Bioinformatics Center and IT Group


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Bioinformatics:  Xixu Cai • Malcolm Cook • Alex Garrett • Madelaine Gogol • Gaye Hattem • Lavanya Kannan • David Kristensen • Hua Li • Arcady Mushegian • Aaron Noll • Ariel Paulson • Boris Rubinstein • Amy Ubben 

 List of former membersFull-time jobs and training opportunities


Software
Publications 

Book: 

Mushegian AR. Foundations of Comparative Genomics. Academic Press, 2007 - Amazon - companion website

Articles: 

2010

Mogilner A, Rubinstein B. Actin disassembly 'clock' and membrane tension determine cell shape and turning: a mathematical model. 2010 J Phys: Condens Matter 22 194118. Abstract.

Fournier ML, Paulson A, Pavelka N, Mosley AL, Gaudenz K, Bradford WD, Glynn E, Li H, Sardiu ME, Fleharty B, Seidel C, Florens L, Washburn MP. Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin. Mol Cell Proteomics. 2010 Feb;9(2):271-84. Epub 2009 Nov 10. Abstract.

Nugent RL, Johnsson A, Fleharty B, Gogol M, Xue-Franzén Y, Seidel C, Wright AP, Forsburg SL. Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation. BMC Genomics. 2010 Jan 22;11:59. Abstract.

Zhang SO, Mathur S, Hattem G, Tassy O, Pourquié O. Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos. BMC Genomics. 2010 Jan 7;11:13. Abstract.

Kristensen DM, Mushegian AR, Dolja VV, Koonin EV. New dimensions of the virus world discovered through metagenomics. Trends Microbiol. 2010 Jan;18(1):11-9. Epub 2009 Nov 26. Abstract.


2009

Weake VM, Swanson SK, Mushegian A, Florens L, Washburn MP, Abmayr SM, Workman JL. A novel histone fold domain-containing protein that replaces TAF6 in Drosophila SAGA is required for SAGA-dependent gene expression. Genes Dev. 2009 Dec 15;23(24):2818-23. Abstract.

Slaughter BD, Das A, Schwartz JW, Rubinstein B, Li R. Dual modes of cdc42 recycling fine-tune polarized morphogenesis. Dev Cell. 2009 Dec;17(6):823-35. Abstract.

Rubinstein B, Fournier MF, Jacobson K, Verkhovsky AB, Mogilner A. Actin-myosin viscoelastic flow in the keratocyte lamellipod. Biophys J. 2009 Oct 7;97(7):1853-63. Abstract.

Tsoy O, Ravcheev D, Mushegian A. Comparative genomics of ethanolamine utilization. J Bacteriol. 2009 Dec;191(23):7157-64. Epub 2009 Sep 25. Abstract.

Camahort R, Shivaraju M, Mattingly M, Li B, Nakanishi S, Zhu D, Shilatifard A, Workman J, Gerton J.Cse4 is part of an octameric nucleosome in budding yeast. Mol Cell. 2009 Sept 24; 35(6):794-805. Abstract.

Wang P, Lin C, Smith ER, Guo H, Sanderson BW, Wu M, Gogol M, Alexander T, Seidel C, Wiedemann LM, Ge K, Krumlauf R, Shilatifard A. Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. Mol Cell Biol. 2009 Nov;29(22):6074-85. Epub 2009 Aug 24. Abstract.

Li H, Kristensen D, Coleman M, Mushegian A. Detection of biochemical pathways by probabilistic matching of phyletic vectors. PLoS ONE. 2009;4(4):e5326. Epub 2009 Apr 24. Abstract.

Asai-Coakwell M, French CR, Ye M, Garcha K, Bigot K, Perera AG, Staehling-Hampton K, Mema SC, Chanda B, Mushegian A, Bamforth S, Doschak MR, Li G, Dobbs MB, Diampietro PF, Brooks BP, Vijayalakshmi P, Sauvé Y, Abitbol M, Sundaresan P, van Heyningen V, Pourquié O, Underhill TM, Waskiewicz AJ, Lehmann OJ. Incomplete penetrance and phenotypic variability characterize Gdf6-attributable oculo-skeletal phenotypes. Hum Mol Genet. 2009 Mar 15;18(6):1110-21. Epub 2009 Jan 6. Abstract.

