Bioinformatics and Computational Biology
  

 

Dr. Lakshmi Kumar Matukumalli Lakshmi Kumar Matukumalli
Research Assistant Professor
Bovine Functional Genomics

Bioinformatics and Computational Biology
Occoquan Building
10900 University Blvd,
Manassas VA 20110
Telephone: 301-504-5979
Fax: 301-504-8414
Email:

Education

Ph.D Bioinformatics (2004)
George Mason University, VA, US

M.Tech Biochemical Engg & Biotechnology (1993)
Indian Institute of Technology, Delhi, INDIA

M.S Biotechnology (1991)
Banaras Hindu University, Varanasi, INDIA

B.S Mathematics Physics and Chemistry (1989)
Osmania University, Hyderabad, INDIA

Research Interests

  • Annotation of the Bovine (Cow) genome
  • Algorithms for SNP Discovery from EST and genome sequence data:
  • Bovine Gene Atlas
  • MicroRNA in Cattle
  • Prediction of genetic merit from Cattle genotype data
  • Copy Number Variation in Cattle
Details for Students Projects

Software Tools

EST-PAGE for EST data analysis

SNP-PHAGE for high throughput SNP Discovery

SNP-PHAGE-ML Application of Machine Learning in SNP Discovery

Publications
  1. Wiggans GR, Sonstegard TS, VanRaden PM, Matukumalli LK, Schnabel RD, Taylor JF, Schenkel FS, Van Tassell CP. Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. J Dairy Sci. 2009 Jul;92(7):3431-6.
  2. Villa-Angulo R, Matukumalli LK, Gill CA, Choi J, Van Tassell CP, Grefenstette JJ. High-resolution haplotype block structure in the cattle genome. BMC Genet.2009 Apr 24;10:19.
  3. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP,O'Connell J, Moore SS, Smith TP, Sonstegard TS, Van Tassell CP. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One.2009;4(4):e5350.
  4. Bovine HapMap Consortium, Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24;324(5926):528-32.
  5. Bovine Genome Sequencing and Analysis Consortium,. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-8.
  6. Liu GE, Weirauch MT, Van Tassell CP, Li RW, Sonstegard TS, Matukumalli LK, Connor EE, Hanson RW, Yang J. Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. Genomics Proteomics Bioinformatics. 2008 Dec;6(3-4):129-43.
  7. Alexander LJ, Kuehn LA, Smith TP, Matukumalli LK, Mote B, Koltes JE, Reecy J, Geary TW, Rule DC, Macneil MD. A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F2 population. J Anim Sci. 2009 May;87(5):1576-81.
  8. McDaneld TG, Smith TP, Doumit ME, Miles JR, Coutinho LL, Sonstegard TS,Matukumalli LK, Nonneman DJ, Wiedmann RT. MicroRNA transcriptome profiles during swine skeletal muscle development. BMC Genomics. 2009 Feb 10;10:77.
  9. Liu GE, Van Tassel CP, Sonstegard TS, Li RW, Alexander LJ, Keele JW, Matukumalli LK, Smith TP, Gasbarre LC. Detection of germline and somatic copy number variations in cattle. Dev Biol (Basel). 2008;132:231-7.
  10. Liu GE, Li RW, Sonstegard TS, Matukumalli LK, Silva MV, Van Tassell CP. Characterization of a novel microdeletion polymorphism on BTA5 in cattle. Anim Genet. 2008 Dec;39(6):655-8.
  11. McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Dias Neto E, Gill CA, Gao C, Mannen H, Wang Z, Van Tassell CP, Williams JL, Taylor JF, Moore SS. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genet. 2008 May 20;9:37.
  12. Curtis P Van Tassell, Timothy P L Smith, Lakshmi K Matukumalli, Jeremy F Taylor, Robert D Schnabel, Cinthia Taylor Lawley, Christian D Haudenschild, Stephen S Moore, Wesley C Warren and Tad S Sonstegard SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries Nature Methods (Adv pub) 2008
  13. David L. Hyten · Qijian Song · Ik-Young Choi · Mun-Sup Yoon · James E. Specht · Lakshmi K. Matukumalli · Randall L. Nelson · Randy C. Shoemaker ·
