dr. dennis r. livesay - wichita state university · dr. dennis r. livesay curriculum vitae june 11,...

Dr. Dennis R. Livesay Curriculum Vitae

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Dr. Dennis R. Livesay 1901 N. Split Rail St., Wichita, KS 67230 p/ 704-773-6296 | e/ [email protected]

1 Academic and Professional History

1.1 Education

PhD in Physical Chemistry (2000) University of Illinois at Urbana-Champaign

BS in Chemistry (1996) Ball State University

1.2 Academic Positions

Wichita State University

-- Dean of the Graduate School (2016-present) -- Associate Vice President of Research and Technology Transfer (2016-present) -- Institutional Officer for both IRB and IACUC (2016-present) -- Professor of Chemistry (2016-present)

University of North Carolina at Charlotte

-- Provost’s Faculty Fellow (2015-2016) -- Chair, Graduate Council (2015-2016) -- Professor of Bioinformatics and Genomics (2014-2016) -- Interim Associate Dean for Graduate Programs (2014-2015) -- Interim Director, Computing and Information Systems PhD program (2014-2015) -- Founding Director, Charlotte Research Scholars (2012-2016) -- President, College of Computing and Informatics Faculty (2012-2013) -- Founding Director, Bioinformatics & Computational Biology PhD program (2011-2015) -- Associate Professor of Bioinformatics and Genomics (2008-2014) -- Chair, Computing and Information Systems PhD Steering Committee (2007-2010) -- Associate Professor of Computer Science (2006-2008)

California State Polytechnic University at Pomona

-- Associate Professor of Chemistry (2005-2006) -- Graduate Coordinator (2000-2006) -- Assistant Professor of Chemistry (2000-2005)


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1.3 Administrative Accomplishments

Dean of the Graduate School and Associate Vice President of Research and Technology Transfer, Wichita State University (2016-present)

-- Successfully developed and implemented a holistic and integrated Graduate Enrollment Management framework to increase enrollment and improve program quality through alignment of all program investments, including graduate teaching and research assistantship allocations

-- Led a critical overhaul of graduate school governing policies and procedures to promote enrollment growth, support new educational opportunities (i.e., badges and MicroMasters), and allow for stackable credentialing

-- Initiated and oversaw university-wide efforts to promote social, cultural, and professional community within our graduate student community

-- Actively involved in President-level discussions and efforts related to sustainable economic development within the immediately surrounding neighborhoods and the greater Wichita region

-- Faculty-facing administrator within the Office of Research and Technology Transfer

-- Oversaw implementation of a new Graduate School admissions and CRM system

-- Developed and oversaw an Interdisciplinary Research Team faculty cluster hire program, and facilitated university-wide discussions regarding new research directions (in progress)

-- Chair of the ad hoc Faculty Senate committee that successfully redesigned the University’s academic honesty policy, which was a collaboration between Academic Affairs and Student Conduct

-- Search committee chair for the dean of the Fairmount College of Arts and Sciences and member of the search committee for provost and vice president of Academic Affairs

About WSU: WSU is a public 4-year university with 14,500 students (2700 graduate students) | $90 million in external research funding, 50.3% of which is industry funded (which is the second highest percentage tracked by NSF) | Carnegie classification = Doctoral University: Higher Research Activity | 12 doctoral and over 40 master’s programs

Provost’s Faculty Fellow; Division of Academic Affairs, UNC Charlotte (2015-2016)

-- Developed a roadmap for a new Undergraduate Research Office to improve access to undergraduate research, which is a key part of the university’s engagement strategy

Chair, Graduate Council; Graduate School, UNC Charlotte (2015-2016)

-- The Council reviews, develops, and makes recommendations regarding policy and all academic proposals

-- Led a campuswide process to reconcile formal program requirements listed within the Graduate Catalog with current practice

-- Served in advisory capacity to the Dean of the Graduate School and Associate Provost


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Interim Associate Dean of Graduate Programs; College of Computing and Informatics, UNC Charlotte (2014-2015)

-- Administrative responsibility for all graduate programs in the College of Computing and Informatics (CCI), totaling more than 700 students

-- Led efforts to strengthen early entry programs and modularize the college’s MS programs

-- Developed an ambitious graduate enrollment projection plan

-- Led redesign of CCI Honors undergraduate program, which led to a focus on developing leadership skills and includes an executive mentoring component

-- Oversaw all of the college’s assessment and accreditation responsibilities

About UNC Charlotte and CCI: UNC Charlotte is a public 4-year university with 28,000 students | Carnegie classification = Doctoral University: Higher Research Activity and is Community Engagement classified | The College of Computing and Informatics has 2,600 students in 3 academic departments (including 700 graduate students) | 2 doctoral programs and 6 master’s degrees | External funding portfolio of nearly $30 million (best externally funded college per capita at UNC Charlotte)

Interim Director of the Computing and Information Systems PhD program; College of Computing and Informatics, UNC Charlotte (2014-2015)

-- Led several curricula and programmatic updates, including overhaul of the qualifying exam and creation of track-specific core class requirements

-- Operational oversight of the program, which included 110 funded doctoral students

Founding Director of the Charlotte Research Scholars; The Graduate School and Division of Academic Affairs, UNC Charlotte (2012-2016)

-- Developed and managed all aspects of the program, including participant selection, mentor matching, professional development, media relations, and the annual capstone symposium

-- Became de facto campus point person for undergraduate research, working across campus on the development and promotion of undergraduate research opportunities

