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S&P DJI Research papers

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Computational Biology

Publications listed in reverse chronological order. For citations, see Google Scholar or PubMed.

Journal articles

  1. Elden Rowland, Jitae Kim, Giulia Friso, Anton Poliakov, Lalit Ponnala, Qi Sun,Klaas J. van Wijk. The CLP and PREP protease systems coordinate maturation and degradation of the chloroplast proteome in Arabidopsis thaliana. New Phytologist, 2022. doi: 10.1111/nph.18426 PMID: 35946374.
  2. Jui-Yun Rei Liao, Giulia Friso, Evan S. Forsythe, Elena J.S. Michel, Alissa M. Williams, Sasha S. Boguraev, Lalit Ponnala, Daniel B. Sloan, Klaas J. van Wijk. Proteomics, phylogenetics, and co-expression analyses indicate novel interactions in the plastid CLP chaperone-protease system. Journal of Biological Chemistry, 2022, 101609, ISSN 0021-9258, https://doi.org/10.1016/j.jbc.2022.101609.
  3. Elena J S Michel, Lalit Ponnala, Klaas J van Wijk. Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks and plastoglobular functions. Journal of Experimental Botany, 2021; https://doi.org/10.1093/jxb/erab175 [data]
  4. Orsi RH, Chaturongakul S, Oliver HF, Ponnala L, Gaballa A, Wiedmann M. Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition. Pathogens. 2021; 10(4):411. https://doi.org/10.3390/pathogens10040411
  5. Nazmul H. Bhuiyan, Elden Rowland, Giulia Friso, Lalit Ponnala, Elena JS Michel, Klaas J. van Wijk. Auto-catalytic processing and substrate specificity of Arabidopsis chloroplast glutamyl peptidase. Plant Physiology 2020 Jul. doi: 10.1104/pp.20.00752
  6. Majeran W, Le Caer J-P, Ponnala L, Meinnel T, Giglione C. Targeted profiling of A. thaliana sub-proteomes illuminates new co- and post-translationally N-terminal Myristoylated proteins. The Plant Cell. 2018 Mar;30(3):543-562. doi: 10.1105/tpc.17.00523.
  7. Mirjam Blattner, Deli Liu, Brian D. Robinson, Dennis Huang, Anton Poliakov, Dong Gao, Srilakshmi Nataraj, Lesa D. Deonarine, Michael A. Augello, Verena Sailer, Lalit Ponnala, Michael Ittmann, Arul M. Chinnaiyan, Andrea Sboner, Yu Chen, Mark A. Rubin, Christopher E. Barbieri. SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling. Cancer Cell. 2017 Mar 13; 31(3):436-451. doi: 10.1016/j.ccell.2017.02.004.
  8. Kenji Nishimura, Janina Apitz, Giulia Friso, Jitae Kim, Lalit Ponnala, Bernhard Grimm and Klaas J. van Wijk. Discovery of a Unique Clp Component, ClpF, in Chloroplasts: A Proposed Binary ClpF-ClpS1 Adaptor Complex Functions in Substrate Recognition and Delivery. The Plant Cell. 2015 Oct;27(10):2677-91. doi: 10.1105/tpc.15.00574.
  9. Jitae Kim, Matthew S. Kimber, Kenji Nishimura, Giulia Friso, Lance Schultz, Lalit Ponnala and Klaas J. van Wijk. Structures, Functions, and Interactions of ClpT1 and ClpT2 in the Clp Protease System of Arabidopsis Chloroplasts. The Plant Cell. 2015 May;27(5):1477-96. doi: 10.1105/tpc.15.00106.
  10. Zuluaga, A.P., Vega-Arreguin, J.C., Fei, Z., Ponnala, L., Lee, S.J., Matas, A.J., Patev, S., Fry, W.E. and Rose, J.K.C. Transcriptional dynamics of Phytophthora infestans during sequential stages of hemibiotrophic infection of tomato. Molecular Plant Pathology 2016 Jan;17(1):29-41. doi: 10.1111/mpp.12263.
  11. Nazmul H. Bhuiyan, Giulia Friso, Anton Poliakov, Lalit Ponnala and Klaas J. van Wijk. MET1 Is a Thylakoid-Associated TPR Protein Involved in Photosystem II Supercomplex Formation and Repair in Arabidopsis. The Plant Cell. 2015 Jan;27(1):262-85. doi: 10.1105/tpc.114.132787.
  12. Lalit Ponnala, Yupeng Wang, Qi Sun, Klaas J. van Wijk. Correlation of mRNA and protein abundance in the developing maize leaf. The Plant Journal 2014 May; 78(3): 424-440. doi: 10.1111/tpj.12482
