Daigle Lab Publications

For further information, consult Google Scholar or PubMed.

2017

Rasha Hammamieh; Nabarun Chakraborty; Aarti Gautam; Seid Muhie; Ruoting Yang; Duncan Donohue; Raina Kumar; Bernie J Daigle Jr.; Yuanyang Zhang; Duna Abu-Amara; Stacy-Ann Miller; Seshmalini Srinivasan; Janine Flory; Rachel Yehuda; Linda Petzold; Owen M Wolkowitz; Synthia H Mellon; Leroy Hood; Francis J Doyle III; Charles Marmar; Marti Jett

Whole-Genome DNA Methylation Status Associated with Clinical PTSD Measures of OIF/OEF Veterans Journal Article

Translational Psychiatry, 7 (7), pp. e1169, 2017.

Abstract | Links | BibTeX

2016

Brian Drawert; Andreas Hellander; Ben Bales; Debjani Banerjee; Giovanni Bellesia; Bernie J Daigle Jr.; Geoffrey Douglas; Mengyuan Gu; Anand Gupta; Stefan Hellander; Chris Horuk; Dibyendu Nath; Aviral Takkar; Sheng Wu; Per Lötstedt; Chandra Krintz; Linda R Petzold

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist Journal Article

PLOS Computational Biology, 12 (12), pp. e1005220, 2016, ISSN: 1553-7358.

Abstract | Links | BibTeX

Min K Roh; Bernie J Daigle Jr.

SParSE++: Improved Event-Based Stochastic Parameter Search Journal Article

BMC Systems Biology, 10 , pp. 109, 2016, ISSN: 1752-0509.

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Eric C Rouchka; Julia H Chariker; Benjamin J Harrison; Juw Won Park; Xueyuan Cao; Stanley Pounds; Susana Raimondi; James Downing; Raul Ribeiro; Jeffery Rubnitz; Jatinder Lamba; Bernie J Daigle Jr.; Deborah Burgess; Stephanie Gehrlich; John C Carmen; Nicholas Johnson; Chandrakanth Emani; Stephanie Gehrlich; Deborah Burgess; John C Carmen; Kalpani De Silva; Michael P Heaton; Theodore S Kalbfleisch; Teeradache Viangteeravat; Rahul Mudunuri; Oluwaseun Ajayi; Fatih c Sen; Eunice Y Huang; Mohammad Mohebbi; Luaire Florian; Douglas J Jackson; John F Naber; AKM Sabbir; Sally R Ellingson; Yuping Lu; Charles A Phillips; Michael A Langston; Rahul K Sevakula; Raghuveer Thirukovalluru; Nishchal K Verma; Yan Cui; Mohammed Sayed; Juw Won Park; Jing Wang; Qi Liu; Yu Shyr; Xiaofei Zhang; Sally R Ellingson; Naresh Prodduturi; Gavin R Oliver; Diane Grill; Jie Na; Jeanette Eckel-Passow; Eric W Klee; Michael M Goodin; Mark Farman; Harrison Inocencio; Chanyong Jang; Jerzy W Jaromczyk; Neil Moore; Kelly Sovacool; Leon Dent; Mike Izban; Sammed Mandape; Shruti Sakhare; Siddharth Pratap; Dana Marshall; Scotty M DePriest; James N MacLeod; Theodore S Kalbfleisch; Chandrakanth Emani; Hanady Adam; Ethan Blandford; Joel Campbell; Joshua Castlen; Brittany Dixon; Ginger Gilbert; Aaron Hall; Philip Kreisle; Jessica Lasher; Bethany Oakes; Allison Speer; Maximilian Valentine; Naga Satya Rao V Nagisetty; Rony Jose; Teeradache Viangteeravat; Robert Rooney; David Hains

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016 Journal Article

BMC Bioinformatics, 17 (10), pp. 297, 2016, ISSN: 1471-2105.

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Nabarun Chakraborty; Seid Muhie; Ruoting Yang; Aarti Gautam; Duncan Donohue; Bernie J Daigle Jr.; Yuanyang Zhang; Duna Abu Amara; Jannie Flory; Rachel Yehuda; Frank Doyle; Rasha Hammamieh; Charles Marmar; Marti Jett

Characterization of the Epigenomic Status of the US OEF/OIF War Veterans: A Pilot Clinical Study Journal Article

The FASEB Journal, 30 (1 Supplement), pp. 831.3–831.3, 2016, ISSN: 0892-6638, 1530-6860.