-- Annual reach: 55 Charlotte Research Scholars + more than 50 additional participants from partnering programs (including three NSF REU programs)

President of the Faculty; College of Computing and Informatics, UNC Charlotte (2012-2013)

-- Led a successful redesign of our faculty governance structure that empowered faculty committees to do impactful work while reducing bureaucratic overhead

Founding Director of the Bioinformatics and Computational Biology PhD program; Department of Bioinformatics and Genomics, UNC Charlotte (2011-2015)

-- Oversaw development and implementation of all academic and operational aspects, including managing the GTA budget and chairing both the Admissions and Advising committees

-- The BCB program has been successful in nearly every metric—a majority of the students were female, our students won NSF and Gates graduate fellowships, the average time to completion was less than five years, and all secured positions in the discipline


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2 Honors and Awards

Outstanding Graduate Teaching Award, College of Computing and Informatics, UNC Charlotte (2014)

7th Annual Goldstein Distinguished Lecture, Cal Poly Pomona (2014)

-- Previous Goldstein lecturers are some of the most influential people in computational chemistry, including journal editors and a Nobelaurate

The National Honor Society of Phi Kappa Phi (2013)

UNC Charlotte Honors Faculty (2013)

Outstanding Faculty Research Award, College of Computing and Informatics, UNC Charlotte (2010)

NATO Advanced Study Institute; Les Houches, France (1998)

Department of Chemistry Graduate Fellowship; University of Illinois (1997)

Undergraduate Award for All-Around Achievement in Chemistry; Ball State University (1996)

1st Place; Midwest Regional Undergraduate Research Poster Competition; University of Kentucky (1996)

Graduated Cum Laude; Ball State University (1996)

Undergraduate Research Fellow; Ball State University (1995)

3 Research Funding

3.1 Summary

Total funded amount = $4.7 million (Based on total amounts for all grants where I am PI or key personnel)

3.2 Funded Research Grants

Graduate fellowships in bioinformatics and computational biology PI: Gibas CJ 2015-2018 US Department of Education (GAANN) Role: co-PI Amount: $738,195 Probing putative binding interactions across the entire antibody molecule PI: Livesay DR 2015-2016 MedImmune, LLC Role: PI Amount: $124,575 Predicting the effects of mutation on antibody stability and flexibility characteristics PI: Livesay DR 2013-2015 MedImmune, LLC Role: PI Amount: $99,495


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Elucidating beta-lactamase functional mechanisms via evolutionary conservation PI: Livesay DR 2013-2015 NIH R15 GM101570 Role: PI Amount: $322,984 Quantitative stability/flexibility relationships within antibody fragments PI: Livesay DR 2013 MedImmune, LLC Role: PI Amount: $32,670 Quantitative stability/flexibility relationships in the GABA transport protein PI: Livesay DR 2012-2013 UNC Charlotte Faculty Research Grant Role: PI Amount: $12,000 Antibody fragment stability: A focus on domain-domain interactions PI: Livesay DR 2011-2012 MedImmune, LLC Role: PI Amount: $99,495 ARRA supplement to: Predicting protein stability and flexibility PI: Jacobs DJ 2010-2011 NIH R01 GM073082-04S2 Role: Investigator Amount: $102,125 (Effectively co-PI, but that option was not available at NIH at that time) High performance computing in computational biology PI: Livesay DR 2010-2011 NIH S10 SRR026514 Role: PI Amount: $474,288 Predicting protein stability and flexibility PI: Jacobs DJ 2006-2011 NIH R01 GM073082 Role: Investigator Amount: $1,459,968 (Effectively co-PI, but that option was not available at NIH at that time) Center for macromolecular modeling and material design PI: Ortiz JM (Cal Poly Pomona President) 2006-2007 W.M. Keck Foundation Role: Co-PI & primary grant writer Amount: $500,000 Phylogenetic similarity maximization: A new algorithm for phylogenetic motif detection PI: Livesay DR 2005-2006 CSUPERB-Joint Venture Grant Role: PI Amount: $21,200 + 2 programmers in Bangalore (in-kind from Agiline, Inc.)


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Acquisition of a workstation network for research in parallel and distributed computing PI: Kuang H 2003-2005 NSF MRI 032-1333 Role: Co-PI Amount: $159,658 Bioinformatics study correlating protein flexibility with function PI: Jacobs DJ 2003 CSUPERB-Joint Venture Matching Grant Role: Co-PI Amount: $25,000 + $75,000 (in-kind from Cengent Therapeutics) Investigation of superoxide dismutase surface electrostatics PI: Livesay DR 2002-2004 NIH S06 GM53933-07 Role: PI Amount: $178,000 Dihedral-angle characterization of conformational flexibility in protein structure PI: Jacobs DJ 2002-2005 NIH S06 GM48680-0952 Role: Paid consultant Amount: $370,328 Conferring thermostability to mesophilic proteins through systematic mutation of surface residues PI: Livesay DR 2001-2003 ACS Petroleum Research Fund 36848-GB4 Role: PI Amount: $25,000

4 Publications

4.1 Summary

Journal publications = 44 Peer-reviewed conference papers = 6

Invited book chapters = 6 H-Index (by Google Scholar) = 23

i10-Index (by Google Scholar) = 41 Total citations (by Google Scholar) = 1452

4.2 Journal Publications

Srivastava A, Tracka MB, Uddin S, Casas-Finet J, Livesay DR, Jacobs DJ (2016). Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations. Biophysical Journal, 110:1933-1942. Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR (2015). Rigidity emerges during antibody evolution in three distinct antibody systems: Evidence from QSFR analysis of Fab fragments. PLOS Computational Biology, 11:e1004327. González LC, Wang H, Livesay DR, Jacobs DJ (2015). A virtual pebble game to ensemble average graph rigidity. Algorithms for Molecular Biology, 10:11.