  13. Nishimura K, Asakura Y, Friso G, Kim J, Oh SH, Rutschow H, Ponnala L, van Wijk KJ. ClpS1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis thaliana. The Plant Cell 2013 Jun; 25(6): 2276-301. doi: 10.1105/tpc.113.112557 [www]
  14. Peter K. Lundquist, Anton Poliakov, Lisa Giacomelli, Giulia Friso, Mason Appel, Ryan P. McQuinn, Stuart B. Krasnoff, Elden Rowland, Lalit Ponnala, Qi Sun and Klaas J. van Wijk. Loss of Plastoglobule Kinases ABC1K1 and ABC1K3 Causes Conditional Degreening, Modified Prenyl-Lipids, and Recruitment of the Jasmonic Acid Pathway. The Plant Cell 2013 May; 25(5): 1818-39. doi: 10.1105/tpc.113.111120 [www]
  15. Jitae Kim, Paul Dominic Olinares, Soo-hyun Oh, Stefania Ghisaura, Anton Poliakov, Lalit Ponnala and Klaas J. van Wijk. Modified Clp protease complex in the ClpP3 null mutant and consequences for chloroplast development and function in Arabidopsis thaliana. Plant Physiology 2013 May; 162(1): 157-79. doi: 10.1104/pp.113.215699 [www]
  16. Lin C, den Bakker HC, Suzuki H, Lefebure T, Ponnala L, Sun Q, Stanhope MJ, Wiedmann M, Duhamel GE. Complete genome sequence of the porcine strain Brachyspira pilosicoli P43/6/78T. Genome Announcements 2013 Jan-Feb 1(1): e00215-12. doi: 10.1128/genomeA.00215-12 [www]
  17. Elizabeth M Takacs, Jie Li, Chuanlong Du, Lalit Ponnala, Diane Janick-Buckner, Jianming Yu, Gary J Muehlbauer, Patrick S Schnable, Marja C P Timmermans, Qi Sun, Dan Nettleton, Michael J Scanlon. Ontogeny of the Maize Shoot Apical Meristem. The Plant Cell 2012 Aug; 24(8): 3219-34. doi: 10.1105/tpc.112.099614 [www]
  18. Judson A. Ward, Lalit Ponnala and Courtney A. Weber. Strategies for transcriptome analysis in nonmodel plants. American Journal of Botany 2012 Feb; 99(2): 267-76. doi: 10.3732/ajb.1100334 [www]
  19. Wojciech Majeran, Giulia Friso, Yukari Asakura, Xian Qu, Mingshu Huang, Lalit Ponnala, Kenneth P. Watkins, Alice Barkan and Klaas J. van Wijk. Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves; a new conceptual framework for nucleoid functions. Plant Physiology 2012 Jan; 158(1): 156-89. doi: 10.1104/pp.111.188474 [www]
  20. A.J. Matas, T.H. Yeats, G.J. Buda, Y. Zheng, S. Chatterjee, T. Tohge, L. Ponnala, A.R. Fernie, R.E. Stark, J. Fei, J.J. Giovannoni, and J.K.C. Rose. Tissue and cell type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. The Plant Cell 2011 Nov; 23(11): 3893-910 [www]
  21. Kukekova AV, Johnson JL, Teiling C, Li L, Oskina IN, Kharlamova AV, Gulevich RG, Padte R, Dubreuil MM, Vladimirova AV, Shepeleva DV, Shikhevich SG, Sun Q, Ponnala L, Temnykh SV, Trut LN, Acland GM. Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes). BMC Genomics 2011 Oct; 12:482. [www]
  22. Poliakov A, Russell CW, Ponnala L, Hoops HJ, Sun Q, Douglas AE, van Wijk KJ. Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis. Molecular and Cellular Proteomics 2011 Jun; 10(6): M110.007039 [www]
  23. Scaria J, Ponnala L, Janvilisri T, Yan W, Mueller LA, Chang YF. Analysis of Ultra Low Genome Conservation in Clostridium difficile. PLoS ONE 2010 Dec; 5(12): e15147. doi: 10.1371/journal.pone.0015147 [www]
  24. Wojciech Majeran, Giulia Friso, Lalit Ponnala, Brian Connolly, Mingshu Huang, Edwin Reidel, Cankui Zhang, Yukari Asakura, Nazmul H. Bhuiyan, Qi Sun, Robert Turgeon and Klaas J. van Wijk. Structural and Metabolic Transitions of C4 Leaf Development and Differentiation Defined by Microscopy and Quantitative Proteomics in Maize. The Plant Cell 2010 Nov; 22(11): 3509-3542. doi: 10.1104/tpc.110.079764 [www]
  25. Pinghua Li, Lalit Ponnala, Neeru Gandotra, Lin Wang, Yaqing Si, S Lori Tausta, Tesfamichael H Kebrom, Nicholas Provart, Rohan Patel, Christopher R Myers, Edwin J Reidel, Robert Turgeon, Peng Liu, Qi Sun, Timothy Nelson and Thomas P Brutnell. The developmental dynamics of the maize leaf transcriptome. Nature Genetics 2010 Dec; 42(12): 1060-1067. doi: 10.1038/ng.703 [www] [press release]