Rubinstein B, Larripa K, Sommi P, Mogilner A. The elasticity of motor-microtubule bundles and shape of the mitotic spindle. Phys Biol. 2009 Feb 4:6(1):16005. Abstract.

Xie Y, Yin T, Wiegraebe W, He XC, Miller D, Stark D, Perko K, Alexander R, Schwartz J, Grindley JC, Park J, Haug JS, Wunderlich JP, Li H, Zhang S, Johnson T, Feldman RA, Li L. Detection of functional haematopoietic stem cell niche using real-time imaging. Nature. 2009 Jan 1;457(7225):97-101. Epub 2008 Dec 3. Abstract.

2008

Rubinstein B. Expression for restricted partition function through Bernoulli polynomials. Ramanujan J. (2008) 15:177-185. Abstract.

Li H, Guo F, Rubinstein B, Li R. Actin-driven chromosomal motility leads to symmetry breaking in mammalian meiotic oocytes. Nat Cell Biol. 2008 Nov;10(11):1301-8. Epub 2008 Oct 5. Abstract.

Box JA, Bunch JT, Zappulla DC, Glynn EF, Baumann P. A flexible template boundary element in the RNA subunit of fission yeast telomerase. J Biol Chem. 2008 Aug 29;283(35):24224-33. Epub 2008 Jun 23. Abstract.

Dequéant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquié O. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS ONE. 2008 Aug 6;3(8):e2856. Abstract.

Baumann D, Cook M, Ma L, Mushegian A, Sanders E, Schwartz J. A family of GFP-like proteins with different spectral properties in lancelet Branchiostoma floridae. Biol Direct. 2008 July 3;3:28. Abstract.

Mushegian AR. Gene content of LUCA, the last universal common ancestor. Frontiers in Bioscience 4657-4666, May 1, 2008. Abstract.

Minakhin L, Goel M, Berdygulova Z, Ramanculov E, Florens L, Glazko G, Karamychev VN, Slesarev AI, Kozyavkin SA, Khromov I, Ackermann HW, Washburn M, Mushegian A, Severinov K. Genome comparison and proteomic characterization of Thermus thermophilus bacteriophages P23-45 and P74-26: siphoviruses with triplex-forming sequences and the longest known tails. J Mol Biol 2008 Apr 25;378(2):468-80. Epub 2008 Feb 15. Abstract.

Li H, Zhu D, Cook M. A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data. BMC Genomics 2008 Apr 24;9:188. Abstract.

Savalia D, Westblade L, Goel M, Florens L, Kemp P, Akulenko N, Pavlova O, Padovan J, Chait B, Washburn M, Ackermann HW, Mushegian A, Gabisonia T, Molineux I, Severinov K. Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage. J Mol Biol 2008 Mar 28;377(3):774-89. Epub 2008 Jan 11. Abstract.

Jones N, Lynn M, Gaudenz K, Sakai D, Aoto K, Rey J, Glynn E, Ellington L, Du C, Dixon J, Dixon M, Trainor P. Prevention of the neurocristopathy Treacher Collins syndrome through inhibition of p53 function. Nat Med. 2008 Feb;14(2):125-33. Epub 2008 Feb 3. Abstract.

Roux M, Radeke M, Goel M, Mushegian A, Foltz K. 2DE identification of proteins exhibiting turnover and phosphorylation dynamics during sea urchin egg activation. Dev Biol. 2008 Jan 15;313(2):630-47. Epub 2007 Nov 13. Abstract.

2007

Glazko G, Makarenkov V, Liu J, Mushegian A. Evolutionary history of bacteriophages with double-stranded DNA genomes. Biol Direct. 2007 Dec 6;2:36. Abstract.

Li H, Gao G, Li J, Page G, Zhang K. Detecting epistatic interactions contributing to human gene expression using the CEPH family data. BMC Proceedings. 2007, 1(Suppl 1):S67. Article.