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Brown JR, Livesay DR (2015). Flexibility correlation between active site regions is conserved across four AmpC β-lactamase enzymes. PLOS ONE, 10:e0125832. Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR (2014). Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier’s principle. PLOS ONE, 9:e92870. Li T, Verma D, Tracka MB, Casas-Finet J, Livesay DR, Jacobs DJ (2014). Thermodynamic stability and flexibility characteristics of antibody fragment complexes. Protein and Peptide Letters, 21:752-65. Verma D, Jacobs DJ, Livesay DR (2013). Variations within class-A β-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity. PLOS Computational Biology, 9:e1003155. Verma D, Jacobs DJ, Livesay DR (2012). Changes in lysozyme flexibility upon mutation are frequent, large and long-ranged. PLOS Computational Biology, 8:e1002409. González LC, Wang H, Livesay DR, Jacobs DJ (2012). Calculating ensemble averaged descriptions of protein rigidity without sampling. PLOS ONE, 7:e29176. Vorov OK, Livesay DR, Jacobs DJ (2011). Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity. Biophysical Journal, 100:1129-1138. KC DB, Livesay DR (2011). Topology improves phylogenetic motif functional site predictions. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8:226-233. Livesay DR (2010). Protein dynamics: Dancing on an ever-changing free energy stage. Current Opinion in Pharmacology, 10:706-708. Verma D, Jacobs DJ, Livesay DR (2010). Predicting the melting point of human c-type lysozyme mutants. Current Protein and Peptide Science, 11:562-572. Mottonen JM, Jacobs DJ, Livesay DR (2010). Allosteric response is both conserved and variable across three CheY orthologs. Biophysical Journal, 99:2245-2254. Chikkagoudar S, Livesay DR, Roshan U (2010). PLAST-ncRNA: Partition function local alignment search tool for non-coding RNA sequences. Nucleic Acids Research, 38:W59-W63. Vorov OK, Livesay DR, Jacobs DJ (2009). Helix/coil nucleation: A local response to global demands. Biophysical Journal, 97:3000-3009. Jasuja R, Ulloor J, Yengo CM, Choong K, Istomin AY, Livesay DR, Jacobs DJ, Swerdloff RS, Miksovska J, Larsen RW, Bhasin S (2009). Kinetic and thermodynamic characterization of dihydrotestosterone-induced conformational perturbations in androgen receptor ligand binding domain. Molecular Endocrinology, 23:1231-1241.


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Mottonen JM, Xu M, Jacobs DJ, Livesay DR (2009). Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family. PROTEINS: Structure, Function, & Bioinformatics, 75:610-627. KC DB, Livesay DR (2008). Improving position specific predictions of protein functional sites using phylogenetic motifs. Bioinformatics, 24:2308-2316. Vorov OK, Livesay DR, Jacobs DJ (2008). Conformational entropy of an ideal cross-linking polymer chain. Entropy, 10:285-308. Livesay DR, Huynh DH, Dallakyan S, Jacobs DJ (2008). Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family. Chemistry Central Journal, 2:17. Roshan U, Chikkagoudar S, Livesay DR (2008). Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. BMC Bioinformatics, 9:61. Istomin AY, Gromiha MM, Vorov OK, Jacobs DJ, Livesay DR (2008). New insight into long-range nonadditivity within protein double-mutant cycles. PROTEINS: Structure, Function, & Bioinformatics, 70:915-924. Istomin AY, Jacobs DJ, Livesay DR (2007). On the role of structural class of a protein with two-state folding kinetics in determining correlations between its size, topology, and folding rate. Protein Science, 16:2564-2569. Livesay DR, Kidd PD, Eskandari S, Roshan U (2007). Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family. BMC Bioinformatics, 8:397. Livesay DR (2007). At the crossroads of biomacromolecular research: highlighting the interdisciplinary nature of the field. Chemistry Central Journal, 1:4. Chea E, Livesay DR (2007). How accurate and statistically robust are catalytic site predictions based on closeness centrality? BMC Bioinformatics, 8:153 (Journal promotional poster was based on a figure from this paper; see it here). Chikkagoudar S, Roshan U, Livesay DR (2007). eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. Nucleic Acids Research, 35:W675-W677. Roshan U, Livesay DR (2006). Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics, 22:2715-2721. Livesay DR, Jacobs DJ, Kanjanapangka J, Chea E, Cortez H, Garcia J, Kidd P, Marquez MP, Pande S, Yang D (2006). Probing the conformational dependence of calculated pKa values. Journal of Chemical Theory and Computation, 2:927-938.