  26. Lalit Ponnala. A plausible role for the presence of internal Shine-Dalgarno sites. Bioinformatics and Biology Insights 2010 Jun; 4: 55-60 [www]
  27. P. B. Olinares, L. Ponnala and K. J. van Wijk. Megadalton complexes in the chloroplast stroma of arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry and hierarchical clustering. Molecular and Cellular Proteomics 2010 Jul; 9(7): 1594-1615. doi: 10.1074/mcp.M000038-MCP201 [www]
  28. Lalit Ponnala. Detecting slow-translating regions in E.coli. International Journal of Bioinformatics Research and Applications 2010; 6(5): 522-530 [pdf]
  29. Ramsey J.S., Rider D.S., Walsh T.K., De Vos M., Gordon K., Ponnala L., Macmil S., Roe B.A. and Jander G. Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae. Insect Molecular Biology 2010 Mar; 19(s2): 155-164. doi: 10.1111/j.1365-2583.2009.00973.x [pdf]
  30. Oliver H.F., R.H. Orsi, L. Ponnala, U. Keich, W. Wang, Q. Sun, S.W. Cartinhour, M. J. Filiatrault, M. Wiedmann, and K.J. Boor. Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 2009 Dec; 10:641. [www]
  31. Schnable PS, D Ware, RS Fulton, JC Stein, F Wei, S Pasternak, C Liang, J Zhang, L Fulton, TA Graves, P Minx, AD Reily, L Courtney, SS Kruchowski, C Tomlinson, C Strong, K Delehaunty, C Fronick, W Courtney, SM Rock, E Belter, F Du, K Kim, RM Abbott, M Cotton, A Levy, P Marchetto, K Ochoa, SM Jackson, B Gillam, W Chen, L Yan, J Higginbotham, M Cardenas, J Waligorski, E Applebaum, L Phelps, J Falcone, K Kanchi, T Thane, A Scimone, N Thane, J Henke, T Wang, J Ruppert, N Shah, K Rotter, J Hodges, E Ingenthron, M Cordes, S Kohlberg, J Sgro, B Delgado, K Mead, A Chinwalla, S Leonard, K Crouse, K Collura, D Kudrna, J Currie, R He, A Angelova, S Rajasekar, T Mueller, R Lomeli, G Scara, A Ko, K Delaney, M Wissotski, G Lopez, D Campos, M Braidotti, E Ashley, W Golser, H Kim, S Lee, J Lin, Z Dujmic, W Kim, J Talag, A Zuccolo, C Fan, A Sebastian, M Kramer, L Spiegel, L Nascimento, T Zutavern, B Miller, C Ambroise, S Muller, W Spooner, A Narechania, L Ren, S Wei, S Kumari, B Faga, M Levy, L McMahan, PV Buren, MW Vaughn, K Ying, CT Yeh, SJ Emrich, Y Jia, A Kalyanaraman, AP Hsia, WB Barbazuk, RS Baucom, TP Brutnell, NC Carpita, C Chaparro, J Chia, J Deragon, JC Estill, Y Fu, JA Jeddeloh, Y Han, H Lee, P Li, DR Lisch, S Liu, Z Liu, DH Nagel, MC McCann, P SanMiguel, AM Myers, DS Nettleton, J Nguyen, BW Penning, L Ponnala, KL Schneider, DC Schwartz, A Sharma, C Soderlund, NM Springer, Q Sun, H Wang, M Waterman, R Westerman, TK Wolfgruber, L Yang, Y Yu, L Zhang, S Zhou, Q Zhu, JL Bennetzen, RK Dawe, J Jiang, N Jiang, GG Presting, SR Wessler, S Aluru, RA Martienssen, SW Clifton, WR McCombie, RA Wing, RK Wilson. The B73 maize genome: complexity, diversity and dynamics. Science 2009 Nov; 326(5956): 1112-1115. doi: 10.1126/science.1178534 [www] [press release]
  32. Ponnala L. On finding poorly translated codons based on their usage frequency. Bioinformation 2009 Sep; 4(2): 63-65 [pdf]
  33. J. Scaria, R. U. Palaniappan, D. Chiu, J. Phan, L. Ponnala, P. McDonough, Y. T. Grohn, S. Porwollik, M. McClelland, C.-S. Chiou, C. Chu, Y.-F. Chang. Microarray for molecular typing of Salmonella enterica serovars. Molecular and Cellular Probes 2008 Aug; 22(4): 238-43. doi: 10.1016/j.mcp.2008.04.002 [www]
  34. Ponnala L, Stomp AM, Bitzer DL, Vouk MA. Analysis of free energy signals arising from nucleotide hybridization between rRNA and mRNA sequences during translation in eubacteria. EURASIP Journal on Bioinformatics and Systems Biology 2006:23613. doi: 10.1155/BSB/2006/23613 [www]

