, 36:W109-W113, 2008. Software available.
Prediction of small, noncoding RNAs in bacteria using heterogeneous data. Brian Tjaden. Journal of Mathematical Biology, 56(1-2):183-200, 2008.
Geographic location determination including inspection of network address. Kingsum Chow, Sumeet Dua, and Brian C. Tjaden. United States Patent (7,454,523), 2008.
A novel Fur and iron-regulated small RNA, NrrF, is required for indirect Fur-mediated regulation of the sdhA and sdhC genes in Neisseria meningitidis. J.R. Mellin, Sulip Goswami, Susan Grogan, Brian Tjaden, and Caroline A. Genco. Journal of Bacteriology, 189(10):3686-3694, 2007.
A multidisciplinary course in computational biology. Brian Tjaden. Journal of Computing Sciences in Colleges, 22(6):80-87, 2007.
Target prediction for small, noncoding RNAs in bacteria. Brian Tjaden, Sarah S. Goodwin, Jason A. Opdyke, Maude Guillier, Daniel X. Fu, Susan Gottesman, and Gisela Storz. Nucleic Acids Research, 34(9):2791-2802, 2006. Software available.
An approach for clustering gene expression data with error information. Brian Tjaden. BMC Bioinformatics, 7:17, 2006. Supplemental data available.
A Survey of Computational Methods used in Microarray Data Interpretation. Brian Tjaden and Jacques Cohen. Applied Mycology and Biotechnology; Volume 6: Bioinformatics, Elsevier, 2006.
Training students to administer and defend computer networks and systems. Brian Tjaden and Brett Tjaden. ACM SIGCSE Bulletin, 38(3):245-249, 2006.
Applications of Genomic Data: Microarrays, Expression Analysis, and Bacterial Genomes. Carsten Rosenow and Brian Tjaden. Microbial Genomes, Humana Press, 2004.
System and method for efficient and adaptive web accesses filtering. Sandeep R. Nair, Kingsum Chow, Ken T. Deeter, and Brian C. Tjaden. United States Patent (6,741,990), 2004.
Global analysis of small RNA and mRNA targets of Hfq. Aixia Zhang, Karen M. Wassarman, Carsten Rosenow, Brian Tjaden, Gisela Storz, and Susan Gottesman. Molecular Microbiology, 50(4):1111-1124, 2003. Supplemental data available.
Coding in tongues: A bilingual programming perspective to data structures. Brian Tjaden and Hannah Tang. Journal of Computing Sciences in Colleges, 18(5):151-158, 2003.
Initial proteome analysis of model microorganism Haemophilus influenzae Rd strain KW20. Eugene Kolker, Samuel Purvine, Michael Y. Galperin, Serg Stolyar, David R. Goodlett, Alexey I. Nesvizhskii, Andrew Keller, Tao Xie, Jimmy K. Eng, Eugene Yi, Leroy Hood, Alex F. Picone, Tim Cherny, Brian C. Tjaden, Andrew F. Siegel, Thomas J. Reilly, Kira S. Makarova, Bernhard O. Palsson, and Arnold L. Smith. Journal of Bacteriology, 185(15):4593-4602, 2003.
Computational Methods for Transcription Analysis Using Oligonucleotide Microarrays. Brian Tjaden. Doctoral Dissertation, University of Washington, 2003.
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Brian Tjaden, Rini Mukherjee Saxena, Sergey Stolyar, David R. Haynor, Eugene Kolker, and Carsten Rosenow. Nucleic Acids Research, 30(17):3732-3738, 2002. Supplemental data available.
Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis. Brian Tjaden, David R. Haynor, Sergey Stolyar, Carsten Rosenow, and Eugene Kolker. Bioinformatics, 18: S337-S344, 2002. Supplemental data available.
Spectral analysis of distributions: finding periodic components in eukaryotic enzyme length data. Eugene Kolker, Brian C. Tjaden, Robert Hubley, Edward N. Trifonov, Andrew F. Siegel. Omics: A Journal of Integrative Biology, 6(1):123-130, 2002.
The inverse nearest neighbor problem with astrophysical applications. Richard Anderson and Brian Tjaden. Proceedings of the Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms, 767-768, 2001.
