Curriculum Vitae

Sudhir Kumar

December ****

PERSONAL DATA

Business Address: Center for Evolutionary Medicine & Informatics (http://cemi.asu.edu)

Biodesign Institute A-240

Arizona State University

1001 S. McAllister Avenue

Tempe, AZ 85827-5301

Laboratory Website: http://www.kumarlab.net

Phone: 623-***-**** (cell)

480-***-**** (Admin Contact: Carol Williams)

Fax: 480-***-****

E-Mail abqgon@r.postjobfree.com

EDUCATION

B. E. (Honors) Electrical & Electronics Engineering* 1990

M. Sc. (Honors) Biological Sciences* (*Concurrent dual degrees) 1990

Birla Institute of Technology & Science, Pilani, Rajasthan (India)

Ph. D. Genetics (Advisor: Masatoshi Nei) 1996

Pennsylvania State University, University Park, Pennsylvania (USA)

MAJOR RESEARCH THEMES

Molecular Evolution, Evolutionary Medicine, and Bioinformatics

PROFESSIONAL APPOINTMENTS

Regents Professor of Life Sciences, Arizona State University (ASU) 2012 Present

Co-Director, Biological Design Graduate Program, ASU 2012 Present

Foundation Professor, School of Life Sciences (SoLS), ASU 2011 Present

Director, Center for Evolutionary Medicine & Informatics, Biodesign Institute 2010 Present

Full Professor, SoLS, ASU 2006 Present

Director, Center for Evolutionary Functional Genomics, Biodesign Institute 2003 2009

Faculty Leader, Genomics, Evolution, and Bioinformatics, SoLS, ASU 2003 2004

Associate Professor, SoLS, ASU 2002 2006

Assistant Professor, Department of Biology, ASU 1998 2002

Postdoctoral Fellow (Nei), Department of Biology, Penn State University 1996 1998

Research Assistant (Nei), Department of Biology, Penn State University 1991 1996

AWARDS & HONORS

President, Society for Molecular Biology and Evolution (SMBE) 2013

President-Elect, Society for Molecular Biology and Evolution (SMBE) 2012

Fellow, American Association for the Advancement of Science (AAAS) 2009

CSE Honorary Professor, School of Computing and Informatics, ASU 2009

Arizona Governor s Celebration of Innovation Academia (Finalist) 2009 & 2011

Top-10 Most-Cited author, Computer Science, Web of Science (series discontinued) 2004 2009

Visiting Fellowship Award, Japanese Society for Promotion of Science (JSPS) 2007 2008

Exemplar Faculty (Promotion to Full Professor), ASU 2006

Secretary (Elected, 2003), Society for Molecular Biology and Evolution (SMBE) 2004 2006

Innovation Award in Functional Genomics, Burroughs-Wellcome Fund 2000

Thomson Reuters ScienceWatch/Web of Science

Current Classic in Multidisciplinary Sciences (PNAS 101:110**-*****) 2010

Current Classic in Biology & Biochemistry (Molecular Biology & Evolution 24:1596 159*-****-****

Sudhir Kumar, Ph.D. (Page 2)

Current Classic Computer Science (Briefings in Bioinformatics 5: 150-163) 2007 2010

Hot Paper in Computer Science (Briefings in Bioinformatics 9:299-306) 2009

Hot Paper in Computer Science (Briefings in Bioinformatics 5:150-163) 2006

Hot Paper in Biology & in Computer Science (Bioinformatics 17:1244-1245), 2004

Hot Paper in Biology (Nature 392: 917-920) 2000

SCIENCE, Editor s Choice, August 25, 2006, Molecular Biology & Evolution 23:1946-1951) 2006

H-index = 51; Total citations to date = 56,000+ (Google Scholar, December) 2012

JOURNAL EDITORIAL AND WEBMASTER SERVICE

Editor in Chief, Molecular Biology & Evolution 2012 Present

Associate Editor, Quarterly Review of Biology 2010 Present

Honorary Editor, Biomolecules 2010 Present

Editorial Board, Bioinformatics and Biology Insights 2009 Present

Associate Editor, Evolutionary Bioinformatics Online 2005 Present

Editorial Board, Molecular and Developmental Evolution (J. Exp. Zool.) 2004 Present

Associate Editor, Molecular Biology & Evolution 2005 2012

Editorial Board, Genome Research 2005 2009

Board of Editors, Gene: Functional Genomics 2005 2006

Webmaster, Society for Molecular Biology and Evolution (www.smbe.org) 2004 2008

Webmaster, American Genetic Association (www.theaga.org) 1999 2007

Associate Editor, Journal of Heredity 1999 2005

RESEARCH GRANT SUPPORT

Current Grants (arranged by start dates)

Principle Investigator

Evolutionary Bioinformatics of Human Mutations (R01) 2010 2013

National Institute of Health (NLM)

Computational Analysis of Gene Expression Pattern Images (R01) 2011 2014

National Institutes of Health (NHGRI)

Comparative Molecular Sequence Analysis (R01) 2011 2014

National Institute of Health (NHGRI)

Computational Methods for Expression Image Analysis (R01; Multi-PI) 2011 2014

National Institutes of Health (NLM)

Identifying disease-associated genome variants through computational prediction 2012 2013

of functional sites in protein structures

ASU/Mayo Seed Grant

Co-Principle or Co-Investigator

Discovering the Hidden Proteome in the Human Genome (EUREKA, R01) 2008 2013

National Institutes of Health

Bioinformatics of Molecular Timetrees 2009 2013

National Science Foundation (DBI)

Center for Membrane Proteins in Infectious Diseases (MIPD, U54) 2010 2015

National Institutes of Health (NIGMS)

A Phylogenetic Approach to Metagenomic Analysis (R21) 2011 2013

National Institutes of Health (NHGRI)

Completed Grants/Contracts (arranged by start dates)

Comparative Molecular Sequence Analysis (R01), Principal Investigator, 2000 2011

National Institutes of Health (includes two renewals, continuing above)

Design of a Bioinformatic Database for Functional Evolutionary Footprints in 2000 2004

Multigene Families, Principal Investigator, National Science Foundation

Emerging Wildlife Diseases: Threats to Amphibian Biodiversity, Co-Investigator, 2000 2008

Sudhir Kumar, Ph.D. (Page 3)

National Science Foundation; PI: J. Collins

Development of an Evolutionary Timescale Database, Co-Principal Investigator, 2001 2004

National Science Foundation

A Computational Biosciences Professional Master s Program, Participating 2001 2003

Investigator, Sloan Foundation

Computational Genomic Analysis to Identify and Dissect Functionally Important 2003 2006

