Topic “bio”

•  “An Integrated Map of Genetic Variation from 1,092 Human Genomes”, The 1000 Genomes Project Consortium, Nature, 2012. 491: 56-65.
• "A Two-Graph Guided Multi-task Lasso Approach for eQTL Mapping”, Chen X*, Shi X*, Xu X, Wang Z, Mills RE, Lee C, and Xu J, In Proceedings of the 15thInternational Conference of Artificial Intelligence and Statistics (AISTATS) 2012, La Palma, Canary Islands, JMLR W&CP 22: 208-217, 2012.
• “Extensive Genetic Diversity and Substructuring among Zebrafish Strains Revealed Through Copy Number Variant Analysis”, Brown KH*, Dobrinski KP*, Lee AS, Gokcumen O, Mills RE, Shi X, Chong W, Chen JY, Yoo P, David S, Petersond SM, Raj T, Choy KW, Stranger BE, Williamson RE, Zon LI, Freeman JL, and Lee C, Proceedings of the National Academy of Sciences of the USA (PNAS), 2012. 109(2):529-534 (cover article).
• “User Identification and Anonymization in 802.11 Wireless LANs”, Xu D, Wang Y, Shi X, and Yin X, Security and Communication Networks (Wiley), 2012. 5(1):15-27.
• “Refinement of Primate CNV Hotspots Identifies Candidate Genomic Regions Evolving under Positive selection”, Gokcumen O*, Babb PL*, Iskow RC, Zhu Q,Shi X, Mills RE, Ionita-Laza I, Vallender EJ, Clark A, Johnson WE, Lee C, Genome Biology, 2011. 12:R52.
• “A Comprehensive Assessment of Array-Based Platforms and Calling Algorithms for Detection of Copy Number Variants”, Pinto D*, Darvishi K*, Shi X, Rigler D, Fitzgerald T, Lionel A, Thiruvahindrapuram B, MacDonald J, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe P, Smith R, Park J.H, Hurles M, Carter N, Lee C, Scherer S, Feuk L, Nature Biotechnology, 2011. 29:512-520.
• “Mapping Copy Number Variation by Population-Scale Genome Sequencing”, Mills R*, Walter K*, Stewart C*, Handsaker R*, Chen K*, Alkan C*, Abyzov A*, Yoon S*, Ye K*, Cheetham R, Chinwalla A, Conrad D, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva L, Iqbal Z, Kang S, Kidd J, Konkel M, Korn J, Khurana E, Kural D, Lam H, Leng J, Li R, Li Y, Lin C, Luo R, Mu X, Nemesh J, Peckham H, Rausch T, Scally A, Shi X, Stromberg M, Stutz A, Urban A, Walker J, Wu J, Zhang Y, Zhang Z, Batzer M, Ding L, Marth G, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eicher E, Gerstein M, Hurles M, Lee C, McCarroll S, and Korbel J, and the 1000 Genomes Project, Nature, 2011. 470: 59-65.
• “Capacity of Data Collection in Randomly-Deployed Wireless Sensor Networks”, Chen S, Wang Y, Li X-Y, Shi X, ACM/Springer Wireless Networks (WINET), 2011. 17: 305-318.
• “A Map of Human Genome Variation from Population Scale Sequencing”, The 1000 Genomes Project Consortium, Nature, 2010. 467: 1061-1073 (cover article).
• “802.11 User Anonymization”, Xu D, Wang Y, Shi X, and Yin X, In Proc. of the IEEE Global Telecommunications Conference (GlobeCom 2010), 1-5, Miami, FL, December 2010.
• “Order-Optimal Data Collection in Wireless Sensor Networks: Delay and Capacity”, Chen S, Wang Y, Li X-Y, and Shi X, In Proc. of the 6th Annual IEEE Communications Society Conference on Sensor, Mesh, and Ad Hoc Communications and Networks (SECON 2009), 1-9, Rome, Italy, June 2009.
• “A Bayesian Approach to High-Throughput Biological Model Generation”, Shi X and Stevens R, In Proc. of the 1st Bioinformatics and Computational Biology Conference (BiCob 2009), Lecture Notes in Bioinformatics (Springer Verlag) 5462: 376-387, New Orleans, LA, April 2009.
