OSU Department of Biomedical Informatics

Daniel A. Janies Ph.D.

Associate Professor

phone: (614) 292-1202
fax: (614) 688-6600

email:



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mailing address
3190 Graves Hall [NOTE: OFFICE IS 216 BRT]
333 W. 10th Ave.
Columbus, OH 43210


Dr Janies received a B.S. in Biology from the University of Michigan, Ann Arbor, and a Ph.D. in Zoology from the University of Florida, Gainsville. He was a NASA Principal Investigator at the American Museum of Natural History, where previously he had been a Postdoctoral Fellow. Since 2003, Dr Janies has been an Associate Professor at BMI.

Dr. Janies was trained as a biologist, however, as a result of the computational demands of the biological questions he was interested in, he began to develop hardware and software. He led the design, construction, and integration of the parallel computing cluster at the American Museum of Natural History. Using off-the-shelf PC components and relying solely on house talent, his team built an inexpensive, internationally ranked 860-processor supercomputer (see an overview of this work).

Research

Project Involvement

Bioinformatics

My research objectives are to continue to develop computational and evolutionary sciences in a comparative genomics context. I have collaborations with phamacogenomicists and microbiologists. To these ends, I have developed novel phylogenetic methods to correlate genotypes and phenotypes and find diagnostic polymorphisms among organisms. In short, I am mining datasets of mutational history implied by phylogenetic trees for two types of information: 1) recurrent changes in phenotype and genotype among lineages to identify disease candidate genes for complex disease and 2) exclusive changes that are vital to design sensitive reagents such a taxon specific oligonucleotides useful in diagnostics.

Genomics promises a new paradigm for scientific and medical research. Soon we will understand the fundamentals of cellular metabolism, development, and evolution at a basic informational level. This understanding will help us attack the mechanics of the disease rather than treat its symptoms. However having a single genome sequence provides little information by itself. It is through sequence alignment and tree search that one can identify functional regions of bimolecular sequences, diagnose affected from unaffected individuals, and better understand infectious disease. Similarity search is vital to database retrieval, annotation, and gene discovery. Comparative organismal approaches lead to the discovery of the shared functional regions. Thus the field of sequence comparison has much to offer for all fields of modern biology and medicine. Progress requires the synergistic development of software and hardware suited to very large datasets.

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Grant Highlights


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Publications

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Daniel A. Janies, "Genome Technology cover & article for Dan Janies & team, July/Aug. 2007", July, 2007.

Steven L. Salzberg, Carl Kingsford, Giovanni Cattoli, David J. Spiro, Daniel A. Janies, Mona Mehrez Aly, Ian Brown, Emmanuel Couacy-Hymann, Gian Mario De Mia, Do Huu Dung, Annalisa Guercio, Tony Joannis, Ali Safar Maken Ali, Azizullah Osmani, Iolanda Padalino, Magdi D. Saad, Vladamir Savic, Naomi A. Sengamalay, Samuel Yingst, Jennifer Zaborsky, Olga Zorman-Rojs, Elodie Ghedin, IIaria Capua, "Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses", Emerging Infectious Diseases, 13 (5) May, 2007.

Daniel A. Janies, Andrew Hill, Rob Guralnick, Farhat Habib, Eric Waltari, Ward C. Wheeler, "Genomic Analysis and Geographic Visualization of the Spread of Avian Influenza (H5N1)", Systematic Biology, Vol. 56 (2) : pp. 321-329, May, 2007.

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Presentations

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Daniel A. Janies, "Applications of large-scale phylogenetic analysis for research in emerging infectious disease", in Proceedings of 2006

Daniel A. Janies, Pablo A. Goloboff, Diego Pol, "Applications of Large-scale Phylogenetic Analysis for Research In Emerging Infectious Disease", in Proceedings of 2005

Diego Pol, Daniel A. Janies, "Host and Antigenic Evolution of Influenza A as Viewed Through Very Large Datasets", in Proceedings of Fagernes, Norway, 2005

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Tech Reports

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Daniel A. Janies, Ward C. Wheeler, "POY version 3.0, Documentation and Command Summary, Phylogeny Reconstruction via Direct Optimization of DNA and other data", Technical Report, No. OSUBMI_TR_2002_n03, Biomedical Informatics, 2002.