Abstract | BibTeX

Yuanyang Zhang; Tie Bo Wu; Bernie J Daigle Jr.; Mitchell Cohen; Linda Petzold

Identification of Disease States Associated with Coagulopathy in Trauma Journal Article

BMC Medical Informatics and Decision Making, 16 , pp. 124, 2016, ISSN: 1472-6947.

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Gunjan S Thakur; Bernie J Daigle Jr.; Meng Qian; Kelsey R Dean; Yuanyang Zhang; Ruoting Yang; Taek-Kyun Kim; Xiaogang Wu; Meng Li; Inyoul Lee; Linda R Petzold; Francis J Doyle III

A Multi-Metric Evaluation of Stratified Random Sampling for Classification: A Case Study Journal Article

IEEE Life Sciences Letters, PP (99), pp. 1–1, 2016.

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2015

Gunjan S Thakur; Bernie J Daigle Jr.; Kelsey Dean; Linda R Petzold; Francis J Doyle III

Metric Focused Feature Selection for Customized Biomarker Identification Inproceedings

The Fifth International Conference on Foundations of Systems Biology in Engineering (FOSBE 2015), 2015.

BibTeX

Gunjan S Thakur; Bernie J Daigle Jr.; Kelsey R Dean; Yuanyang Zhang; Maria Rodriguez-Fernandez; Rasha Hammamieh; Ruoting Yang; Marti Jett; Joseph Palma; Linda R Petzold; Francis J Doyle III

Systems Biology Approach to Understanding Post-Traumatic Stress Disorder Journal Article

Molecular BioSystems, 11 (4), pp. 980–993, 2015, ISSN: 1742-2051.

Abstract | Links | BibTeX

Bernie J Daigle Jr.; Mohammad Soltani; Linda R Petzold; Abhyudai Singh

Inferring Single-Cell Gene Expression Mechanisms Using Stochastic Simulation Journal Article

Bioinformatics, 31 (9), pp. 1428–1435, 2015, ISSN: 1367-4803, 1460-2059.

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Yuanyang Zhang; Bernie J Daigle Jr.; Mitchell Cohen; Linda R Petzold

A Cure Time Model for Joint Prediction of Outcome and Time-to-Outcome Inproceedings

2015 IEEE International Conference on Data Mining (ICDM), pp. 1117–1122, 2015.

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2014

Yuanyang Zhang; Bernie J Daigle Jr.; Lisa Ferrigno; Mitchell Cohen; Linda R Petzold

Data-Driven Mortality Prediction for Trauma Patients Journal Article

Selected for presentation at the Machine Learning in Computational Biology workshop (MLCB 2014) in the Twenty-eighth Annual Conference on Neural Information Processing Systems (NIPS 2014), 2014.

BibTeX

Gunjan S Thakur; Bernie J Daigle Jr.; Linda R Petzold; Francis J Doyle III

A Multivariate Ensemble Approach for Identification of Biomarkers: Application to Breast Cancer Inproceedings

The 19th World Congress of the International Federation of Automatic Control (IFAC), pp. 809–814, 2014.

BibTeX

2013

Linda Petzold; Yuanyang Zhang; Bernie J Daigle Jr.; Lisa Ferrigno; Mitch Cohen

Toward a Data-Driven Model of Trauma Dynamics Journal Article

Journal of Critical Care, 28 (6), pp. e37, 2013, ISSN: 0883-9441.

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Ruoting Yang; Bernie J Daigle Jr.; Seid Y Muhie; Rasha Hammamieh; Marti Jett; Linda Petzold; Francis J Doyle III

Core Modular Blood and Brain Biomarkers in Social Defeat Mouse Model for Post Traumatic Stress Disorder Journal Article

BMC Systems Biology, 7 (1), pp. 80, 2013, ISSN: 1752-0509.

Abstract | Links | BibTeX

2012

Ruoting Yang; Bernie J Daigle Jr.; Linda R Petzold; Francis J Doyle III

Core Module Biomarker Identification with Network Exploration for Breast Cancer Metastasis Journal Article

BMC Bioinformatics, 13 (1), pp. 12, 2012, ISSN: 1471-2105.