Zhu D, Hero AO 3rd. Bayesian hierarchical model for large-scale covariance matrix estimation. J Comput Biol. 2007 Dec;14(10):1311-26. Abstract.

Pan L, Chen S, Weng C, Call G, Zhu D, Tang H, Zhang N, Xie T. Stem cell aging is controlled both intrinsically and extrinsically in the Drosophila ovary. Cell Stem Cell. 1, 458-469, October 2007. Article.

Emmert-Streib F. The chronic fatigue syndrome: a comparative pathway analysis. J Comput Biol. 2007 Sep;14(7):961-72. Abstract.

Emmert-Streib F, Mushegian A. A topological algorithm for identification of structural domains of proteins. BMC Bioinformatics. 2007 Jul 3;8:237. Abstract.

Zhu D, Li Y, Li H. Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data. Bioinformatics. 2007 Sep 1; 23(17):2298-305. Epub 2007 Jun 22. Abstract.

Sandell LL, Sanderson BW, Moiseyev G, Johnson T, Mushegian A, Young K, Rey JP, Ma JX, Staehling-Hampton K, Trainor PA. RDH10 is essential for synthesis of embryonic retinoic acid and is required for limb, craniofacial, and organ development. Genes Dev. 2007 May 1;21(9):1113-24. Abstract.

Banks CAS, Kong SE, Spahr H, Florens L, Martin-Brown S, Washburn MP, Conaway JW, Mushegian A, Conaway RC. Identification and characterization of a Schizosaccharomyces pombe RNA polymerase II elongation factor with similarity to the metazoan transcription factor ELL. J Biol Chem. 2007 Feb 23;282(8):5761-9. Epub 2006 Dec 6. Abstract.

2006

Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Conaway JW, Florens L, and Washburn MP. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci USA. 2006 Dec12;103(50):18928-33. Abstract.

Dequéant M, Glynn E, Gaudenz K, Wahl M, Chen J, Mushegian A, Pourquie O. A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science. 2006 Dec 8:314(5805):1595-8. Abstract.

Naryshkina T, Liu J, Florens L, Swanson SK, Pavlov AR, Pavlova NV, Inman R, Minakhin L, Kozyavkin SA, Washburn M, Mushegian A, Severinov K. Thermus thermophilus Bacteriophage φ YS40 Genome and Proteomic Characterization of Virions. J Mol Biol. 2006 Dec 8;364(4):667-77. Abstract.

Bradham CA, Foltz KR, Beane WS, Arnone MI, Rizzo F, Coffman JA, Mushegian A, Goel M, Morales J, Geneviere AM, Lapraz F, Robertson AJ, Kelkar H, Loza-Coll M, Townley IK, Raisch M, Roux MM, Lepage T, Gache C, McClay DR, Manning G. The sea urchin kinome: a first look. Dev Biol. 2006 Dec 1;300(1):180-93. Abstract.

Goel M, Mushegian A. Intermediary metabolism in sea urchin: the first inferences from the genome sequence. Dev Biol. 2006 Dec 1;300(1):282-92. Abstract.

Florens L, Carozza MJ, Swanson SK, Fournier M, Coleman MK, Workman JL, Washburn MP. Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods. 2006 Dec;40(4):303-11. Abstract.

Sea Urchin Genome Sequencing Consortium. The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science. 2006 Nov 10:314(5801):941-52. Abstract.

Emmert-Streib F. Algorithmic computation of knot polynomials of secondary structure elements of proteins. J Comput Biol. 2006 Oct:13(8):1503-12. Abstract.

Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res. 2006 Sep;5(9):2339-47. Abstract.

Jaspersen S, Martin A, Glazko G, Giddings TH Jr, Morgan G, Mushegian A, Winey M. The Sad1-UNC-84 homology domain in Mps3 interacts with Mps2 to connect the spindle pole body with the nuclear envelope. J Cell Biology 2006 Aug 28;174(5):665-75. Abstract.

Emmert-Streib F, Dehmer, M. Topological mappings between graphs, trees and generalized trees. Appl Math Comput 2006, doi:10.1016/j.amc.2006.07.162

Rai R, Mushegian A, Makarova K, Kashina A. Molecular dissection of arginyltransferases guided by similarity to bacterial peptidoglycan synthases. EMBO Reports. 2006 July 7. Abstract.