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Jacobs DJ, Livesay DR, Hules J, Tasayco ML (2006). Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a Distance Constraint Model. Journal of Molecular Biology, 358:882-904. Livesay DR, Jacobs DJ (2006). Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair. PROTEINS: Structure, Function, & Bioinformatics, 62:130-143. La D, Livesay DR (2005). MINER: Software for phylogenetic motif identification. Nucleic Acids Research, 33:W267-W270. La D, Livesay DR (2005). Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics, 6:116. Livesay DR, La D (2005). Probing the evolutionary origins and catalytic importance of conserved electrostatic networks in TIM-barrel proteins. Protein Science, 14:1158-1170. La D, Sutch B, Livesay DR (2005). Predicting protein functional sites with phylogenetic motifs. PROTEINS: Structure, Function, & Bioinformatics, 58:309-320 (Featured on the cover). Livesay DR, Dallakayan S, Woods GG, Jacobs DJ (2004). A flexible approach for understanding protein thermodynamics. FEBS Letters, 576:468-476. Livesay DR, Subramaniam S (2004). Conserved sequence and structure association motifs in antibody-protein and antibody-hapten complexes. Protein Engineering, Design, & Selection, 17:463-472. Alsop E, Silver MA, Livesay DR (2003). Optimized electrostatic surfaces parallel increased thermostability: A structural bioinformatics analysis. Protein Engineering, 16:871-874. Torrez M, Schultehenrich M, Livesay DR (2003). Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces. Biophysical Journal, 85:2845-2853. La D, Silver MA, Edgar RC, Livesay DR (2003). Using motif-based methods in multiple genome analyses: A case study comparing orthologous mesophilic and thermophilic proteins. Biochemistry, 42:8988-8998. Livesay DR, Jambeck P, Rojnuckarin A, Subramaniam S (2003). Conservation of electrostatic properties within enzyme families and superfamilies. Biochemistry, 42:3464-3473 (Faculty of 1000 “Must Read”). Rojnuckarin A, Livesay DR, Subramaniam S (2000). Reaction rate prediction with weighted ensemble Brownian dynamics and the University of Houston Brownian Dynamics program. Biophysical Journal, 79:686-693. Livesay DR, Linthicum SD, Subramaniam S (1999). pH dependence of antibody-hapten association. Molecular Immunology, 36:397-410.


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4.3 Peer Reviewed Conference Papers

Barlow S, Yang J, Jacobs DJ, Livesay DR, Alsakran J, Zhao Y, Verma D, Mottonen J (2013). A visual analytics approach to exploring protein flexibility subspaces. PacificVis, 193-200. González LC, Livesay DR, Jacobs DJ (2011). Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual pebble game. Second ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 294-298. Barlow S, Liu Y, Yang J, Livesay DR, Jacobs DJ, Mottonen J, Verma D (2011). WaveMap: Interactively discovering features from protein flexibility matrices using wavelet-based visual analytics. Computer Graphics Forum, 30:1001-1010. Pande S, Raheja A, Livesay DR (2007). Prediction of enzyme catalytic sites from sequence using neural networks. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 247-253. Roshan U, Livesay DR, Chikkagoudar S (2006). Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees. Sixth IEEE Symposium on Bioinformatics and Bioengineering, 159-164. Roshan U, Livesay DR, La D (2005). Improved phylogenetic motif detection using parsimony. Fifth IEEE Symposium on Bioinformatics and Bioengineering, 19-26.

4.4 Peer Reviewed Book Chapters

Verma D, Guo JT, Jacobs DJ, Livesay DR (2014). Towards comprehensive analysis of protein family quantitative stability/flexibility relationships using homology models. In Protein Dynamics: Methods and Protocols, D.R. Livesay (Ed.), Springer, ISBN: 978-1-62703-657-3. Brown M, Verma D, Russell C, Jacobs DJ, Livesay DR (2014). A case study comparing quantitative stability/flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1. In Protein Dynamics: Methods and Protocols, D.R. Livesay (Ed.), Springer, ISBN: 978-1-62703-657-3. Jacobs DJ, Livesay DR, Mottonen JM, Vorov OK, Istomin AY, Verma D (2012). Ensemble properties of network rigidity reveal allosteric mechanisms. In Allostery: Methods and Protocols, A. Fenton (Ed.), Springer, ISBN: 978-1-61779-333-2. Livesay DR, Kreth KE, Fodor AA (2012). A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms. In Allostery: Methods and Protocols, A. Fenton (Ed.), Springer, ISBN: 978-1-61779-333-2. Livesay DR, KC DB, La D. Predicting protein functional sites with phylogenetic motifs: Past, present and beyond (2011). In Protein Function Prediction for the Omics Era, D. Kihara (Ed.), Springer, ISBN: 978-94-007-0880-8. KC DB, Livesay DR. A spectrum of phylogenetic-based approaches for predicting protein functional sites (2009). In Bioinformatics for Systems Biology, S. Krawetz (Ed.), Humana Press, ISBN: 978-1-934115-02-2.


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4.5 Editor

Book: Protein Dynamics: Methods and Protocols, D.R. Livesay (Ed.), Springer, ISBN: 978-1-62703-657-3, 2014. Special Issue: Current Opinion in Pharmacology on “The importance of protein dynamics,” D.R. Livesay (Ed.), 2010.

4.6 Patents Awarded

Jacobs DJ, Livesay DR (2013). Computer implemented system for protein and drug target design utilizing quantitative stability/flexibility relationships. United States Patent 8374828.

4.7 Doctoral Dissertation

Livesay DR (2000). Conservation of electrostatically mediated function across protein families and superfamilies. Advisor: Shankar Subramaniam.

5 Professional Presentations

5.1 Invited Research Talks at Professional Conferences

Entangled relationships: protein flexibility, allostery, and mutation. 253rd American Chemical Society National Meeting, San Francisco, CA, 2017. Revealing the complicated relationships between antibody fragment stability, structural flexibility, and allosteric response. 7th Annual Biotherapeutics Analytical Summit, Bethesda, MD 2016 (Keynote Speaker). Structural flexibility and allosteric responses are widely redistributed within antibody fragments upon mutation. PEGS: The Essential Protein Engineering Summit, Boston, MA, 2015.