Mutations in Protein Sequences, Principal Investigator,

Burroughs-Wellcome Fund, USA

Computational Analysis of Gene Expression Pattern Images (R01) 2003 2011

Principal Investigator, National Institutes of Health

(includes one renewal, continuing above)

LSAMP Biodesigned Bridges to the Doctorate, Co-Principal Investigator, 2004 2006

National Science Foundation

Developing a Bioinformatic Database for Stoichioproteomics 2006 2010

National Science Foundation; PI: W. Fagan

Machine Learning Approaches for Biological Image Informatics 2006 2010

National Science Foundation; PI: J. Ye

Bioinformatics of Assembling the Timescale of Life, Principal Investigator, 2007 2008

Science Foundation of Arizona

Re-engineering the MEGA Software Package (R01), Principal Investigator, 2007 2011

National Institutes of Health (NIGMS/ARRA)

Team Approach to Translate Novel Biomarkers for Diabetes 2009 2010

Co-Investigator; R. Nelson, PI, National Institutes of Health

MEMBERSHIPS IN SCIENTIFIC AND PROFESSIONAL ORGANIZATIONS

American Association for the Advancement of Science

Arizona Arts, Sciences, and Technology Academy (founding fellow)

American Genetic Association

The Genetics Society of America

International Society of Computational Biologists

Society for Molecular Biology and Evolution

Society for the Study of Evolution

CONFERENCE/SYMPOSIA/OUTREACH ORGANIZED

Society for Molecular Biology and Evolution satellite-Symposium on Phylomedicine 2012

Arizona State University, Tempe Arizona (March 23 24)

SMBE competitively awarded $30K for this symposium

Global Organizing Committee (GOC) of the Annual meeting of the Society for 2011

Molecular Biology and Evolution, Kyoto Japan (July 26 - 30)

Biodesign Data Club (with Joshua LaBaer), Arizona State University (Fall) 2010

Evolutionary Biology in Health and Medicine, Annual meeting of the Society for

Molecular Biology and Evolution, Lyon France (July 4 - 8) 2010

(co-organized with Joel Dudley and Atul Butte)

Molecular Phylogenetics Symposium, Russia (May 17 21) 2010

Hosted FlyBase outreach meeting at ASU (March) 2007

Member, Program Committee, International Conference on Computational 2007

Phylogenetics and Molecular Systematics, Moscow State University, Russia

(November 16 19)

Chair, Annual meeting of the Society for Molecular Biology and Evolution, 2006

Arizona State University, Tempe, Arizona (May 24 28)

Organizer, Genome Database Workshop @ National Evolutionary Synthesis 2005

Center, Wilmington Beach, North Carolina, (May 31 Jun 3)

Sudhir Kumar, Ph.D. (Page 4)

Symposium on Evolutionary and Population Genomics in the Future of Statistics 2004

Conference at Indian School of Business, Hyderabad, India (Dec. 29 Jan. 1)

PROFESSIONAL AFFILIATIONS

Coordinator, Academic Exchange and Collaboration, Tokyo Metropolitan University, 2012 Present

Japan and Arizona State University

Guest Professor, Center for Computational and Evolutionary Biology (CCEB), 2007 Present

Institute of Zoology at Beijing, China

Affiliate Professor, School of Computing, Informatics, and Decision Support 2002 Present

Engineering, ASU

Member, NASA Astrobiology/Evolutionary Genomics Focus Group 2000 Present

Associate Member, Penn State Astrobiology Research Center 1998 Present

Affiliate Professor, Department of Biomedical Informatics, ASU 2005 2007

Adjunct Senior Investigator, Translational Genomics Research Institute 2004 2007

(TGen), Phoenix, Arizona

Member, Genetics Program, ASU 1998 2005

ORGANIZATIONAL REVIEWER & CONSULTANT

Member, review committee, Genomic Sciences review, NC State University 2013

Raleigh, North Carolina (Upcoming)

Member, 10-year review committee, Institute for Genomics and Bioinformatics 2010

(IGB) @ University of California, Irvine

Consultant, Amerigenics, Inc., USA 2006 2007

Consultant, Advisory Committee on Evolutionary Bioinformatics, University of 2006

South Dakota, USA

Member, five-year review committee, Institute for Genomics and Bioinformatics 2005

(IGB) @ University of California, Irvine

Consultant, Pharmacia Corporation, USA 2002 2003

PROFESSIONAL ADVISORY BOARDS / WORKING GROUPS

Advisory Board Member, M nster Graduate School of Evolution (MGSE) 2011 Present

FlyBase Advisory Group 2007 2008

Standing Member, BioData Management and Analysis (BDMA) Study Section, 2006 2010

National Institutes of Health, USA

Member, Informatics Advisory Committee, National Center for Evolutionary 2006 2009

Synthesis (NESCent), USA

Member, Working Group: Evolutionary Informatics: Supporting Interoperability 2006 2008

in Evolutionary Analysis, NESCent, USA

EXTRAMURAL TEACHING

Molecular Evolution and Phylogenetics (July 13 14) Centers for Disease 2009

Control (CDC), Atlanta, Georgia, USA

Distance and Parsimony Methods (June) in Molecular Evolution and Systematics 2004

workshop, Chinese Academy of Sciences, Beijing, China

SOFTWARE AND DATABASES

MEGA (1993 ): Molecular Evolutionary Genetics Analysis. Integrated tool for molecular

evolutionary and comparative sequence analyses

(http://www.megasoftware.net)

PhylTest (1995): Phylogenetic Hypothesis Testing Software. A simple utility to conduct four

cluster analysis (http://www.kumarlab.net/pdf_new/phyltst.zip)

FlyExpress (2003 ): Drosophila melanogaster Expression Pattern Search Engine. A knowledge -base

to discover genes with similar patterns of expression

(http://www.flyexpress.net and iPHONE application)

Sudhir Kumar, Ph.D. (Page 5)

TimeTree (2006 ): Knowledge-base of species timetrees. A discovery platform to identify all

published molecular time estimates for chosen organisms

(http://www.timetree.org and iPHONE application)

GRASP (2010 ): Genomic Resource Access for StoichioProteomics. A resource containing

stoichiometric information on Drosophila proteins (http://www.graspdb.net)

PUBLICATIONS

1990 1999

1. Hedges SB, Kumar S, Tamura K & Stoneking M (1992) Human origins and analysis of mitochondrial DNA

sequences. Science 255:737 739.