• “Enhanced Feature Selection and Generation for 802.11 User Identification”, Xu D, Wang Y, and Shi X, In Proc. of The 18th International Conference on Computer Communications and Networks (ICCCN 2009), 1-6, San Francisco, CA, August 2009.
• “Self-Organizing Fault Tolerant Topology Control in Large-Scale Three-Dimensional Wireless Networks”, Wang Y, Cao L, Dahlberg T, Li F, and Shi X, ACM Transactions on Autonomous and Adaptive Systems (TAAS), 2009. 3:19.1-19.21.
• “SWARM: A Scientific Workflow for Supporting Bayesian Approaches to Improve Metabolic Models”, Shi X and Stevens R, In Proc. of The 6th ACM/IEEE International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 2008), 25-34, Boston, MA, March, 2008.
• “The National Microbial Pathogen Database Resource (NMPDR): A Genomics Platform Based on Subsystem Annotation”, McNeil L, Reich C, Aziz R, Bartels D, Cohoon M, Disz T, Edwards R, Gerdes S, Hwang K, Kubal M, Margaryan G, Meyer F, Mihalo W, Olsen G, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch G, Rodionov D, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R, Nucleic Acids Research, 2007.35:D347-D353.
• “Efficient On-Demand Topology Control for Wireless Ad Hoc Networks”, Wang Y and Shi X, In Proc. of 14th IEEE International Conference on Computer Communications and Networks (ICCCN 2005), 159-164, San Diego, California, October 2005.

• Daniel A. Janies, Jonathon Studer, Samuel K. Handelman, Gregorio Linchangco. A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets. Cladistics. DOI: 10.1111/cla.12014. February 18, 2013. http://onlinelibrary.wiley.com/doi/10.1111/cla.12014/full.
• Janies, D., Pomeroy, L., Aaronson, J., Handelman, S., Hardman, J., Kawalec, K., Bitterman, T., Wheeler, W.C. (2012) Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service.Cladistics. DOI: 10.1111/j.1096-0031.2012.00401.x
• Chakrabarty, P., Lam, C., Hardman, J., Aaronson, J., House, P., Janies, D. (2012) Speciesmap: A Web-Based Application for Determining the Effects of the 2010 Gulf Of Mexico Oil Spill on Wildlife, with a Preliminary List of Fishes Put at Risk. Biodiversity and Conservation.                                                                                                                 http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s10...
• Newman S., Hill, N., Spragens, K., Janies, D., Voronkin, I., Prosser, D., Baoping, Y., Lei, F., Batbayar, N., Tseveenmyadag, N., Bishop, C., Butler, P., Wikelski, M., Sivananinthaperumal, B., Mundkur, T., Douglas, D., and Takekawa, J. (2012) An Eco-Virological Approach for Assessing the Role of Wild Birds in the Spread of Avian Influenza H5N1 Along the Central Asian Flyway. PloS ONE. 7(2): e30636. doi:10.1371/journal.pone.0030636
• Bokhari, S., Pomeroy, L., Janies, D. (2012) Reassortment Networks and the Evolution of Pandemic H1N1 Swine-origin Influenza. IEEE Transactions on Computational Biology and Bioinformatics.                                         http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2011.95
• Janies D., Embi P.J., Payne P.R. Health-care hit or miss?: Collect genetic data on pathogens. Nature. Vol. 470, no. 7334. (February 17, 2011):329.                                                                                                                                                       http://www.nature.com/nature/journal/v470/n7334/full/470327a.html
• Janies, D., Voight, J., Daly, M., (2011) Echinoderm Phylogeny including Xyloplax, a Progenetic Asteroid. Systematic Biology. 604:420-438 doi: 10.1093/sysbio/syr044
• Studer, J. and Janies. D. (2011) Global spread and evolution of viral hemorrhagic septicemia virus. Journal of Fish Diseases. 34: 741–747. doi: 10.1111/j.1365-2761.2011.01290.x
• Griffen, A., Beall C., Firestone, N., Gross, E., DiFranco J., Hardman, H., Vriesendorp, B., Faust, R., Janies, D., Leys, E., CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome. PLoS ONE 6(4):e19051. doi:10.1371/journal.pone.0019051
• Kumar, S., Handelman, S., Voronkin I., Mwapasa V., Janies D., Rogerson S., Meshnick S., Kwiek J. (2011) Different Regions of HIV-1 Subtype C Env are Associated  with Placental Localization and in Utero Mother-to-Child Transmission. Journal of Virology.                                                                                                                                                                             http://jvi.asm.org/cgi/reprint/JVI.01955-10v1?view=long&pmid=21543508
• Gross, E., E. Leys, S. Gasparovich, N. Firestone, J. Schwartzbaum, D. Janies, K. Asnani, A. Griffen, (2010) Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth. Journal of Clinical Microbiology. 48:4121-8
  http://jcm.asm.org/cgi/content/abstract/JCM.01232-10v1
• Bulach, D., R. Halpin, D. Spiro, L. Pomeroy, D. Janies, D. Boyle (2010) Molecular analysis of H7 avian influenza viruses from Australia and New Zealand: Genetic diversity and relationships – 1976 to 2007. Journal of Virology.
