Research

 

My research spans the intersection between Computer Science and Genetics. The development of high-throughput biological methods (e.g. DNA sequencing, mass spectrometry, etc) has required the parallel development of new analysis and visualization approaches to translate these raw data into useful knowledge. To this end, my work focuses on the development and application of new algorithms, visualization techniques, and software tools to address import biological problems, with a specific focus on diseases of aging, such as cancer and osteoporosis.


Computational Areas of Interest:

  1. Machine Learning & Data Mining

  2. Large-scale Data Visualization

  3. Sequence/String Analysis Methods

  4. Graph analysis algorithms


Biological Areas of Interest:

  1. Gene Expression Profiling & Analysis

  2. Cell-type Specific Gene Function Prediction

  3. High-throughput Sequencing Analysis

  4. Diseases of Aging, including cancer and osteoporosis


Publication List:

  1. Munger SC, Raghupathy N, Choi KB, Simons AK, Gatti DM, Hinerfeld DA, Svenson KL, Keller MP, Attie AD, Hibbs MA, Graber JH, Chesler EJ, Churchill GA. RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations. Genetics (2014) 198:75-86.

  2. Kemp JP, Medina-Gomez C, Estrada K, St Pourcain B, Heppe DHM, Warrington NM, Oei L, Ring SM, Kruithof CJ, Timpson NJ, Wolber LE, Reppe S, Gautvik K, Grundberg E, Ge B, van der Eerden B, van de Peppel J, Hibbs MA, Ackert-Bicknell CL, Choi KB, Koller DL, Econs MJ, Williams FMK, Foroud T, Zillikens MC, Ohlsson C, Hofman A, Uitterlinden AG, Smith GD, Jaddoe VWV, Tobias JH, Rivadeneira F, Evans DM. Phenotypic Dissection of Bone Mineral Density Reveals Skeletal Site Specificity and Facilitates the Identification of Novel Loci in the Genetic Regulation of Bone Mass Attainment. PLoS Genetics (2014) 10(6): e1004423. doi:10.1371/journal.pgen.1004423.

  3. Dowell KG, Simons AK, Bai H, Kell B, Wang ZZ, Yun K, Hibbs MA.  Novel Insights into Embryonic Stem Cell Self-Renewal Revealed Through Comparative Human and Mouse Systems Biology Networks.  Stem Cells (2014) 32(5): 1161-1172.

  4. Choi KB, Shultz K, Godfrey D, Yuan R, Hibbs MA, Gatti D, Churchill GA, Paigen B, Beamer W, Ackert-Bicknell CL.  Identification of Slc9a9 as a candidate gene for a bone mineral density locus on mouse Chromosome 9.  Journal of Bone and Mineral Research (2013) 28.

  5. Dowell KG, Simons AK, Wang ZZ, Yun K, Hibbs MA.  Cell-Type-Specific Predictive Network Yields Novel Insights into Mouse Embryonic Stem Cell Self-Renewal and Cell Fate.  PLoS ONE (2013) 8(2): e56810.

  6. Gu T, Buaas FW, Simons AK, Ackert-Bicknell CL, Braun RE*, Hibbs MA*.  Canonical A-to-I and C-to-U RNA editing is enriched at 3’UTRs and microRNA target sites in multiple mouse tissues.  PLoS ONE (2012) 7(3):e33720. (*Co-senior authors)

  7. Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ*, Hibbs MA*, Troyanskaya OG*. Tissue-specific functional networks for prioritizing disease genes. PLoS Comp Biol (2012) 8(9):e1002694. (*Co-senior authors)

  8. Ackert-Bicknell CL and Hibbs MA. The need for mouse models in osteoporosis genetics research. BoneKEY (2012) 1:98.

  9. Aljakna A, Choi S, Savage H, Hageman-Blair R, Gu T, Svenson K, Churchill GA, Hibbs MA, Korstanje R.  Pla2g12b and Hpn are HDL-regulating Genes Identified by ENU Mutagenesis in the Mouse and HPN is Associated with HDL Cholesterol Levels in Human.  PLoS ONE (2012) 7(8):e43139.

  10. Li Y*, Hibbs MA*, Gard AL*, Shylo NA, Yun K.  Genome-wide analysis of N1ICD/RBPJ targets in vivo reveals direct transcriptional regulation of Wnt, SHH, and Hippo pathway effectors by Notch1. Stem Cells (2012) 30(4):741-752. (*Equal contribution)

  11. GR Howell GR, Macalinao DG, Sousa GL, Walden M, Soto I, Kneeland SC, Barbay JM, King BL, Marchant JK, Hibbs MA, Stevens B, Barres BA, Clark AF, Libby RT, John SW.  Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma. Journal of Clinical Investigation (2011) 121(4):1429-1444.