2. Kumar S, Tamura K & Nei M (1993) A Guide to Molecular Evolutionary Genetics Analysis Program

for Microcomputers, Institute of Molecular Evolutionary Genetics, Pennsylvania State University,

University Park, PA (140 pp; >2500 printed manuals distributed).

3. Kumar S, Tamura K & Nei M (1994) MEGA: Molecular Evolutionary Genetics Analysis software for

microcomputers. Computer Applications in Biosciences 10:189 191.

4. Kumar S (1995) PhylTest: A Program for Testing Phylogenetic Hypotheses. Pennsylvania State

University, University Park.

5. Rzhetsky A, Kumar S & Nei M (1995) Four-cluster analysis: A simple method to test phylogenetic

hypotheses. Molecular Biology & Evolution 12:163 167.

6. Yang Z, Kumar S & Nei M (1995) A new method of inference of ancestral nucleotide and amino acid

sequences. Genetics 141:1641 1650.

7. Winnepenninckx W, Backeljau T, Mackey LY, Brooks JM, De -Wachter R, Kumar S & Garey JR (1995) 18S

rRNA data indicate that Aschelminthes are polyphyletic in origin and consist of at least three distinct

clades. Molecular Biology and Evolution 12:1132 1137.

8. Hedges SB, Parker PH, Sibley CG & Kumar S (1996) Continental breakup and the ord inal diversification

of birds and mammals. Nature 381:226 229.

9. Kumar S (1996) A stepwise algorithm for finding minimum evolution trees. Molecular Biology and

Evolution 13:584 593.

10. Kumar S (1996) Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates.

Genetics 143:537 548.

11. Kumar S, Balczarek KA & Lai Z-C (1996) Evolution of the hedgehog gene family. Genetics 142:965

972.

12. Kumar S & Rzhetsky A (1996) Evolutionary relationships of eukaryotic kingdoms. Journal of Molecular

Evolution 42:183 193.

13. Yang Z & Kumar S (1996) Approximate methods for estimating the pattern of nucleotide substitution

and the variation of substitution rates among sites. Molecular Biology and Evolution 13:650 659.

14. Balczarek KA, Lai Z-C & Kumar S (1997) Evolution and functional diversification of the Paired box (Pax)

DNA-binding domains. Molecular Biology and Evolution 14:829 842.

15. Zhang J & Kumar S (1997) Detection of convergent and pa rallel evolution at the amino acid sequence

level. Molecular Biology and Evolution 14:527 536.

16. Zhang J, Kumar S & Nei M (1997) Small-sample tests of episodic adaptive evolution: A case study of

primate lysozymes. Molecular Biology and Evolution 14:1335 1338.

17. Yeager M, Kumar S & Hughes AL (1997) Sequence convergence in the peptide -binding region of primate

and rodent MHC class Ib molecules. Molecular Biology and Evolution 14:1035 1041.

18. Leitner TL, Kumar S & Albert J (1997) Tempo and mode of nucleotide substitutions in gag and env gene

fragments in Human Immunodeficiency Virus Type 1 populations with a known transmission history.

Journal of Virology 71:4761 4770.

Sudhir Kumar, Ph.D. (Page 6)

19. Kumar S & Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392:917 920.

20. Nei M, Kumar S & Takahashi K (1998) The optimization principle in phylogenetic analysis tends to give

incorrect topologies when the number of nucleotides or amino acids used is small. Proceedings of the

National Academy of Sciences (USA) 95:123**-*****.

21. Hedges SB & Kumar S (1999) Divergence times of eutherian mammals. Science 285:2031a.

22. Newfeld SJ, Wisotzkey RG & Kumar S (1999) Molecular evolution of a development pathway:

Phylogenetic analyses of transforming growth factor- family ligands, receptors, and Smad signal

transducers. Genetics 152:783 795.

23. Wang Y-C, Kumar S & Hedges SB (1999) Divergence time estimates for the early history of animal phyla

and the origin of plants, animals, and fungi. Proceedings of the Royal Society, London. B 266:163

171.

24. O Brien S, Eisenberg JF, Miyamoto M, Hedges SB, Kumar S & Wilson DE (1999) Genome Maps 10.

Comparative Genomics. Mammalian radiations. Wall Chart. Science 286:463 478.

2000 2009

25. Nei M & Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York (333

pp). (Translated in Chinese, Japanese, and Russian)

26. Kumar S, Mitnik C, Valente G & Floyd-Smith G (2000) Expansion and molecular evolution of the

interferon-induced 2 -5 oligoadenylate synthetase gene family. Molecular Biology and Evolution

17:738 750.

27. Kumar S, Hedrick P, Dowling T & Stoneking M (2000) Questioning evidence for recombination in human

mitochondrial DNA. Science 288:1931a.

28. Kumar S & Gadagkar SR (2000) Efficiency of the neighb or-joining method in reconstructing deep and

shallow evolutionary relationships in large phylogenies. Journal of Molecular Evolution 51:544 553.

29. Purdom PW, Bradford PG, Tamura K & Kumar S (2000) Single column discrepancy and dynamic max -

mini optimizations for quickly finding the most parsimonious evolutionary trees. Bioinformatics

16:140 151.

30. Kumar S (2000) A review of the book Genomes by TA Brown. The Quarterly Review of Biology 75:316

317.

31. Kumar S, Tamura K, Jakobsen IB & Nei M (2001) MEGA2: Molecular Evolutionary Genetics Analysis

software. Bioinformatics 17:1244 1245.

32. Gerber AS, Loggins R, Kumar S & Dowling TE (2001) Does non-neutral evolution shape observed

patterns of DNA variation in animal mitochondrial genomes? Annual Review of Genetics 35:539 566.

33. Kumar S & Filipski A (2001 and 2008) Molecular Phylogeny Reconstruction. Encyclopedia of Life

Sciences Macmillan Reference Ltd, Oxford, UK. (www.els.net)

34. Kumar S & Filipski A (2001) Molecular Clock Testing. Encyclopedia of Life Sciences, Macmillan

Reference Ltd, Oxford, UK. (www.els.net).

35. Kumar S, Gadagkar SR, Filipski A & Gu X (2001) Determination of the number of conserved

chromosomal segments between species. Genetics 157:1387 1395.

36. Kumar S & Gadagkar SR (2001) Disparity Index: A simple statistic to measure and test the homogeneity

of substitution patterns between molecular sequences. Genetics 158:1321 1327.

37. Kumar S & Panchanathan S (2001) Elucidating gene interaction networks based on gene expression

pattern image analysis. Proceedings of the International Conference on Biomedical Engineering

5A:232 234.