Glazko G, Coleman M, Mushegian A. Similarity searches in genome-wide numerical data sets. Biology Direct 2006, 1:13. AbstractSupplementary Information.

Liu J, Glazko G, Mushegian A. Protein repertoire of double-stranded DNA bacteriophages. Virus Res. 2006 Feb 18. Abstract.

Glynn EF, Chen J, Mushegian AR. Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics. 2006;22(3):310-6. Abstract.  Supplementary Information

Glazko GV, Babenko VN, Koonin EV, Rogozin IB. Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection. Biology Direct. 1:4. Abstract.

2005

Li B, Pattenden S, Lee D, Gutierrez J, Chen J, Seidel C, Gerton J, Workman J. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. PNAS. 2005;102:18385-18390. Abstract.

Alder MN, Rogozin IB, Iyer LM, Glazko GV, Cooper MD, Pancer Z.  Diversity and function of adaptive immune receptors in a jawless vertebrate.  Science. 2005;310(5756): 1892-3.  Abstract.

Jin J, Cai Y, Yao T, Gottschalk A, Florens L, Swanson SK, Gutiérrez JL, Coleman M, Workman J, Mushegian A, Washburn MP, Conaway RC, and Conaway JW.  A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. J Biol Chem. 2005;280:41207-12Abstract.

Minakhin L, Semenova E, Liu J, Vasilov A, Severinova E, Gabisonia T, Inman R, Mushegian A, Severinov K. Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah. J Mol Biol. 2005;354:1-15. Abstract.

Kozbial PZ, Mushegian AR. Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol . 2005;5:19Abstract.

Mushegian AR. Protein content of minimal and ancestral ribosome. RNA. 2005;11:1400-6.  AbstractSupplementary Information

Glazko G, Gordon A, Mushegian A. The choice of optimal distance measure in genome-wide data sets. Bioinformatics. 2005;21 Suppl 3:iii3-iii11.  AbstractSupplementary Information

Zybailov B, Coleman M, Florens L, Washburn M.  Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem. 2005;77:6218-6224.  Abstract.

Koonin EV, Rogozin IB, Glazko GV. p53 Gain-of-Function -- Tumor biology and bioinformatics come together. Cell Cycle. 2005;4:e6-e8.  Abstract

Glazko GV, Koonin EV, Rogozin IB. Molecular dating: ape bones agree with chicken entrails. Trends Genet. 2005;21:89-92. Abstract.

2004
Gensheimer M, Mushegian A. Chalcone isomerase family and fold: no longer unique to plants. Protein Sci. 2004;13:540-544. Abstract  PDF

Glazko GV, Koonin EV, Rogozin IB. Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection. Biochim Biophys Acta. 2004;1679:95-106. Abstract 

Glazko GV, Mushegian AR. Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biol. 2004;5:R32. Abstract  PDF

Glazko GV, Gensheimer M, Mushegian A.  Phylogenetic tree inference from local gene content.  Unpublished

Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL. Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. PLoS Biol. 2004;2:E259. Abstract  PDF [9.2 MB]   Supplementary Information

Liu J, Mushegian A. Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages. J Bacteriol. 2004;186:4369-4375. Abstract  PDF [3.9 MB]   Supplementary Information

Melko OM, Mushegian AR. Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes. Bioinformatics. 2004;20:67-74. Abstract  PDF

Mushegian A. Evolution and function of processosome, the complex that assembles ribosomes in eukaryotes: clues from comparative sequence analysis. Practical bioinformatics. Berlin ; New York: Springer; 2004;15:xvii, 265 p.  Publisher

Petyuk V, McDermott J, Cook M, Sauer B. Functional mapping of Cre recombinase by pentapeptide insertional mutagenesis. J Biol Chem. 2004;279:37040-37048. Abstract   PDF [1.1 MB]

Yan Q, Kamura T, Cai Y, Jin J, Ivan M, Mushegian A, Conaway RC, Conaway JW. Identification of Elongin C and Skp1 sequences that determine Cullin selection.  J Biol Chem. 2004 Oct; 279(41): 43019-26. Abstract   PDF