    Nevin D. Young · Perry B. Cregan High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet (Adv. Pub) 2008
  14. Choi,I.Y., Hyten,D.L., Matukumalli,L.K., Song,Q., Chaky,J.M., Quigley,C.V., Chase,K., Lark,K.G., Reiter,R.S., Yoon,M.S., Hwang,E.Y., Yi,S.I., Young,N.D., Shoemaker,R.C., van Tassell,C.P., Specht,J.E., & Cregan,P.B. A Soybean Transcript Map: Gene Distribution, Haplotype and SNP Analysis. Genetics (2007).
  15. McKay,S.D., Schnabel,R.D., Murdoch,B.M., Aerts,J., Gill,C.A., Gao,C., Li,C., Matukumalli,L.K., Stothard,P., Wang,Z., van Tassell,C.P., Williams,J.L., Taylor,J.F., & Moore,S.S. Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping. Anim Genet38, 120-125 (2007).
  16. Coutinho,L.L., Matukumalli,L.K., Sonstegard,T.S., van Tassell,C.P., Gasbarre,L.C., Capuco,A.V., & Smith,T.P. Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues. Physiol Genomics29, 35-43 (2007).
  17. Sonstegard,T.S, G.Liu, Matukumalli,L.K., and Van Tassell,C.P. (2007) SNPs to Chips: Changing the paradigm of mapping and selection in cattle. Journal of Animal Genetics, 35, 205-217.
  18. Snelling, W. M.; Chiu, R.; Schein, J. E.; Hobbs, M.; Abbey, C. A.; Adelson, D. L.; Aerts, J.; Bennett, G. L.; Bosdet, I. E.; Boussaha, M.; Brauning, R.; Caetano, A. R.; Costa, M. M.; Crawford, A. M.; Dalrymple, B. P.; Eggen, A.; Everts-van der Wind, A.; Floriot, S.; Gautier, M.; Gill, C. A.; Green, R. D.; Holt, R.; Jann, O.; Jones, S. J.; Kappes, S. M.; Keele, J. W.; de Jong, P. J.; Larkin, D. M.; Lewin, H. A.; McEwan, J. C.; McKay, S.; Marra, M. A.; Mathewson, C. A.; Matukumalli, L. K.; Moore, S. S.; Murdoch, B.; Nicholas, F. W.; Osoegawa, K.; Roy, A.; Salih, H.; Schibler, L.; Schnabel, R. D.; Silveri, L.; Skow, L. C.; Smith, T. P.; Sonstegard, T. S.; Taylor, J. F.; Tellam, R.; Van Tassell, C. P.; Williams, J. L.; Womack, J. E.; Wye, N. H.; Yang, G.; Zhao, S. A physical map of the bovine genome Genome Biol. 2007, 8, R165
  19. Matukumalli,L.K., Grefenstette,J.J., Hyten,D.L., Choi,I.Y., Cregan,P.B., & van Tassell,C.P. SNP-PHAGE--High throughput SNP discovery pipeline. BMC Bioinformatics.7, 468 (2006).
  20. Liu,G.E., Matukumalli,L.K., Sonstegard,T.S., Shade,L.L., & van Tassell,C.P. Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences. BMC Genomics7, 140 (2006).
  21. Matukumalli,L.K., Grefenstette,J.J., Hyten,D.L., Choi,I.Y., Cregan,P.B., & van Tassell,C.P. Application of machine learning in SNP discovery. BMC Bioinformatics.7, 4 (2006).
  22. Baumann,R.G., Baldwin,R.L., van Tassell,C.P., Sonstegard,T.S., & Matukumalli,L.K. Characterization of a normalized cDNA library from bovine intestinal muscle and epithelial tissues. Anim Biotechnol.16, 17-29 (2005).
  23. Min,W., Lillehoj,H.S., Ashwell,C.M., van Tassell,C.P., Dalloul,R.A., Matukumalli,L.K., Han,J.Y., & Lillehoj,E.P. Expressed sequence tag analysis of Eimeria-stimulated intestinal intraepithelial lymphocytes in chickens. Mol. Biotechnol.30, 143-150 (2005).
  24. da Mota,A.F., Sonstegard,T.S., van Tassell,C.P., Shade,L.L., Matukumalli,L.K., Wood,D.L., Capuco,A.V., Brito,M.A., Connor,E.E., Martinez,M.L., & Coutinho,L.L. Characterization of open reading frame-expressed sequence tags generated from Bos indicus and B. taurus mammary gland cDNA libraries. Anim Genet35, 213-219 (2004).
  25. Matukumalli,L.K., Grefenstette,J.J., Sonstegard,T.S., & van Tassell,C.P. EST-PAGE--managing and analyzing EST data. Bioinformatics.20, 286-288 (2004).
  26. Zhu,Y.L., Song,Q.J., Hyten,D.L., van Tassell,C.P., Matukumalli,L.K., Grimm,D.R., Hyatt,S.M., Fickus,E.W., Young,N.D., & Cregan,P.B. Single-nucleotide polymorphisms in soybean. Genetics163, 1123-1134 (2003)
  
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Bioinformatics and Computational Biology