38. Rosenberg MS & Kumar S (2001) Traditional phylogenetic reconstr uction methods reconstruct shallow

and deep evolutionary relationships equally well. Molecular Biology and Evolution 18:1823 1827.

Sudhir Kumar, Ph.D. (Page 7)

39. Rosenberg MS & Kumar S (2001) Incomplete taxon sampling is not a problem for phylogenetic

inference. Proceedings of the National Academy of Sciences (USA) 98:107**-*****.

40. Miller MP & Kumar S (2001) Understanding human disease mutations through the use of interspecific

genetic variation. Human Molecular Genetics 10: 2319 2328.

41. Hedrick P & Kumar S (2001) Mutation and linkage disequilibrium in human mtDNA. European Journal

of Human Genetics 9:969 972.

42. Hedges SB, Chen H, Kumar S, Wang DY-C, Thompson AS & Watanabe H (2001) A genomic timescale for

the origin of eukaryotes. BMC Evolutionary Biology 1:4 (10 pp).

43. Jayaraman K, Panchanathan S & Kumar S (2001) Classification and indexing of gene expression images.

Proceedings of Society of Photo-optical Instrumentation Engineers 4472:471 481.

44. Hedges SB & Kumar S (2002) Vertebrate genomes compared. Science 297:1283 1285.

45. Kumar S & Newfeld SJ (2002) A review of the book Modern Genetic Analysis: Integrating Genes and

Genomes (second edition) by Griffiths AJF, Gelbart WM, Lewontin RC & Miller JH. The Quarterly

Review of Biology 77:456 457.

46. Rawls A & Kumar S (2002) A review of the book Genomic Regulatory Systems: Development and

Evolution by E. H. Davidson. The Quarterly Review of Biology 77:456.

47. Kumar S & Subramanian S (2002) Mutation rates in mammalian genomes . Proceedings of the

National Academy of Sciences (USA) 99:803 808.

48. Kumar S, Jayaraman K, Panchanathan S, Gurunathan R, Marti-Subirana A & Newfeld SJ (2002) BEST: A

novel computational approach for comparing gene expression patterns from early stages of Drosophila

melanogaster development. Genetics 162:2037 2047.

49. Tamura K & Kumar S (2002) Evolutionary distance estimation under heterogeneous substitution pattern

among lineages. Molecular Biology & Evolution 19:1727 1736.

50. Jiang Z, Melville JS, Cao H, Kumar S, Filipski A & Verrinder Gibbins AM (2002) Measuring conservation of

contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the

human genome. Genome 45:769 776.

51. Hedges SB & Kumar S (2003) Genomic clocks and evolutionary timescales. Trends in Genetics

19:200 206.

52. Lorson C & Kumar S (2003) A review of the book Genomes (second edition) by T.A. Brown. The

Quarterly Review of Biology 78:225.

53. Kumar S (2003) MacTrees made easy, a review of the book Phylogenetic trees made easy: a how-to-

manual for molecular biologists by Hall BG. Molecular Evolution and Phylogenetics 27:165 167.

54. Subramanian S & Kumar S (2003) Neutral substitutions occur as a faster rate in exons than in

noncoding DNA in primate genomes. Genome Research 13:838 844.

55. Rosenberg MS & Kumar S (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic

Biology 52:119 124.

56. Rosenberg MS, Subramanian S & Kumar S (2003) Patterns of transitional mutation biases within and

among mammalian genomes. Molecular Biology and Evolution 20:988 993.

57. Rosenberg MS & Kumar S (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages

and phylogenetic inference. Molecular Biology and Evolution 20:610 621.

58. Miller MP, Parker JD, Rissing SW, & Kumar S (2003) Quantifying the intragenic distribution of human

disease mutations. Annals of Human Genetics 67:567 579.

59. Jancovich J, Mao J, Chinchar VG, Wyatt C, Case S, Kumar S, Valente G, Subramanian S, Davidson EW,

Collins JP & Jacobs BL (2003) Genomic sequence of a ranavirus (family Iridoviridae) associated with

salamander mortalities in North America. Virology 316:90 103.

Sudhir Kumar, Ph.D. (Page 8)

60. Kumar S, Tamura K & Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics

Analysis and sequence alignment. Briefings in Bioinformatics 5:150 163.

61. Hedges SB & Kumar S (2004) Precision of molecular time estimates. Trends in Genetics 20:242 247.

62. Kumar S & Filipski A (2004) Phylogenetic Analysis. Dictionary of Bioinformatics and Computational

Biology edited by Hancock J & Zvelebil M, Wiley-Liss, New York.

63. Tamura K, Subramanian S & Kumar S (2004) Temporal patterns of fruit fly evolution revealed by

mutation clocks. Molecular Biology and Evolution 21:36 44.

64. Briscoe A, Gaur C & Kumar S (2004) The spectrum of human rhodopsin disease mutations through the

lens of interspecific variation. Gene 332:107 118.

65. Tamura K, Masatoshi Nei, & Kumar S (2004) Prospects for inferring very large phylogenies using the

neighbor-joining method. Proceedings of the National Academy of Sciences (USA) 101:11030

11035.

66. Subramanian S & Kumar S (2004) Gene expression intensity shapes evolutionary rates of the proteins

encoded by the vertebrate genome. Genetics 168:373 381.

67. Gurunathan R, Van Emden B, Panchanathan S & Kumar S (2004) Identifying spatially similar gene

expression patterns in early stage fruit fly embryo images: Binary feature versus invariant moment

digital representations. BMC Bioinformatics 5:202 (13 pp).

68. Gargesha M, Antin P, Van Emden B, Panchanathan S & Kumar S (2004) Image registration and

similarity computation for chicken gene expression patterns. Genomic Signal Processing and

Statistics (GENSIPS), IEEE Signal Processing Society (4 pp).

69. Kumar S (2005) Molecular clocks: four decades of evolution. Nature Reviews Genetics 6:654 662.

70. Kumar S & Hedges SB (2005) Pushing back the expansion of introns in animal genomes. Cell

123:1182 1184.

71. Filipski A & Kumar S (2005) Comparative Genomics in Eukaryotes. In The Evolution of the Genome

edited by Ryan TG. Elsevier, San Diego, pp 521 583.

72. Kumar S & Filipski A (2005) Reconstructing Vertebrate Phylogeny. Encyclopedia of Genetics,

Genomics, Proteomics and Bioinformatics edited by Subramaniam S. John Wiley & Sons, New York.

73. Kumar S, Filipski A, Swarna V, Walker A & Hedges SB (2005) Placing confidence limits on the molecular

age of the human-chimpanzee divergence. Proceedings of the National Academy of Sciences

(USA) 102:188**-*****.