J. Harshman, Daniel A. Janies, "Summary Report of the Workshop on Evolutionary Biology, held at The American Museum of Natural History, NY, March 3-5, 1999", Technical Report, No. OSUBMI_TR_1999_n01, Biomedical Informatics, 1999.

Daniel A. Janies, Ward C. Wheeler, "MALIGN version 2.7", Technical Report, No. OSUBMI_TR_1998_n01, Biomedical Informatics, 1998.


Publications

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Daniel A. Janies, Diego Pol, Andrew Hill, Boyan Alexandrov, Farhat Habib, "Evolution of genomes, host shifts, and geographic spread of SARS-CoV and related coronaviruses", Cladistics, Vol. 24 (2) : pp. 111-130, April, 2008.

Daniel A. Janies, Diego Pol, "Phylogenetic analysis of emerging infectious diseases", Tutorials in Mathematical Biosciences IV: Evolution and Ecology, Vol. 1922 : pp. 39-76, January, 2008.

Daniel A. Janies, "Genome Technology cover & article for Dan Janies & team, July/Aug. 2007", July, 2007.

Daniel A. Janies, Pablo A. Goloboff, Diego Pol, "Large-scale phylogenetic analysis for the study of zoonosis and assessment of influenza surveillance", Scalable Computing: Practice and Experience, 8 (2) : pp. 143-146, June, 2007.

Daniel A. Janies, Andrew Hill, Rob Guralnick, Farhat Habib, Eric Waltari, Ward C. Wheeler, "Genomic Analysis and Geographic Visualization of the Spread of Avian Influenza (H5N1)", Systematic Biology, Vol. 56 (2) : pp. 321-329, May, 2007.

Steven L. Salzberg, Carl Kingsford, Giovanni Cattoli, David J. Spiro, Daniel A. Janies, Mona Mehrez Aly, Ian Brown, Emmanuel Couacy-Hymann, Gian Mario De Mia, Do Huu Dung, Annalisa Guercio, Tony Joannis, Ali Safar Maken Ali, Azizullah Osmani, Iolanda Padalino, Magdi D. Saad, Vladamir Savic, Naomi A. Sengamalay, Samuel Yingst, Jennifer Zaborsky, Olga Zorman-Rojs, Elodie Ghedin, IIaria Capua, "Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses", Emerging Infectious Diseases, 13 (5) May, 2007.

Farhat Habib, Andrew Johnson, Ralf Bundschuh, Daniel A. Janies, "Large scale genotype-phenotype correlation analysis based on phylogenetic trees", Bioinformatics, 23 (7) : pp. 785-788, February, 2007.

Ward C. Wheeler, Lone Aagesen, Claudia P. Arango, Julian Faivovich, Taran Grant, Cyrille D'Haese, Daniel A. Janies, William L. Smith, Andres Varon, Gonzalo Giribet, "Dynamic Homology and Phylogenetic Systematics: A Unified Approach Using POY", : pp. 365, December, 2006.

X. Zhang, M. Hasoksuz, D. Spiro, R. Halpin, S. Wang, S. Stollar, Daniel A. Janies, N. Hadya, Y. Tang, E. Ghedin, Linda J. Saif, "Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus.", Virology, : pp. 424-435, October, 2006.

Tahsin M. Kurc, Daniel A. Janies, Andrew Johnson, Stephen Langella, Scott Oster, Shannon L. Hastings, Farhat Habib, Terry Camerlengo, David W. Ervin, Umit V. Catalyurek, Joel H. Saltz, "An XML-based System for Synthesis of Data from Disparate Databases", Journal of the American Medical Informatics Association, 13 : pp. 289-301, January, 2006.