Abstract | Links | BibTeX

Bernie J Daigle Jr.; Min K Roh; Linda R Petzold; Jarad Niemi

Accelerated Maximum Likelihood Parameter Estimation for Stochastic Biochemical Systems Journal Article

BMC Bioinformatics, 13 (1), pp. 68, 2012, ISSN: 1471-2105.

Abstract | Links | BibTeX

Robin E White; Curtis Palm; Lijun Xu; Evelyn Ling; Mitchell Ginsburg; Bernie J Daigle Jr.; Ruquan Han; Andrew Patterson; Russ B Altman; Rona G Giffard

Mice Lacking the $B$2 Adrenergic Receptor Have a Unique Genetic Profile before and after Focal Brain Ischaemia Journal Article

ASN Neuro, 4 (5), pp. AN20110020, 2012, ISSN: , 1759-0914.

Abstract | Links | BibTeX

Ruoting Yang; Bernie J Daigle Jr.; Linda R Petzold; Francis J Doyle III

Core Module Network Construction for Breast Cancer Metastasis Inproceedings

2012 10th World Congress on Intelligent Control and Automation (WCICA), pp. 5083–5089, 2012.

Abstract | Links | BibTeX

2011

Min K Roh; Bernie J Daigle Jr.; Dan T Gillespie; Linda R Petzold

State-Dependent Doubly Weighted Stochastic Simulation Algorithm for Automatic Characterization of Stochastic Biochemical Rare Events Journal Article

The Journal of Chemical Physics, 135 (23), pp. 234108, 2011, ISSN: 0021-9606, 1089-7690.

Abstract | Links | BibTeX

Bernie J Daigle Jr.; Min K Roh; Dan T Gillespie; Linda R Petzold

Automated Estimation of Rare Event Probabilities in Biochemical Systems Journal Article

The Journal of Chemical Physics, 134 (4), pp. 044110, 2011, ISSN: 0021-9606, 1089-7690.

Abstract | Links | BibTeX

2010

Jesse M Engreitz; Bernie J Daigle Jr.; Jonathan J Marshall; Russ B Altman

Independent Component Analysis: Mining Microarray Data for Fundamental Human Gene Expression Modules Journal Article

Journal of Biomedical Informatics, 43 (6), pp. 932–944, 2010, ISSN: 1532-0464.

Abstract | Links | BibTeX

Bernie J Daigle Jr.; Alicia Deng; Tracey McLaughlin; Samuel W Cushman; Margaret C Cam; Gerald Reaven; Philip S Tsao; Russ B Altman

Using Pre-Existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance Journal Article

PLoS Comput Biol, 6 (3), pp. e1000718, 2010.

Abstract | Links | BibTeX

Bernie J Daigle Jr.; Balaji S Srinivasan; Jason A Flannick; Antal F Novak; Serafim Batzoglou

Current Progress in Static and Dynamic Modeling of Biological Networks Incollection

Sangdun Choi (Ed.): Systems Biology for Signaling Networks, pp. 13–73, Springer New York, 2010, ISBN: 978-1-4419-5796-2 978-1-4419-5797-9.

Abstract | Links | BibTeX

2008

Bernie J Daigle Jr.; Russ B Altman

M-BISON: Microarray-Based Integration of Data Sources Using Networks Journal Article

BMC Bioinformatics, 9 (1), pp. 214, 2008, ISSN: 1471-2105.

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2004

Stephen R Yant; Xiaolin Wu; Yong Huang; Bernie J Daigle Jr.; Brian A Garrison; Shawn M Burgess; Mark A Kay

Nonrandom Insertion Site Preferences for the SB Transposon in Vitro and in Vivo Journal Article

Molecular Therapy, 9 , pp. S309–S310, 2004.

BibTeX

2003

Stephen R Yant; Brian A Garrison; Bernie J Daigle Jr.; Mark A Kay

Analysis of Target Site Selection for the Sleeping Beauty Transposon in Mouse Liver Journal Article

Molecular Therapy, 7 (5), pp. S63–S63, 2003.

BibTeX

2002

Garth D Ehrlich; Richard Veeh; Xue Wang; William J Costerton; Jay D Hayes; Fen Z Hu; Bernie J Daigle Jr.; Miles D Ehrlich; Christopher J Post

Mucosal Biofilm Formation on Middle-Ear Mucosa in the Chinchilla Model of Otitis Media Journal Article

JAMA, 287 (13), pp. 1710–1715, 2002, ISSN: 0098-7484.

Abstract | Links | BibTeX