74. Gadagkar SR, Rosenberg MS & Kumar S (2005) Inferring species phylogenies from multiple genes:

Concatenated sequence tree versus consensus gene tree. Journal of Experimental Zoology

(Molecular & Developmental Evolution) 304B:64 74.

75. Gadagkar SR & Kumar S (2005) Maximum likelihood outperforms maximum parsimony even when

evolutionary rates are heterotachous. Molecular Biology and Evolution 22:2139 2141.

76. Gargesha M, Yang J, Van Emden B, Panchanathan S & Kumar S (2005) Automatic annotation techniques

for gene expression images of the fruit fly embryo. Proceedings of Society of Photo-optical

Instrumentation Engineers 5960:576 583.

77. Hedges SB, Dudley J & Kumar S (2006) TimeTree: A public knowledge-base of divergence times among

organisms. Bioinformatics 22: 2971 2972.

78. Hedges SB, Kumar S & van Tuinen M (2006) Constraining fossil calibrations for molecular clocks.

BioEssays 28:770 771.

79. Elser JJ, Fagan WF, Subramanian S & Kumar S (2006) Signatures of ecological resource availability in

the animal and plant proteomes. Molecular Biology and Evolution 23:1946 1951.

80. Subramanian S & Kumar S (2006) Higher intensity of natural selection on >90% of the human genes

revealed by the intrinsic replacement mutation rates. Molecular Biology and Evolution 23:2283

2287.

Sudhir Kumar, Ph.D. (Page 9)

81. Subramanian S & Kumar S (2006) Evolutionary anatomies of positions and types of disease -associated

and neutral amino acid mutations in the human genome. BMC Genomics 7:306 (9 pp).

82. Ye J, Chen J, Li Q & Kumar S (2006) Classification of Drosophila embryonic developmental stage range

based on gene expression pattern images. Computational Systems Bioinformatics Conference

4:293 298.

83. Xia X & Kumar S (2006) Codon-based detection of positive selection can be biased by heterogeneous

distribution of polar amino acids along protein sequences. Computational Systems Bioinformatics

Conference 4:335 340.

84. Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Anal ysis (MEGA)

software version 4.0. Molecular Biology & Evolution 24:1596 1599.

85. Kumar S & Filipski A (2007) Multiple sequence alignment: In pursuit of homologous DNA positions.

Genome Research 17:127 135.

86. Kumar S & Dudley J (2007) Bioinformatics software for biologists in the genomics era. Bioinformatics

23:1713 1717.

87. Filipski A, Prohaska S & Kumar S (2007) Detecting molecular signatures of adaptive evolution. In

Evolutionary Genomics and Proteomics edited by Pagel M & Pomiankowski A. Sinauer Associates,

Massachusetts, pp 241 254.

88. Kumar S with many authors (2007) Sequence Assembly and Alignment Tech Guide. In Genome

Technology (10 pp).

89. Colbourn CJ & Kumar S (2007) Lower bounds on multiple sequence alignment using exact 3 -way

alignment. BMC Bioinformatics 8:140 (8 pp).

90. Zhang Y, Sturgill D, Parisi M, Kumar S & Oliver B (2007) Constraint and turnover in sex -biased gene

expression in the genus Drosophila. Nature 450:233 237.

91. Clark AG,, Kumar S,, Drosophila 12 Genomes Consortium (2007) Evolution of genes an d genomes

on the Drosophila phylogeny. Nature 450:203 218.

92. Acquisti C, Poste G, Curtiss D & Kumar S (2007) Nullomers: Really a matter of natural selection? PLoS

ONE 2 (3 pp).

93. Kumar S, Van Emden B, Acquisti C, Fagan WF & Elser JJ (2008) GRASP: Genomic Resource Access for

Stoichioproteomics. Arizona State University, Tempe, Arizona. (www.graspdb.net)

94. Ye J, Janardan R & Kumar S (2008) Biological Image Analysis via Matrix Approximation, Encyclopedia

of Data Warehousing and Mining (2nd Ed.) edited by John Wang, Idea Group, Inc., Pennsylvania

(Pp. 166-170).

95. Ye J, Chen J, Janardan R & Kumar S (2008) Developmental stage annotation of Drosophila gene

expression pattern images via an entire solution path for LDA. ACM Transactions on Knowledge

Discovery from Data 2:1 21.

96. Ji S, Sun L, Jin R, Kumar S & Ye J (2008) Automated annotation of Drosophila gene expression patterns

using a controlled vocabulary. Bioinformatics 24:1881 1888.

97. Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A b iologist-centric software for evolutionary

analysis of DNA and protein sequences. Briefings in Bioinformatics 9:299 306.

98. Hedges SB & Kumar S (2009) The Timetree of Life. Oxford University Press, New York (550 pp; edited

volume with 81 contributions).

99. Hedges SB & Kumar S (2009) Discovering the Timetree of Life. In The Timetree of Life edited by

Hedges SB & Kumar S. Oxford University Press, New York, pp 3 18.

100. Kumar S, Suleski M, Markov GJ, Lawrence S, Marco A & Filipski AJ (2009) Positional conservation and

amino acids shape the correct diagnosis and population frequencies of benign and damaging personal

amino acid mutations. Genome Research 19:1562-1569.

Sudhir Kumar, Ph.D. (Page 10)

101. Suzuki Y, Gojobori T & Kumar S (2009) Methods for incorporating the hypermutability of CpG

dinucleotides in detecting natural selection operating at the amino acid sequence level. Molecular

Biology & Evolution 26: 2275-2284.

102. Acquisti C, Elser JJ & Kumar S (2009) Ecological Nitrogen-limitation shapes the DNA composition of

plant genomes. Molecular Biology and Evolution 26:953 956.

103. Horiike T, Miyata D, Hamada K, Saruhashi S, Shinozawa T, Kumar S, Chakraborty R, Komiyama T &

Tateno Y (2009) Phylogenetic construction of 17 bacterial phyla by new method and carefully selected

orthologs. Gene 429:59 64.

104. Acquisti C, Kumar S & Elser JJ (2009) Signatures of nitrogen limitation in the elemental composition of

the proteins involved in the metabolic apparatus. Proceedings of the Royal Society, London, B

276:2605-2610.

105. Mikhailov KV, Konstantinova AV, Nikitin MA, Troshin PV, Rusin LY, Lyubetsky VA, Panchin YV, Mylnikov

AP, Moroz LL, Kumar S & Aleoshin VV (2009) The origin of Metazoa: a transition from temporal to

spatial cell differentiation. BioEssays 31:758-768.

