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Faculty and Student Research

Saint Louis University's bioinformatics faculty is engaged in cutting-edge research, both in the development of novel algorithms used in bioinformatics and also application of a variety of bioinformatics and computational tools to interesting and challenging questions at the intersection of life sciences and computer science. 

Our faculty members present work at national and international conferences and publish results in renowned journals. They are principal investigators, currently leading projects funded the NSF, NIH and other funding agencies. They are also educators, teaching the courses and involving many of our graduate students in these research efforts. (See highlights of our students' research at left.)

Research Areas

Our research areas span both computational and biological questions, often within the same project. Details of our research activities can be found on individual faculty member's profiles. 

Computational Research Areas


Algorithms

Artificial Intelligence and Machine Learning

Computational Topology

Data Science

Cloud Computing and HPC

Biological Research Areas


Genome Evolution

Microbiome and Genome Assembly

Plant Phenotyping and Evolution

Protein Evolution and Structure Prediction

Data Mining for Multiple Omics

Biostatistics and Modeling

Recent Faculty Publications

Tae-Hyuk (Ted) Ahn, Ph.D.
Gerado Camilo, Ph.D.
  • Kleinschmidt LM, Kinney ME, Camilo GR, Thier T, Fischer M, Hanley CS, Padilla LR. Comparison of Propofol Constant Rate Infusionand Isoflurane for Maintenance of Anesthesia in Speke's Gazelle, Gazella Spekei. J Zoo Wildl Med. 2018 Sep;49(3):722-731.
  • Hall DM, Camilo GR, Tonietto RK, Ollerton J, Ahrné K, Arduser M, Ascher JS, Baldock KC, Fowler R, Frankie G, Goulson D, Gunnarsson B, Hanley ME, Jackson JI, Langellotto G, Lowenstein D, Minor ES, Philpott SM, Potts SG, Sirohi MH, Spevak EM, Stone GN, Threlfall CG. “The city as a refuge for insect pollinators” in Conserv Biol. 2017 Feb;31(1):24-29. 
Maureen Donlin, Ph.D.
  • Cao F, Orth C, Donlin MJ, Adegboyega P, Meyers MJ, Murelli RP, Elagawany M, Elgendy B, Tavis JE. “Synthesis and Evaluation of Troponoids as a New Class of Antibiotics”, in ACS Omega. 2018 Nov 30;3(11):15125-15133.
  • Upadhya R, Baker LG, Lam WC, Specht CA, Donlin MJ, Lodge JK. “Cryptococcus neoformans Cda1 and Its Chitin Deacetylase Activity Are Required for Fungal Pathogenesis”, in MBio. 2018 Nov 20;9(6). pii: e02087-18.

Brian Downes, Ph.D.
  • Lu X, Malley KR, Brenner CC, Koroleva O, Korolev S, Downes BP. “A MUB E2 structure reveals E1 selectivity between cognate ubiquitin E2s in eukaryotes”, in Nat Commun. 2016 Aug 23;7:12580.  
Haijun Gong, Ph.D. 
  • Zi Wang*, Yun Guo*, Haijun Gong,  “An Integrative Analysis of Time-varying Regulatory Networks from High-dimensional Data”, IEEE International Conference on Big Data, Page 3798-3807 (2018)
Jack Kennell, Ph.D.
  • Vijayraghavan S, Kozmin SG, Strope PK, Skelly DA, Lin Z, Kennell J, Magwene PM, Dietrich S, McCusker JH. Mitochondrial Genome Variation Affects Multiple Respiration and Nonrespiration Phenotypes in Saccharomyces cerevisiae. Genetics.  2019 Feb;211(2):773-786
Zhenguo Lin, Ph.D.
  • J. McMillan, Z. Lu, J. Rodriguez, T.-H. Ahn*, and Z. Lin*, "YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites", Database (Oxford), (2019:baz048 (*: co-corresponding authors), 2019.
  • Vijayraghavan S, Kozmin SG, Strope PK, Skelly DA, Lin Z, Kennell J, Magwene PM, Dietrich S, McCusker JH. Mitochondrial Genome Variation Affects Multiple Respiration and Nonrespiration Phenotypes in Saccharomyces cerevisiae. Genetics.  2019 Feb;211(2):773-786

  • Wang J, Alvin Chew BL, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu CF, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC. Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Nucleic Acids Res. 2019 Sep 2. pii: gkz751.  

  • Lu Z, Lin Z. “Pervasive and dynamic transcription initiation in SaccharomycesCerevisiae”, in Genome Res. 2019 Jul;29(7):1198-1210 

Allison Miller, Ph.D.
  • Li M, Klein LL, Duncan KE, Jiang N, Chitwood DH, Londo J, Miller AJ, Topp CN. “Characterizing grapevine 3D inflorescence architecture using X-ray imaging and advanced morphometrics: implications for understanding cluster density”, in J Exp Bot. 2019 Aug 31. pii: erz394.
  • Gaut BS, Miller AJ, Seymour DK. “Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution”, in Annu Rev Genet. 2019 Aug 19. doi: 10.1146/annurev-genet-112618-043545.
  • Migicovsky Z, Harris ZN, Klein LL, Li M, McDermaid A, Chitwood DH, Fennell A, Kovacs G, Kwasniewski M, Londo JP, Ma Q, Miller AJ. “Rootstock effects on scion phenotypes in a Chambourcin' experimental vineyard”, in Hortic Res. 2019 May 1;6:64.
Dapeng Zhang, Ph.D.
  • Makarova KS, Wolf YI, Karamycheva S, Zhang D, Aravind L, Koonin EV, “Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts” in MBio. 2019 10(3). pii: e00715-19.
Brent Znosko, Ph.D.
  • Adams MS, Znosko BM. “Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions”, in Nucleic Acids Res. 2019 Apr 23;47(7):3658-3666. 
  • Lisowiec-Wachnicka J, Znosko BM, Pasternak A. “Contribution of 3'T and 3'TT overhangs to the thermodynamic stability of model siRNA duplexes”, in Biophys Chem. 2019 Mar;246:35-39.
  • Wright DJ, Force CR, Znosko BM. “Stability of RNA duplexes containing inosine·cytosine pairs”, in Nucleic Acids Res. 2018 Dec 14;46(22):12099-12108.