Daniel A. Janies, Linda J. Saif, "Genetic Diversity and Recombination of Porcine Sapoviruses", Journal of Clincal Microbiology, 43 (12) : pp. 5963-72, December, 2005.

Ron M. Clouse, Daniel A. Janies, Alexander M. Kerr, "Resurrection of Bohadschia bivittata from B. marmorata (Holothuroidea: Holothuriidae) based on behavioral, morphological, and mitochondrial DNA evidence", Zoology, 108 (1) : pp. 27-39, March, 2005.

Shannon L. Hastings, Stephen Langella, Scott Oster, Tahsin M. Kurc, Tony C. Pan, Umit V. Catalyurek, Daniel A. Janies, Joel H. Saltz, "Grid-based Management of Biomedical Data using an XML-based Distributed Data Management System", Proceedings of the 19th Annual ACM Symposium on Applied Computing (SAC '05), : pp. 105-109, March, 2005.

Alexander M. Kerr, Daniel A. Janies, Ron M. Clouse, J. Kuszak, J. Kim, "Molecular phylogeny of coral-reef sea cucumbers (Holothuroidea: Aspidochirotida) based on 16S mt rDNA sequence", Marine Biotechnology, 7 (1) : pp. 53-60, February, 2005.

Ward C. Wheeler, Daniel A. Janies, J. DeLaet, "DNA sequence alignment and parallel processing", McGraw-Hill 2004 Yearbook of Science & Technology, August, 2004.

Daniel A. Janies, Farhat Habib, Andrew Johnson, "Comparative Methods of Discovery of Exclusive or Functional Regions of Biomolecular Sequences", June, 2004.

Daniel A. Janies, "Please explain the basics of bioinformatics. What questions in biology are currently being addressed with computer methods?", September, 2003.

Daniel A. Janies, "Reversibility in life cycle and larval evolutionary among echinoderms", Cladistics, 19 March, 2003.

Daniel A. Janies, Ward C. Wheeler, "A Primer for combined Analysis of DNA and Phenotypic Data in Cluster Computers", January, 2003.

Daniel A. Janies, Ward C. Wheeler, "Theory and practice of parallel direct optimization", Techniques in Molecular Systematics and Evolution, : pp. 115-123, June, 2002.

Daniel A. Janies, "Phylogenetic relationships of extant echinoderm classes", Canadian Journal of Zoology, 79 (7) : pp. 1232-1250, July, 2001.

D. Frost, R. Etheridge, Daniel A. Janies, T. Titus, "Total evidence, sequence alignment, evolution of polychrotid lizards, and a reclassification of the Iguania (Squamata Iguanania)", American Museum Novitates, 1 (343) : pp. 1-39, June, 2001.

Daniel A. Janies, Ward C. Wheeler, "Efficiency of Parallel Direct Optimization", Cladistics, 17 (1) : pp. S71-S82, March, 2001.

Gonzalo Giribet, Daniel A. Janies, Ward C. Wheeler, "Introduction", Cladistics, 17 (1) : pp. S1-S2, March, 2001.

D. Frost, Daniel A. Janies, P. le Fras Mouton, T. Titus, "A molecular perspective on the phylogeny of the girldes lizards (Cordylidae, Squamata)", American Museum Novitates, (3310) : pp. 1-12, January, 2001.

A. Phillips, Daniel A. Janies, Ward C. Wheeler, "Multiple Sequence Alignment in Phylogenetic Analysis", Molecular Phylogenetics and Evolution, 16 (3) : pp. 317-330, September, 2000.

Daniel Blake, Daniel A. Janies, R. Mooi, "Evolution of Starfishes: Morphology, Molecules, Development, and Paleobiology", American Zoologist, 40 (3) : pp. 311-315, June, 2000.