-- Also chaired a discussion session on Emerging Computational Technologies to Streamline the Development of Protein Therapeutics

Dissecting cooperativity one H-bond at a time (presenter: Smith BK). 29th Annual Gibbs Conference on Biothermodynamics, Carbondale, IL, 2015. Modulating allosteric response in scFv antibody fragments through mutation is linked to changes in the hydrogen bond network (presenter: Srivastava A). 10th EBSA European Biophysics Congress, Dresden, Germany, 2015. WaveMap: Feature discovery using visual analytics. Informs 2011 Annual Meeting, Charlotte, NC, 2011. Conservation of electrostatic properties across protein family divergence. Modeling Electrostatics in Molecular Biology Conference, Clemson, SC, 2011. FAST predictions of protein stability and flexibility. 240th American Chemical Society National Meeting, Boston, MA, 2010.


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5.2 Invited Research Talks at Universities, Industry, and Research Labs

Does nature love chemistry and physics as much as I do? A biophysical chemist attempts to explain protein family evolution. 7th Annual Chevy Goldstein Distinguished Lecture, Pomona, CA, 2014. Predicting allosteric sites in antibody fragments. MedImmune, LLC, Gaithersburg, MD, 2014. Linking the sensitivity within protein dynamics to evolutionary processes. Department of Physics, Clemson University, Clemson, SC, 2013. Antibody fragment stability: A focus on domain-domain interactions (with D.J. Jacobs). MedImmune, LLC, Gaithersburg, MD, 2012 Quantifying protein stability and flexibility relationships. Department of Chemistry, Davidson College, Davidson, NC, 2011. FAST predictions of protein stability and flexibility (with D.J. Jacobs). MedImmune, LLC, Gaithersburg, MD, 2010. Predicting Protein Functional Sites from Multiple Sequence Alignments. Ensenada Center for Scientific Research and Higher Education, Ensenada, BC, Mexico, 2009. A unified description of protein folding cooperativity. Department of Physics, Appalachian State University, Boone, NC, 2009. Understanding protein family sequence/structure/function relationships: From biophysics to empiricism and back. Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, MO 2009. Quantitative stability/flexibility relationships (QSFR) within protein families. Department of Physics, Wake Forest University, Winston-Salem, NC 2007. Deciphering complex protein family sequence/structure/function relationships. College of Sciences, Washington State University, Pullman, WA, 2006.

-- Also presented at: Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 2006; Case Proteomics Center, Case Western Reserve University, Cleveland, OH, 2006; Wadsworth Center, New York State Department of Health, Albany, NY, 2006; Western University of Health Sciences, Department of Basic Medical Sciences, Pomona, CA, 2006

Toward improved understanding of protein family sequence/structure/function relationships. Department of Pharmacy, University of Southern California, Los Angeles, CA, 2005.

-- Also presented at: Albert Einstein College of Medicine, Bronx, NY, 2005; CUNY Staten Island, New York, NY, 2005

Engineering thermostability: Toward development of a protein design strategy that doesn’t compromise function at standard conditions. Keck Graduate Institute, Claremont, CA, 2004.

-- Also presented at: Program in Bioinformatics and Computational Biology, George Mason University, Manassas, VA, 2004; Department of Chemistry, San Diego State University, San Diego, CA, 2004; Bioinformatics/Statistical Genomics Seminar Series, Purdue University,


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West Lafayette, IN, 2004; Program in Bioinformatics, University of Michigan, Ann Arbor, MI, 2003

Understanding protein thermostability: Recent results from sequence and structure. Department of Chemistry, Loyola Marymount University, Los Angeles, CA, 2003. Sequence and structure insights into the molecular basis of thermostability. Bioinformatics and Computational Biology Group, University of California San Diego, La Jolla, CA, 2002. Using bioinformatics and molecular simulation to understand enzyme function. Department of Chemistry, California State University, San Bernardino, San Bernardino, CA, 2002. Conservation of electrostatically mediated function across protein families and superfamilies. Department of Physics, California State University, Northridge, Northridge, CA, 2001.

-- Also presented at: Department of Biology, Wabash College, Crawfordsville, IN, 2000

5.3 Research Poster Presentations (Selected from well over 100 posters)

Smith B, Jacobs DJ, Livesay DR (2015). Fluctuations within the hydrogen bond network modulate cooperativity across the conformational ensemble of protein structures. Biophysical Society 59th Annual Meeting, Baltimore, MD. Srivastava A, Track MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR (2015). Dynamic characteristics of allosteric pathways in scFv antibody fragments. Biophysical Society 59th Annual Meeting, Baltimore, MD. Brown JR, Livesay DR (2014). Flexibility correlation between active site regions is conserved across three AmpC β-lactamase enzymes. State of North Carolina Undergraduate Research and Creativity Symposium, Raleigh, NC. Brown JR, Livesay DR (2014). Quantitative stability/flexibility relationships in the class-C β-lactamase enzyme family. UNC Charlotte Summer Research Symposium, Charlotte, NC (Best poster in the Natural Sciences and Public Health category). Brown MC, Rabinowitz TM, Jacobs DJ, Livesay DR (2014). It’s hard to forget: 100ns simulations of β-lactamase mutants retain memory of starting conditions. CBES Research Poster Competition, Charlotte, NC. Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR (2014). Redistribution of flexibility in stabilizing antibody fragments follows Le Chatelier’s Principle. 58th Annual Meeting of the Biophysical Society, San Francisco, CA. Brown M, Verma D, Russell C, Jacobs DJ, Livesay DR (2013). Do stability/flexibility relationships explain antibiotic resistance activities within metallo-b-lactamases? Gordon Research Conference-Proteins, Holderness, NH. Li T, Verma D, Jacobs DJ, Livesay DR (2012). Thermodynamic stability and flexibility characteristics of antibody fragment complexes. 13th Annual Structure Based Drug Design Conference, Boston, MA.