106. Li Y-X, Ji S, Kumar S, Ye J, and Zhou Z-H. (2009) Drosophila gene expression pattern annotation

through multi-instance multi-label learning. International Joint Conference on Artificial

Intelligence, 1445-1450.

107. Ji S, Li Y-X, Zhou Z-H, Kumar S & Ye J (2009) A bag-of-words approach for Drosophila gene expression

pattern annotation. BMC Bioinformatics 10:119 (16 pp).

108. Marco A, Konikoff C, Karr TL & Kumar S (2009) Relationship between gene co -expression and sharing of

transcription factor binding sites in Drosophila melanogaster. Bioinformatics 25:2473-2477.

109. Goering LM, Hunt PK, Heighington C, Busick C, Pennings P, Hermisson J, Kumar S & Gibson G (2009)

Association of orthodenticle with natural variation for early embryonic patterning in Drosophila

melanogaster. Journal of Experimental Zoology (Molecular & Developmental Evolution)

312B:841-854.

110. Ji S, Yuan L, Li Y-X, Zhou Z-H, Kumar S & Ye J (2009) Drosophila gene expression pattern annotation

using sparse features and term-term interactions. ACM SIGKDD International Conference on

Knowledge Discovery and Data Mining. 407-416.

2010 Present

111. Battistuzzi FU, Filipski A, Hedges SB & Kumar S (2010) Performance of relaxed clock methods in

estimating evolutionary divergence times and their credibility intervals. Molecular Biology and

Evolution 27: 1289-1300.

112. Stone AC, Battistuzzi FU, Kubatko LS, Perry GH, Trudeau E, Lin H & Kumar S (2010) More reliable

estimates of divergence times in Pan using complete mtDNA sequences in and accounting for population

structure. Philosophical Transactions of Royal Society B 365: 3277-3288.

113. Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar

S, Wolfe SA, Brodsky MH & Sinha S (2010) Quantitative analysis of the Drosophila segmentation

regulatory network using pattern generating potentials. PLoS Biology 17: 8 (8 pp).

114. Kumar S. (2010) Foreword for the book GENES: Conceptual, Molecular, and Developmental by S Mitra.

MacMillan Press, India.

115. Kumar S & Hedges SB (2011) TimeTree2: Species divergence times on the iPhone. Bioinformatics 27:

2023-2024. [http://www.timetree.org].

116. Kumar S, Dudley JT, Filipski A & Liu L (2011) Phylomedicine: An evolutionary telescope to explore and

diagnose the universe of disease mutations. Trends in Genetics 27:377-386.

117. Kumar S, Konikoff C, Van Emden B, Busick C, Davis KT, Ji S, Wu L -W, Ramos H, Brody T, Panchanathan

S, Ye J, Karr TL, Gerold K, McCutchan M & Newfeld SJ (2011) FlyExpress: Visual mining of

spatiotemporal patterns for genes and publications in Drosophila embryo genesis. Bioinformatics

27:3319-3320.

Sudhir Kumar, Ph.D. (Page 11)

118. Battistuzzi FU, Billing-Ross P, Paliwal A & Kumar S (2011) Fast and slow programs implementing relaxed

clock methods show similar accuracies in estimating divergence times. Molecular Biology and

Evolution 28:2439-2442.

119. Elser JJ, Acquisti C & Kumar S (2011) Stoichiogenomics: The evolutionary ecology of macromolecular

elemental composition. Trends in Ecology & Evolution 26:38-44.

120. Tamura K, Peterson D, Peterson N, Stecher G, Nei M & Kumar S (2011) MEGA5: Molecular Evolutionary

Genetics Analysis using Maximum Likelihood, evolutionary distance, and Maximum Parsimony methods.

Molecular Biology & Evolution 28:2731-2739.

121. Battistuzzi FU, Filipski A & Kumar S (2011) Molecular clock: testing (version 2.0). Encyclopedia of Life

Sciences. John Wiley & Sons, Ltd, Chichester, UK (7pp) (www.els.net).

122. Gray VE & Kumar S (2011) Rampant purifying selection conserves positions with post-translational

modifications in human proteins. Molecular Biology and Evolution 28:1565-1568.

123. Pacheco MA, Battistuzzi FU, Lentino M, Aguilar R, Kumar S & Escalante AA (2011) Evolution of modern

birds revealed by Mitogenomics: timing the radiation and origin of major orders. Molecular Biology

and Evolution 28: 1927-1942.

124. Kumar S, Filipski A, Battistuzzi FU, Kosakovsky Pond SL & Tamura K (2012) Statistics and truth in

phylogenomics. Molecular Biology and Evolution 29:457-472.

125. Kumar S, Sanderford M, Gray VE, Ye J & Liu L (2012) Evolutionary diagnosis methods for variants in

personal exomes. Nature Methods 9:855-856.

126. Kumar S, Stecher G, Peterson D & Tamura K (2012) MEGA-CC: computing core of molecular

evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics

28:2685-2686.

127. Kumar S, Boccia K, McCutchan M & Ye J (2012) Exploring spatial patterns of gene expression from Fruit

Fly embryogenesis on the iPhone. Bioinformatics 28:2847-2848.

128. Konikoff C, Karr TL, McCutchan M, Newfeld SJ & Kumar S (2012) Comparison of embryonic expression

within multigene families employing the FlyExpress discovery platform reveals significantly more spatial

than temporal divergence. Developmental Dynamics 241:150-160.

129. Dudley JT, Chen R, Sanderford M & Kumar S (2012) Evolutionary meta-analysis of association studies

reveals ancient constraints affecting disease marker discovery. Molecular Biology and Evolution

29:2087-2094.

130. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ & Kumar S (2012) Human genomic

disease variants: A neutral evolutionary explanation. Genome Research 22:1383-94.

131. Gray VE, Kukurba KR & Kumar S (2012) Performance of computational tools in evaluating the functional

impact of laboratory-induced amino acid mutations. Bioinformatics 28:2093-2096.

132. Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A & Kumar S (2012) Estimating divergence

times in large molecular phylogenies. Proceedings of the National Academy of Sciences

109:193**-*****.

133. Li Y-X, Ji S, Kumar S, Ye J & Zhou Z-H (2012) Drosophila gene expression pattern annotation through

multi-instance multi-label learning. ACM/IEEE Transactions on Computational Biology and

Bioinformatics 98-112.

134. Yuan L, Woodard A, Ji S, Jiang Y, Zhou Z-H, Kumar S & Ye J (2012) Learning sparse representations for

fruit-fly gene expression pattern image annotation and retrieval. BMC Bioinformatics 13:107.