Daniel A. Janies, Rob Desalle, "Development, Evolution, and Corroboration", The Anatomical Record, 257 (1) : pp. 6-14, December, 1999.

Daniel A. Janies, Larry McEdward, "Heterotopy, pelagic direct development, and new body plans in velatid asteroids", : pp. 319-324, December, 1998.

Daniel A. Janies, R. Mooi, "Xyloplax is an asteroid", Echinoderm Research, 1998: Proceedings of the 5th European Conference on Echinoderms, : pp. 311-316, October, 1998.

Larry McEdward, Daniel A. Janies, "Relationships among development, ecology, and morphology in the evolution of echinoderm larvae and life cycles", Biological Journal of the Linnean Society, 60 (3) : pp. 381-400, March, 1997.

Daniel A. Janies, "Reconstructing the Evolution of Morphogenesis and Dispersal among Velatid Asteroids", December, 1995.

Daniel A. Janies, Larry McEdward, "A hypothesis for the evolution of the concentricycloid water-vascular system", : pp. 246-257, December, 1994.

Daniel A. Janies, Larry McEdward, "Highly Derived Coelomic and Water-Vascular Morphogenesis in a Starfish with Pelagic Direct Development", Biological Bulletin, 185 (1) : pp. 56-76, August, 1993.

Daniel A. Janies, Larry McEdward, "Life Cycle Evolution in Asteroids: What is a Larva?", Biological Bulletin, 184 (3) : pp. 255-268, June, 1993.

Daniel A. Janies, X. Zhang, M. Hasoksuz, David J. Spiro, S. Wang, R. Halpin, E. Ghedin, Linda J. Saif, A Vlasova, L. Jones, "Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation", Virology, : pp. 1-10, December, 0000.

Presentations

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Daniel A. Janies, Ward C. Wheeler, Andres Varon, L. Vinh, "Towards Phylogenomic Reconstruction", in Proceedings of BIOCOMP, Las Vegas, Nevada, 2007

Daniel A. Janies, "Applications of large-scale phylogenetic analysis for research in emerging infectious disease", in Proceedings of 2006

Daniel A. Janies, Pablo A. Goloboff, Diego Pol, "Applications of Large-scale Phylogenetic Analysis for Research In Emerging Infectious Disease", in Proceedings of 2005

Diego Pol, Daniel A. Janies, "Host and Antigenic Evolution of Influenza A as Viewed Through Very Large Datasets", in Proceedings of Fagernes, Norway, 2005

Daniel A. Janies, "Evolution of Genomes and Host Shifts Among SARS Associated and Related Coronaviruses", in Proceedings of Evolution of Infectious Disease, Fairbanks, Alaska, 2005

Farhat Habib, Daniel A. Janies, "Intersection and Exclusion Analysis of Genomic Changes Implied by Phylogenetic Trees", in Proceedings of 2005

Daniel A. Janies, "Novel Method for Inferring Genotype-Phenotype Associations to Identify Disease Susceptibility Loci", in Proceedings of 2005

Daniel A. Janies, "Research Summary", in Proceedings of IBGP 705, 2003

Tech Reports

click to hide (-)

Daniel A. Janies, Ward C. Wheeler, "POY version 3.0, Documentation and Command Summary, Phylogeny Reconstruction via Direct Optimization of DNA and other data", Technical Report, No. OSUBMI_TR_2002_n03, Biomedical Informatics, 2002.

J. Harshman, Daniel A. Janies, "Summary Report of the Workshop on Evolutionary Biology, held at The American Museum of Natural History, NY, March 3-5, 1999", Technical Report, No. OSUBMI_TR_1999_n01, Biomedical Informatics, 1999.

Daniel A. Janies, Ward C. Wheeler, "MALIGN version 2.7", Technical Report, No. OSUBMI_TR_1998_n01, Biomedical Informatics, 1998.


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