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Verma D, Livesay DR (2012). Is rigidity conserved across the class-A b-lactamase family. 56th Annual Biophysical Society Meeting, San Diego, CA. Verma D, Jacobs DJ, Livesay DR (2012). Elucidating the Effects of Mutation upon c-type Lysozyme Quantitative Stability/Flexibility Relationships. 55th Annual Biophysical Society Meeting, Baltimore, MD. Livesay DR, Jacobs DJ, Vorov OK (2010). A Unified Model of Protein Folding Cooperativity. Gordon Research Conference-Protein Dynamics, Ventura, CA.

5.4 Other Academic Presentations

The balancing act: Program quality, enrollment targets and budget pressure (co-facilitator with J. Brown and P. Monaco). Council of Graduate Schools 2018 Summer Workshop, Chicago, IL, 2018.

Catalyzing change through graduate enrollment management. Midwest Association of Graduate Schools Annual Meeting, Grand Rapids, MI, 2018. Mentoring undergraduate student researchers: Best practices and lessons learned. Smith Institute for Applied Research, Johnson C. Smith University, Charlotte, NC, 2016. Making big plans: Growing honors through disciplinarily diverse capstone experiences (with M. Pereira and J. Warner). National Collegiate Honors Council Conference, Chicago, IL, 2015. What is bioinformatics? And why should I care? Department of Biology, Johnson C. Smith University, Charlotte, NC, 2011. Developing an "Intro to Bioinformatics" course: Content, pitfalls, & logistics. School of Information Science, Claremont Graduate University, Claremont, CA, 2002.

6 Research Trainee Supervision

6.1 Research Student Awards

Natural Sciences and Public Health best poster award, 3rd Annual Charlotte Summer Research Symposium (Jenna Brown, 2014) Graduate Dean’s Distinguished Dissertation Award, which is a university-wide competition (Deeptak Verma, 2013) Molecular Engineering and Design best poster award, 4th Annual CBES Graduate Student Poster Competition (Deeptak Verma, 2012) Cal Poly Pomona International Center Merit Scholarship (Swati Pande, 2006) Best Poster, Sigma Xi Graduate Research Poster Competition (David La, 2006) Howard Hughes Undergraduate Research Fellowship (Eric Chea, 2005)


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Don Eden Graduate Student Research Award, which is a CSU system-wide competition (David La, 2004) Poster Award, Annual Meeting of the Protein Society (David La and Melanie Silver, 2002)

6.2 Post-Doctoral Research Associates Supervised

Dr. Amit Srivastava (2014-2015); research topic: Computational methods to predict and understand allostery within antibodies; currently a research fellow at the School of Computational Sciences, Korea Institute for Advanced Study Dr. Tong Li (2012-2013); research topic: Computational methods to predict and understand quantitative stability/flexibility relationships (QSFR) within antibodies; currently a Bioinformatics Data Scientist at BASF Dr. Chuanbin Du (2008-2011); research topic: Development of sparse grids methods for interpolating high-dimensional free energy landscapes Dr. Hui Wang (2008-2010); research topic: Development and testing of an updated computational distant constraint model; currently a Vice President at Goldman Sachs Dr. James Mottonen (2006-2009); research topic: Computational methods to predict and understand quantitative stability/flexibility relationships (QSFR) across protein families Dr. Dukka KC (2006-2009); research topic: Functional site prediction using phylogenetic motifs; currently an Associate Professor of Computational Science and Engineering at NC A&T University Dr. Oleg Vorov (2006-2010); research topic: Theoretical investigations of the distant constraint model for studying protein stability and dynamics; RIP Dr. Andrei Istomin (2006-2008); research topic: Quantitative stability/flexibility relationships (QSFR) within proteins; currently a Vice President of Engineering at Bidz.com Dr. Jaydutt Bhalshankar (2006); research topic: Development and testing of a phylogenetic similarity maximization functional site prediction algorithm; currently a Bioinformatics Engineer at the Curie Institute

6.3 Doctoral Students Supervised

Dr. Deeptak Verma. PhD in Bioinformatics and Computational Biology (2012); dissertation title: Elucidating the effects of mutation and evolutionary divergence upon protein structure quantitative stability/flexibility relationships; currently a protein design research scientist at Merck Dr. Luis Carlos Gonzalez. PhD in Information Technology—Bioinformatics track (2011); dissertation title: A virtual pebble game to ensemble average graph rigidity; currently a Professor of Computer Science at the Autonomous University of Chihuahua


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6.4 Other Doctoral Dissertation Committees