135. Stoltzfus SA, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF & and Vos RA (2012)

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Research

Notes 5:574 doi:10.1186/175*-****-*-***.

136. Maruki T, Kumar S & Kim Y. (2012) Purifying selection modulates the estimates of population

differentiation and confounds genome-wide comparisons across single nucleotide polymorphisms.

Molecular Biology and Evolution 29:3617-3623.

Sudhir Kumar, Ph.D. (Page 12)

INVITED PRESENTATIONS

SMBE Annual Meeting @ Chicago, Illinois (July 7-11), Nei Lecture (Upcoming) 2013

Sigma Xi, Oakland University, Rochester, Michigan (April 3) (Upcoming) 2013

Plenary Speaker, Society for Evolutionary Studies Annual Meeting @ Tokyo 2012

Metropolitan University (August 21-24)

Title: New methods and tools for the next generation of phylogenetics

SMBE Annual Meeting @ Dublin, Ireland 2012

Workshop on The animal tree of life and its application

Title: Bioinformatics Resources for Enabling Discoveries from Genomes to Phenotypes

Biomedicine: Big Data and New Paths to Personalized Medicine, ASU 2012

Title: Making Sense of the Molecular Data

International Conference on Bioinformatics & Computational Biology @ BKK, Thailand 2012

Title: Phylomedicine

ORSP Research Seminar Series @ Midwestern University, Phoenix, Arizona 2011

Molecular Biosciences Seminar Presentation on Phylomedicine at Montana State 2011

Young Scientists Workshop on Evolutionary Genomics @ Tokyo, Japan 2011

SMBE Annual Meeting @ Kyoto, Japan 2011

Workshop on Methods for multiple alignment and phylogenetic tree making for large

sequence datasets

Title: Maximum likelihood methods in MEGA5

International Society for Molecular Biology/ECCB @ Vienna, Austria 2011

SNPSigs Selection: Comparative Genomics as an Evolutionary Telescope for

Genomic Medicine to Peer into the Universe of Human Mutations

Workshop on Bioinformatic Software for Comparative Genomics and Metagenomics.

The Smithsonian Institution (SI), American Museum of Natural History (AMNH) 2011

and the Food and Drug Administration (FDA)

Title: MEGA software: Philosophy and Future

Department of Biomedical Informatics, ASU 2011

Barrett Honors College, ASU 2011

SMBE Symposium on Molecular and Genomic Evolution @ Penn State University 2011

Invited Keynote speaker, Mini-symposium on Data Mining for Biomedical Informatics 2011

@ SIAM International Conference on Data Mining, Mesa, Arizona

Keynote Speaker, Interdisciplinary Graduate Student's Symposium on 2011

Evolution Across Fields @ Institute for Evolution and Biodiversity,

Muenster, Germany (February 18)

Title: Molecular Evolution in Personal Medicine

Plenary Speaker, Molecular Phylogenetics Symposium, Russia (May 17-21) 2010

Stanford University, California, USA 2009

Symphogen Corporation (Copenhagen) 2009

Chalk Talk, Physics Department, ASU 2009

Spirit of Senses Group, Phoenix, Arizona 2009

University of Cologne, Germany 2009

Quantitative Expression Analysis workshop @ Drosophila Research Conference, 2009

Chicago, Illinois

Title: Challenges in Integrative Analysis of High-Throughput Datasets

University of North Carolina, Charlotte, NC 2008

Washington University, St. Louis, MO 2008

Symposium on Evolutionary Bioinformatics, Keynote address, Lava Springs, 2008

Idaho State University (Oct 3-5)

Title: Software tools and Knowledge-bases for discoveries from

genomes to phenotypes

Sudhir Kumar, Ph.D. (Page 13)

Japan Biological Information Research Center (JBIRC), Tokyo, Japan 2008

Symposium on New Insight of Genome Evolution into Fundamental Activities of 2008

Life, National Institute of Genetics (NIG) and the Tokyo Institute of Technology

(TIT), Japan

Global Center for Excellence, Hokkaido University, Sapporo, Japan 2008

Discussion leader, Computational and Statistical Advances, Gordon Conference 2008

in Molecular Evolution @ Ventura, California (Feb 3-8, 2008)

SOLUR Program, Arizona State University 2007

Department of Biomedical Informatics, Arizona State University 2007

FlyExpress: The Next Steps. FlyBase Advisory Group @ Harvard University, 2007

Boston, MA (Sept 15-18)

Keynote Speaker, Ohio Collaborative Conference on Bioinformatics (OCCBIO) 2007

@ Miami University, Oxford, Ohio

Title: Evolutionary anatomies of disease mutations in proteins

EMBO workshop on Human Evolution and Disease @ Center for Cellular and 2006

Molecular Biology, Hyderabad, India

Title: Evolutionary anatomies of the locations and types of disease-

associated nonsynonymous mutations in the human genome

Department of Biological Sciences, University of Idaho, Moscow, ID 2006

Microbiology Department, Montana State University, Bozeman, MT 2006

ASU Emeritus Faculty Association Luncheon, Tempe, AZ 2005

Title: Evolutionary Functional Genomics in the Biodesign Institute:

Taking a Computational Approach to Understanding and Harnessing

the Biological Design

Symposium on Molecular Evolution @ Moscow Conference on Computational 2005

Molecular Biology, Moscow State University, Russia

Title: Placing Confidence Limits on the Molecular Age of the Human-

Chimpanzee Divergence

Symposium on Systems Biology @ Moscow Conference on Computational 2005

Molecular Biology, Moscow State University, Russia

Title: Automating Discovery of Gene Interactions by in silico

Analysis of in situ Gene Expression Patterns in Fruit Fly Embryos

Special presentation to the Panel on Chemical Imaging, National Academies 2005

(USA), Washington DC

Title: In silico Analysis and Management of Fruit Fly Gene Expression

Pattern Images

Symposium on Evolutionary and Population Genomics @ Future of Statistics 2004

Conference, Hyderabad, India

Title: Genomic Bounds on the Timing of the Evolutionary Divergence

of Humans and Chimpanzees

Symposium on Advances in Methods for Estimating Species Divergence Dates 2004

Using Molecular Data @ International Congress of Zoology, Beijing, China

Title: Genomic Timescales: Precision & Robustness

Symposium on Molecular Phylogeny and Molecular Clocks @ Annual Meeting 2004

of the Society for Molecular Biology & Evolution, Penn State University,

University Park, PA

Title: Genomic Timescales: Precision & Robustness

Hexapodium, Center for Insect Research, University of Arizona 2004

Techniques Workshop @ 44th Annual Drosophila Research Conference,

2003

Chicago, IL

Sudhir Kumar, Ph.D. (Page 14)