2003
Liu J, Mushegian A. Three monophyletic superfamilies account for the majority of the known glycosyltransferases. Protein Sci. 2003;12:1418-1431.   Abstract   PDF [4.3 MB]   Supplementary Information

Rennert J, Coffman JA, Mushegian AR, Robertson AJ. The evolution of runx genes I. A comparative study of sequences from phylogenetically diverse model organisms. BMC Evol Biol. 2003;3:4.  Abstract   PDF

Yuzenkova J, Nechaev S, Berlin J, Rogulja D, Kuznedelov K, Inman R, Mushegian A, Severinov K. Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage. J Mol Biol. 2003;330:735-748.   Abstract   PDF [1.9 MB]

2002
Golden, T. A., Schauer, S. E., Lang, J. D., Pien, S., Mushegian, A. R., Grossniklaus, U., Meinke, D. W., Ray, A. (2002). Short Integuments1/Suspensor1/Carpel Factory, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis. Plant Physiol, 130(2), 808-822.  Abstract  PDF

Mushegian, A. (2002). Refining structural and functional predictions for secretasome components by comparative sequence analysis. Proteins, 47(1), 69-74.  Abstract

2001
Iyer, L. M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A. R., Zhulin, I. B., Koonin, E. V. (2001). Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biol, 2(12), RESEARCH0051.  Abstract   PDF

Mushegian, A., & Medzhitov, R. (2001). Evolutionary perspective on innate immune recognition. J Cell Biol, 155(5), 705-710.  Abstract  PDF  Supplementary Material

 


Alumni (position when in the lab/current location): Joe Adams (IT dept) • Rich Brown (IT dept) • Jay Casillas (IT dept) • Jie Chen (sabbatical visitor / Mathematics Department Chair at UMKC) • Mike Coleman (scientific programmer/programmer at TradeBot Systems) • Steve De Gennaro (IT dept) • Deendayal Dinakarpandian (summer visitor / faculty at UMKC) •  David Duerr (IT dept) • Ognen Duzlevski (Unix administrator / financial industry in Florida) • Frank Emmert-Streib (postdoc / lecturer at Queen's University in Belfast, Northern Ireland)  • Mike Gensheimer (summer intern / medical intern at Johns Hopkins University) • Galina Glazko (postdoc / Assistant Professor at the University of Rochester) • Earl Glynn (scientific programmer / investigative reporter for independent press) • Manisha Goel (postdoc / Assistant Professor, University of Delhi) • Dirk Hacker (IT dept) • Chad Harvey (IT dept) • Steve Jones (IT dept) • Piotr Kozbial (postdoc / Biostatistician, University of California - San Diego) • Jing Liu (Ph.D. student / law associate, Knobbe Martens Olson and Bear LLP) • Chris Locke (IT dept) • Anna Lyubetskaya (research scholar / graduate student, Boston University)• Mark Matson (IT dept) • Jennifer McGee (IT dept) • Mike Melko (postdoc / faculty at Northern State University)• Mike Newhouse (IT dept)  • Shaun Price (IT dept) • Bob Reece (IT dept) • Shaili Sharma (summer intern / graduate student, Purdue University)• Dan Stranathan (IT dept) • Dan Thomasset (Unix administrator / Google) • Olga Tsoy (research scholar / graduate student, Russian Academy of Sciences) • Brandon Young (IT dept) • Marina Yurjeva (research scholar / Graduate Student, Open University at Stowers Institute) • Dongxiao Zhu (biostatistician / assistant professor at the University of New Orleans)

      


If you are interested in full-time professional positions at Bioinformatics Center or the IT Department of Stowers Institute, check the Institute jobs page.

• If you are interested in a postdoctoral position or short-term training opportunities, inquire with Arcady Mushegian, Director of Bioinformatics Center.

• If you are interested in graduate training, note that we are affiliated with two graduate programs, one at Kansas University Medical Center and the other at the Open University . Please contact these programs and simultaneously Dr. Mushegian.