Dr. Ivetth Corona. PhD in Bioinformatics and Computational Biology (2016); dissertation title: Structural analysis of protein-DNA binding specificity and its application to protein-DNA docking assessment; currently a post-doctoral research associate at Cedars-Sinai Hospital in Los Angeles Dr. Sajedeh Safari. PhD in Bioinformatics and Computational Biology (2016); dissertation title: Evolution of flavonoid pathway in legumes Dr. Kyle Kreth. PhD in Bioinformatics and Computational Biology (2014); dissertation title: Studies on correlated mutations algorithms of proteins providing structural, spatial, and allostery information from multiple sequence alignments; currently a director at CenturyLink Cognilytics Dr. Wei Song. PhD in Bioinformatics and Computational Biology (2013); dissertation title: Modeling, simulation and analysis of the reaction field for electrostatic interactions in aqueous solution; currently a post-doctoral research associate at University of Maryland School of Medicine Dr. Charles David. PhD in Bioinformatics and Computational Biology (2012); dissertation title: Essential dynamics of proteins using geometrical simulations and subspace analysis; currently a bioinformatician at the New Zealand Institute for Plant & Food Research Dr. Scott Barlow. PhD in Information Technology—Computer Science track (2011); dissertation title: A visual analytics approach to feature discovery and subspace exploration in protein flexibility matrices; currently an Assistant Professor of Computer Science at Western Carolina University Dr. Melanie Spencer. PhD in Bioinformatics and Computational Biology (2011); dissertation title: Stability, resistance and change in mammalian microbiota and their associations with host health; currently an Associate Vice President of Clinical and Outcomes Research at Carolinas HealthCare System

6.5 Masters Students Supervised

Brittany Smith. PSM in Bioinformatics (2015); research topic: Cooperativity within protein stability/flexibility relationships; currently a doctoral student at Washington University, St. Louis Tony Dao. PSM in Bioinformatics (2013); research topic: Predicting stability/flexibility relationships with the distant constraint model Swati Pande. MS in Biological Sciences (2007); thesis title: Predicting enzyme catalytic sites with neural networks; currently a Staff Research Associate in the School of Public Health at UC-Berkeley Dr. Julie Kanjanapangka. MS in Biological Sciences (2006); thesis title: Investigating protein stability and per residue pKa values using Poisson-Boltzmann continuum electrostatic theory; later completed her PhD at the City of Hope Graduate College of Biological Sciences; currently Adjunct Professor at Santa Monica College


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Dr. David La. MS in Biological Sciences (2005); thesis title: Robust large-scale protein functional site prediction using phylogenetic motifs; later completed his PhD at Purdue University; currently a research associate in David Baker’s lab at the University of Washington Michael Torrez. MS in Chemistry (2004); thesis title: Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces; currently a chemistry instructor at San Bernardino Valley College Dr. Brian Lin. MS in Chemistry (2004); thesis title: Understanding polymer based sensing films; later completed his PhD at the University of California at Santa Barbara; currently at IBM

6.6 Undergraduate Students Supervised

Jenna Brown. BS in Biology (2016); research topic: Stability/flexibility relationships across the AmpC b-lactamase family; currently a pharmacology student at Wingate University Kavitha Eechambadi. BS in Neurobiology at Virginia Tech (2014); research topic: Stability/flexibility relationships across the class-D b-lactamase family Michael Ross. BS in Engineering (2012); research topic: Stability/flexibility relationships within membrane transport proteins; currently a software developer at Wells Fargo Securities Christian Russell. BS in Chemistry (2012); research topic: Functional site prediction; currently a community engineer at iTalent Dr. Eric Chea. BS in Biology (2006); research topic: Network centrality methods to predict protein functional sites; later completed his PhD at the Weill Cornell Graduate School / Sloan-Kettering Cancer Institute; currently the Senior Data Manager at McKesson Steve Fregoso. BS in Chemistry (2005); thesis title: Computational redesign of RNase Sa2 surface electrostatics Alfonso Faris. BS in Chemistry (2005); research topic: Protein electrostatics using continuum Poisson-Boltzmann methods Dr. Brian Sutch. BS in Chemistry (2005); research topic: Development and testing of a phylogenetic motif functional site prediction algorithm; later completed his PhD at the University of Southern California; currently the Chief Technical Officer at Sarcix, Inc. Dr. Erik Kish-Trier. BS in Chemistry (2004); research topic; protein sequence/structure/functional relationships; later completed his PhD at the State University of New York Upstate Medical University; currently R&D Scientist II at ARUP Laboratories Melanie Silver. BS in Biological Sciences (2003); research topic: Molecular origins of protein thermostability, currently Senior Chemist at Southwest Regional Laboratory Eric Alsop. BS in Chemistry (2003); thesis title: Optimized electrostatic surfaces parallel increased thermostability: A structural bioinformatics analysis; later completed his PhD at Arizona State University; currently a bioinformatician at Translational Genomics Research Institute (TGen)


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Hank Lam. BS in Chemistry (2002); thesis title: Identification of factors leading to increased thermostability in iron-manganese superoxide dismutase

7 Teaching († Indicates courses that I developed)

7.1 Graduate Courses at UNC Charlotte

BINF 6101/8101 Energy & Interaction in Biological Modeling† BINF 6202/8202 Computational Structural Biology† BINF 6311/8311 Biophysical Modeling†

7.2 Graduate Courses at Cal Poly Pomona

CHEM 513/561 Advanced Topics in Biochemistry (proteomics) †

7.3 Undergraduate Courses at UNC Charlotte

HONR 3700 Antibiotic Resistance: A Looming Pandemic† CHEM 4165/5165 Principles of Biochemistry I

7.4 Undergraduate Courses at Cal Poly Pomona

CHEM 121 General Chemistry I CHEM 321 Elements of Biochemistry CHEM 321L Elements of Biochemistry Lab CHEM 327 Biochemistry I CHEM 327L Biochemistry I Lab CHEM 328 Biochemistry II CHEM 328L Biochemistry II Lab CHEM 329 Biochemistry III CHEM 329L Biochemistry III Lab CHEM 417 Computational Biochemistry† CHEM 416 Macromolecular Modeling† BIOL 499 Introduction to Bioinformatics (team taught)