  http://jvi.asm.org/cgi/content/abstract/JVI.00930-10v1
• Janies, D., I. Voronkin, M. Das, J. Hardman, T. Treseder, J. Studer. (2010) Genome Informatics of Influenza A. From data sharing to shared analytical capabilities.Animal Health Research Reviews. 11: 73-79
  http://journals.cambridge.org/repo_A78auyCI
• Janies, D., T. Treseder, B. Alexandrov, F. Habib, J. Chen, R. Ferreira, Ü. Çatalyürek, A. Varón, W.C. Wheeler. (2010) The Supramap project: Linking pathogen genomes with geography to fight emergent infectious diseases. Cladistics. 27: 61-
  66 http://dx.doi.org/10.1111/j.1096-0031.2010.00314.x
• Janies, D., I. Voronkin, J. Studer, J. Hardman, B. Alexandrov, T. Treseder, C. Valson. (2010) Selection for resistance to oseltamivir in seasonal and pandemic H1N1 influenza and widespread co-circulation of the lineages. International Journal of Health Geographics. 9:13 http://dx.doi.org/10.1186/1476-072X-9-13
• Hovmöller, R., B. Alexandrov, J. Hardman, D. Janies. (2010) Tracking the Geographic Spread of Avian Influenza (H5N1) with Multiple Phylogenetic Trees. Cladistics. 26:1–13.
  http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2009.00297.x/full
• Bokhari, S. and D. Janies. (2010) Reassortment Networks for Investigating the Evolution of Segmented Viruses. IEEE Transactions on Computational Biology and Bioinformatics 7:288-298
  http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=04585355
• Hill, A.W., R. Guralnick, M. Wilson, F. Habib, D. Janies. (2009) Evolution of drug resistance in multiple distinct lineages of H5N1 avian influenza. Infection, Genetics, and Evolution. 9: 169-178. Top 10 most downloaded for the journal for 2009. http://linkinghub.elsevier.com/retrieve/pii/S1567134808001913
• Yilmaz, A., M. Nishiyama, B. Garcia-Fuentes, G. Souza, D. Janies, J. Gray, E. Grotewold. (2009) GRASSIUS: A Platform for Comparative Regulatory Genomics Across the Grasses. Plant Physiol. doi:10.1104/pp.108.128579
• Janies, D., F. Habib, B. Alexandrov, A. Hill, D. (2008) Pol. Evolution of genomes, host shifts, and geographic spread of SARS-CoV and related coronaviruses. Cladistics.
  24: 111–130. http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2008.00199.x/full
• Ott, M., J. Zola, S. Aluru, A. Johnson, D. Janies, A. Stamatakis. (2008) Large-scale Phylogenetic Analysis on Current HPC Architectures. Scientific Programming. 16:255-270.