Title: Basic Expression Search Tool (BEST): Computational

Framework for in silico Analysis of in situ Hybridization Data

Comparative and Functional Genomics Workshop, Sponsored by the Wellcome 2003

Trust and Department of Energy, Hinxton, Camridgeshire, UK

Title: Patterns of Point Mutation and Protein Substitution Rates Revealed

by Comparative Mammalian Genomics

Annual Meeting of the Society for Molecular Biology & Evolution, Newport 2003

Beach, CA

Department of Biology, Duke University, Durham, NC 2003

Bioinformatics Research Center, North Carolina State University, Raleigh, NC 2003

Symposium on Evolutionary Genetics @ Annual meeting of the American 2002

Genetic Association, Arizona State University, Tempe, Arizona

Title: Rates of Point Mutation in Mammals

The 12th International Workshop on Beyond the Identification of Transcribed

2002

Sequences: Functional, Evolutionary, and Expression Analysis sponsored by

Department of Energy, Washington, DC

Title: Building Fruit Fly Developmental Networks: in silico Approaches

for analyzing in situ Gene Expression Patterns

The 18th International Symposium in Conjunction with Award of the International

2002

Prize for Biology, Tokyo, Japan

Title: Building Fruit Fly Developmental Networks: in silico approaches

for Analyzing in situ Gene Expression Patterns

Department of Biology, Indiana University, Bloomington, Indiana 2002

Department of Computer Science, Arizona State University, Tempe, AZ 2002

Department of Biology, University of Michigan, Ann Arbor, MI 2002

International Workshop on Population Genetics @ University of Montreal, 2001

Montreal, Canada

Title: Estimating Neutral Evolutionary Rates in Mammals

ASU President s Community Enrichment Program, Phoenix, Arizona 2001

Department of Biology, Ohio State University, Columbus, Ohio 2001

Department of Biology, Hong Kong University, Hong Kong, China (2 lectures) 2001

Department of Biology, Syracuse University, Syracuse, New York 2001

Program in Ecology and Evolutionary Biology, University of Illinois, Urbana 2001

Champaign, Illinois

Department of Biology, Grand Canyon University, Phoenix, Arizona 2001

Ecology & Evolutionary Biology Program/IGERT, Indiana University, 2001

Bloomington, Indiana

Department of Biology, Tokyo Metropolitan University, Tokyo, Japan 2001

Biomedical Engineering, Indian Institute of Science, Bangalore, India 2001

Department of Biology, Tokyo Metropolitan University, Tokyo, Japan 2000

Graduate University for Advanced Studies, Hayama, Japan 2000

Genetics Program, University of Arizona, Tucson, Arizona 2000

Birla Institute of Technology & Sciences, Pilani, India 2000

University of South Carolina, Columbia, South Carolina 2000

Symposium on Genomic Diversity @ Annual meeting of the American Genetic 1999

Association, Pennsylvania State University, University Park, PA

Title: Genomic Divergence between Species in terms of the Number

of Chromosomal Rearrangements

Department of Biology, Arizona State University-West, Phoenix, Arizona 1999

Department of Zoology and Genetics, Iowa State University, Ames, Iowa 1998

Sudhir Kumar, Ph.D. (Page 15)

Symposium on Large Phylogenies @ Annual meeting of the Society for the 1997

Study of Systematic Biology, University of Colorado, Boulder, Colorado

Title: Inferring Large Phylogenies

National Cancer Institute, Frederick, Maryland 1997

Department of Biology, Arizona State University, Tempe, Arizona 1997

TEACHING, MENTORING, UNIVERSITY SERVICE

Classroom Instruction

(Average rating in parentheses; SCALE: 1 = BEST; 4 = WORST)

BIO 494 Evolutionary Medicine (41 students) 2012

BIO 455 (1.2) Introduction to Comparative Genomics (41 students) 2011

BIO 494 (1.1) Evolutionary Medicine (30 students) 2010

BIO 455 (1.2) Introduction to Comparative Genomics (25 students) 2009

BIO 455 (1.2) Introduction to Comparative Genomics (10 students) 2008

BIO 494 (1.2) Introduction to Comparative Genomics (12 students) 2007

BIO 345 (1.4) Organic Evolution (180 students) 2006

BIO 345 (1.6) Organic Evolution (150 students) 2005

BIO 494 (1.3) Introduction to Comparative Genomics (11 students) 2004

BIO 345 (1.4) Organic Evolution (185 students) 2003

BIO 494 (1.2) Introduction to Comparative Genomics (12 students) 2003

BIO 445 (1.4) Organic Evolution (180 students) 2001

BIO 494 (1.3) Computational Genomics (7 students) 2001

BIO 445 (1.7) Organic Evolution (106 students) 2000

BIO 594 (1.3) Molecular Evolutionary Genetics (7 students) 2000

BIO 594 (1.5) Molecular Evolutionary Genetics (10 students) 1999

BIO 494 (1.2) Advanced Evolution (14 students) 1999

Current Postdoctoral Fellows / Research Scientists

Sayaka Miura, Ph.D., Biology, Pennsylvania State University 2012 Present

Project: Phylomedicine of gene duplicates in the human genome

Lifang Liu, Ph.D., Computer Science, Xidian University, China 2012 Present

Project: Integrative analysis of gene expression phenotypes and genome sequences

Li Liu, MS, MD, Research Scientist 2010 Present

Project: Bioinformatics Analysis Research Nexus (BARN) core facility

Nevin Gerek, Ph.D., Chemical Engineering, University of Akron, OH 2010 Present

Project: Protein structure dynamics in human diseases

Alan Filipski, Ph.D., Computer Science, Michigan State 2001 Present

Project: Molecular Phylogenetics and Metagenomics

Past Postdoctoral Fellows Mentored

Fabia Battistuzzi, Ph.D., Biology/Astrobiology 2008 2012

Current Position: Assistant Professor, Oakland University, Michigan

Yingqin Luo, Ph.D., Bioinformatics 2008 2011

Project: Microbial Genome Evolution.

Claudia Acquisti, Ph.D., Molecular Evolution, Italy 2006 2010

Current Position. Assistant Professor, Institute for Evolution and Biodiversity,

University of Muenster, Germany

Antonio Marco-Castillo, Ph.D., Genetics, Spain 2008 2009

Current Position. Faculty of Life Sciences, The University of Manchester, England

Bao Hong Shen, Ph.D., Computer Science, Ariz. State Univ.

Contact this candidate