7.5 Other Courses

Introduction to Bioinformatics Methods (short course in Kuala Lumpur, Malaysia, 2005)†

8 Service Outside of Home Institution

8.1 Grant Reviews

National Science Foundation, Panelist (2017) Research Corporation – Cottrell College Science Award (2011 and 2012) W.M. Keck Foundation (2010)


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NIH-ZRG1 BST-F – S10 ARRA proposals (2009) National Science Foundation, Panelist (2006) NIH-Special Emphasis study section – R15 and R21 proposals (2005) NIH-MBRS ad hoc study section – SCORE (S06) proposals (2002) California State Program for Education and Research in Biotechnology (2004 & 2005)

8.2 Editorial Service

Protein Dynamics: Methods and Protocols, Springer, Editor (2014) Journal of Proteome Science and Computational Biology, Editorial Board (2012-2016) PLOS Computational Biology, Associate Editor (2011-2016) BMC Bioinformatics, Associate Editor (2010-2016) Current Protein and Peptide Science, Editorial Board (2010-2016) Protein and Peptide Letters, Editorial Board (2010-2016) Advances in Bioinformatics, Editorial Board (2010-2015) Current Opinion in Pharmacology, Editor of special issue on protein dynamics (2010) Chemistry Central Journal, Editorial Board (2010-2016) Chemistry Central Journal, Section Editor: Biomacromolecules (2006-2010)

8.3 Journal Reviews (typically multiple times per journal)

Advances in Bioinformatics Antibiotics Astrobiology BBA – Proteins and Proteomics Biochemistry and Cell Biology Bioinformatics Biophysical Journal BMC Bioinformatics BMC Structural Biology Chemistry Central Journal Chemical Reviews ChemPhysChem Communications in Computational Physics Current Bioinformatics Current Protein and Peptide Science Current Opinion in Pharmacology FEBS Letters Human Mutation IEEE Transactions on Computational Biology and Bioinformatics Infection, Genetics and Evolution Genome Biology


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Journal of Bioinformatics and Computational Biology Journal of Biophysics and Structural Biology Journal of Chemical Information and Modeling Journal of Chemical Theory and Computation Journal of Computational Chemistry Journal of Molecular Biology Journal of Molecular Recognition Journal of Physical Chemistry Journal of the Royal Society – Interface Journal of Structural Biology Nature Communications Nature Protocols Nucleic Acids Research PLOS Computational Biology PLOS ONE Protein Engineering, Design, and Selection Protein and Peptide Letters PROTEINS: Structure, Function & Bioinformatics

8.4 Miscellaneous External Service

Board of Directors member for BioKansas, which is a trade organization representing the biological and life sciences in the state of KS and surrounding areas (2017-present) Institutional Review Board member for Via Christi-Wichita; Via Christi is the largest hospital system in the state of Kansas (2017-present) Chair, Kansas Graduate Deans Council (2017-2018)

9 In the Press

9.1 Expert Commentary

Charlotte Talks: Preventing Antibiotic-Resistance. I was part of a panel on the Charlotte Talks daily WFAE National Public Radio program discussing antibiotic resistance (November 23, 2015). Nautilus Magazine: The Great Bioterror Threat is Modern Society. Article discussing how human actions can promote the evolution of antibiotic resistance (February 26, 2014). Niner Times: Gamers Working to Find Cure for HIV and AIDS. Article describing the online puzzle video game FoldIt, and summary of some of gamers’ real-world successes in the protein-folding problem (March 15, 2012).


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9.2 Non-Scientific Reports Commenting on our Research

Millennial Magazine (Charlotte, NC): Perilous Resistance. Overview of our findings the β-lactamase enzyme family (Fall 2013/Winter 2014, Vol. 3, Issue 3, Pages 5-8). UNC-TV Science Blog (Chapel Hill, NC): Doing a Little Reconnaissance. Summary of the findings within our recent paper describing evolution of the class-A β-lactamase enzyme family (July 25, 2013) The Poly Post (Pomona, CA): Livesay Leaves Cal Poly for North Carolina. The Poly Post is the independent student newspaper at Cal Poly Pomona. The article described our recent accomplishments and the fact that I was leaving Cal Poly Pomona for a new position at UNC Charlotte (April 11, 2006). The Republic (Columbus, IN): East Grad’s Chemistry Skills Focused on Battling Diseases. The Republic is the only daily newspaper in Columbus, IN. The article described my current work, our successes and the influences of my high school and community college teachers on my career development (April 6, 2006). PolyTrends (Pomona, CA): More Than Innovative, Research Center is Surprisingly Interdisciplinary. PolyTrends is a bi-annual publication of Cal Poly Pomona Development Office designed to highlight “excellence on campus.” The article described the Center for Macromolecular Modeling & Materials Design and our recent W.M. Keck Foundation grant (January, 2006). The New Straight Times (Kuala Lumpur, Malaysia): Expert to Discuss Bioinformatics in KL. The New Straight Times is the leading English-language paper in Malaysia. The article briefly described my Bioinformatics Short Course at Technology Park Malaysia (May 5, 2005). Panorama (Pomona, CA): Taking a Byte out of Complex Research. Panorama is a quarterly community newsletter published by the Cal Poly Pomona Development Office. This article described our funded NSF-MRI grant, which allowed us to create a new state-of-the-art computer lab and a 64-CPU research cluster (Winter, 2004)

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