• Janies, D. and D. Pol. (2008) Phylogenetic analysis of emerging infectious diseases. In Tutorials in Mathematical Biosciences IV: Evolution and Ecology (Lecture Notes in Mathematics / Mathematical Biosciences Sub series) A. Friedman ed. http://www.springerlink.com/content/978-3-540-74328-6#section=246925&page=1
• Janies, D., A. Hill, R. Guralnick, F. Habib, E. Waltari, W. Wheeler. (2007) Genomic Analysis and Geographic Visualization of the Spread of Avian Influenza (H5N1). Systematic Biology. 56:321-9. http://sysbio.oxfordjournals.org/content/56/2/321.full
• Habib, F., A. Johnson, R. Bundschuh, D. Janies. (2007) Large scale genotype-phenotype correlation analysis based on phylogenetic trees. Bioinformatics. 23:785-788 http://bioinformatics.oxfordjournals.org/content/23/7/785.abstract
• Janies, D., P. Goloboff, D. Pol, Large-scale phylogenetic analysis for the study of zoonosis and assessment of influenza surveillance. Scalable Computing: Practice and Experience. Volume 8, Number 2, pp. 143–146. 2007
• Salzberg, S., C. Kingsford, G. Cattoli, D. Spiro, D. Janies, et al., (2007) Genome analysis links recent European and African H5N1 influenza viruses and shows them to be distinct from earlier outbreak strains. Emerging Infectious Diseases. 13:5
• Zhang, X., M. Hasoksuz, D. Spiro, R. Halpin, S. Wang, A. Vlasova, D. Janies, L. Jones, E. Ghedin, L. Saif. (2007) Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation. Virology. 363:1-10
• Vinh, L., A. Varon, D. Janies, W. Wheeler. (2007) Towards Phylogenomic Reconstruction. International Conference on Bioinformatics and Computational Biology. BIOCOMP'07. CSREA Press Vol. 1, page: 98-104.
• Zhang X., M. Hasoksuz, D. Spiro, R. Halpin, S. Wang, S. Stollar, D. Janies, N. Hadya, Y. Tang, E. Ghedin, L. Saif. (2007) Complete genomic sequences, a key residue in the spike protein and deletions in non-structural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus. Virology. 358:424-35.

• Time Series Microarray Gene Expression Profiling and Temporal Regulatory Pathway Analysis of BMP6 Induced Osteoblast Differentiation and Mineralization. Luo W, Friedman M, Hankenson KD, Woolf JP, BMC Syst Biol. 2011, 5(1):82
• GAGE: Generally Applicable Gene Set Enrichment for Pathways Analysis. Luo W, Friedman M, Shedden K, Hankenson KD, Woolf JP, BMC Bioinformatics 2009, 10:161
• Learning Transcriptional Regulatory Network from High Throughput Gene Expression Data Using Continuous Three-Way Mutual Information. Luo W, Hankenson KD, Woolf JP, BMC Bioinformatics. 2008. 9(1):467
• Disruption of cell-matrix interactions by heparin enhances mesenchymal progenitor adipocyte differentiation. Luo W, Shitaye H, Friedman M, Bennett C, Miller J, MacDougald OM, Hankenson KD, Exp. Cell Res., 2008, 314(18):3382-91
• Targeting a Myb-mediated self-renewal program eradicates chemotherapy-resistant AML. Zuber J, Rappaport AR, Luo W, et al, Genes Dev. In press
• A common telomeric gene silencing assay is affected by nucleotide metabolism. Rossmann MP, Luo W, Tsaponina O, Chabes A, Stillman B, Molecular Cell, 2011, 42(1):127-36. Mouse models of human AML accurately predict chemotherapy response. Zuber J, Radtke I, Pardee TS, Zhao Z, Rappaport AR, Luo W, et al. Genes Dev. 2009, 23(7):877-89.
• Synthesis and Characterization of Poly(L-lactide)-Poly(ethylene glycol) Multiblock Copolymers, Luo W, Li S, Bei J, Wang S, J. Appl. Polym. Sci., 2002, 84(9):1729-1736
• Dependence of Morphology on Composition of Poly(L-lactide)- Poly(ethylene glycol) Multiblock Copolymers, Luo W, Li S, Bei J, Wang S, Polym. Advan. Tech., 2002, 13: 233-238
• Synthesis and properties of poly(L-lactide)-poly (ethylene glycol) multiblock copolymers by coupling triblock copolymers, Chen W, Luo W, Bei J, Wang S, Polym. Advan. Tech., 2003, 14:245-253
• Poly(L-lactide)-Poly(ethylene glycol) Multiblock Copolymers: Synthesis and Properties, Luo W, Li S, Bei J, Wang S, Chin. Chem. Lett., 2002, 84(9):1729-1736

RESEARCH AREAS High throughput genomic data analysis Computational method development and implementation Systems biology on complex diseases and processes Biomedical informatics and computing Personal genome and personalized medicine