  12. Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA.  Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations.  PLoS Comp Biol (2010) 6(11):e1000991.

  13. Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs MA, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL.  Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.  Nat Methods (2010) 7(12):1017-1024.

  14. Hibbs MA.  Advanced Bioinformatics Tools and Strategies, in Principles and Practices of Plant Genomics: Volume 3: Advanced Genomics, Eds. Kole C and Abbott AG. Science Publishers Inc: New Hampshire (2010).

  15. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin A.  Visualization of omics data for systems biology. Nat Methods (2010) 7(3):S56-S68.

  16. Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG.  Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data. Methods Mol Biol (2009) 548:273-93.

  17. Hibbs MA. The Effects of Pre-processing and Parameter Choices on Searches Through Large Gene Expression Data Collections. IEEE Int Conf on Genomic Signal Processing and Statistics (2009).

  18. Huttenhower C*, Hibbs MA*, Myers CL*, Caudy AA, Hess DC, Troyanskaya OG. The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics (2009) doi10.1093. (*Equal contribution)

  19. Hibbs MA*, Myers CL*, Huttenhower C*, Hess DC, Caudy AA, Li K, Troyanskaya OG. Analysis of Computational Functional Genomic Approaches for Directing Experimental Biology: a Case Study in Mitochondrial Inheritance.  PLoS Computational Biology (2009) 5(3):e1000322. (*Equal contribution)

  20. Hess DC, Myers CL*, Huttenhower C*, Hibbs MA*, Hayes A, Paw J, Clore J, Mendoza R, San Luis B, Costanzo M, Boone C, Caudy AA, Troyanskaya OG.  Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.  PLoS Genetics (2009) 5(3):e1000407. (*Equal contribution)

  21. Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. Exploring the human genome with functional maps. Genome Res (2009) 19(6):1093-106.

  22. Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. Exploring the functional landscape of gene expression:  directed search of large microarray compendia.  Bioinformatics (2007) 23(20):2692-9.

  23. Huttenhower C, Flamholz A, Landis J, Sahi S, Myers CL, Olszewski K, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA. Nearest Neighbor Networks: Clustering Expression Data Based on Gene Neighborhoods. BMC Bioinformatics (2007) 8:250.

  24. Hibbs MA, Wallace G, Dunham M, Li K, Troyanskaya OG. Viewing the Larger Context of Genomic Data through Horizontal Integration.  Proceedings of IEEE-CS 11th Int. Conf. on Information Visualization (2007) pp326-334.

  25. Wallace G, Hibbs MA, Dunham M, Sealfon RSG, Troyanskaya OG, Li K. Scalable, Dynamic Analysis and Visualization for Genomic Datasets.  Proceedings of IPDPS 2007 Workshop on Next Generation Software (2007).

  26. Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC. Modeling Complex Genetic Interactions in a Simple Eukaryotic Genome: Actin Displays a Rich Spectrum of Complex Haploinsufficiencies. Genes & Development (2006) 21(2):148-59.

  27. Sealfon RSG, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene ontology navigation and analysis tool. BMC Bioinformatics (2006) 7:443.

  28. Myers CL, Barrett D, Hibbs MA, Huttenhower C, Troyanskaya OG. Finding function: evaluation methods for functional genomic data. BMC Genomics (2006) 7:187.

  29. Huttenhower C, Hibbs MA, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray data sets. Bioinformatics (2006) 22:2890.

  30. Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG. Discovery of biological networks from diverse functional genomic data. Genome Biology (2005) 6(13):R114.

  31. Hibbs MA, Dirksen NC, Li K, Troyanskaya OG. Visualization Methods for Statistical Analysis of Microarray Clusters. BMC Bioinformatics (2005) 6:115.

  32. Wallace G, Chen H, Chen Y, Liu Z, Samanta R, Bi P, Gupta A, Hibbs MA, Li K, Finkelstein A, Funkhouser T, Cook P, Sukthankar R, and Troyanskaya OG. Tools and Applications for Large Scale Display Walls. Special Issue on Large Format Displays, IEEE Computer Graphics and Applications, July/August 2005.

  33. Li K, Hibbs MA, Wallace G, Troyanskaya OG. Dynamic Scalable Visualization for Collaborative Scientific Applications. Proceedings of IPDPS 2005 Workshop on Next Generation Software (2005).