Conference papers

  1. Ponnala L, Bitzer DL, Stomp A, Vouk MA. A computational model for reading frame maintenance. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:4540-3. ISBN: 1-4244-0032-5 [pdf]
  2. Ponnala L, Stomp A, Bitzer DL, Vouk M. Statistical significance and biological relevance of a sinusoidal pattern detected in translational free energy signals. Proc IEEE International Workshop on Genomic Signal Processing and Statistics. 2006; 55-56. ISBN: 1-4244-0384-7 [pdf]
  3. Ponnala L, Barnes TM, Bitzer DL, Vouk M, Stomp A. A signal processing-based model for analyzing programmed frameshifts. Proc IEEE International Workshop on Genomic Signal Processing and Statistics. 2005; 2:2-3 [pdf]
  4. Ponnala L, Barnes TM, Bitzer DL, Vouk M. Ribosome tail ends as signal detectors for protein production in prokaryotes. Proc NC Symp Biotech Bioinf. 2004; 15-23. ISBN: 0-7803-8826-7 [pdf]
  5. Ponnala L, Barnes TM, Bitzer DL, Vouk M. The search for the optimal ribosome 3' tail end in E. coli. Conf Proc IEEE Eng Med Biol Soc. 2004; 4:2824-7. ISBN: 0-7803-8439-3 [pdf]
  6. Ponnala L, Bitzer DL, Vouk M. On finding convolutional code generators for translation initiation of Escherichia Coli K-12. Conf Proc IEEE Eng Med Biol Soc. 2003; 4:3854-7. ISBN: 0-7803-7789-3 [pdf]

Preprints

  1. L. Ponnala. On the clustering of rare codons and its effect on translation. arXiv:0910.0429v1 [q-bio.GN]
  2. L. Ponnala, D. L. Bitzer, A. Stomp, M. A. Vouk. A mechanistic model for +1 frameshifts in eubacteria. arXiv:0712.2068v1 [q-bio.GN]

Theses

  1. Ponnala L. Analysis of Genetic Translation Using Signal Processing. PhD Dissertation, North Carolina State University, Feb. 2007 ISBN: 978-0-549-54768-6 [pdf]
  2. Ponnala L. Algorithmic Approach for finding Convolutional Code generators for the Translation Initiation of Escherichia coli K-12. M.S. Thesis, North Carolina State University, Nov. 2003 [pdf]

Presentations

  1. Mingshu Huang, Giulia Friso, Yukari Asakura, Robert Turgeon, Lalit Ponnala, Qi Sun, Klaas van Wijk. A High Resolution Structural and Proteomic Atlas of the Developing Rice Leaf. Plant & Animal Genomes XVII Conference, San Diego, CA, Jan 12-16, 2013
  2. Giulia Friso, Mingshu Huang, Yukari Asakura, Robert Turgeon, Lalit Ponnala, Qi Sun, Klaas J. Van Wijk. A high resolution structural and proteomics atlas of the developing rice leaf. 60th ASMS Conference on mass spectrometry and allied topics , May 20 - 24, 2012 , Vancouver, Canada
  3. Anton Poliakov, Yukari Asakura, Lalit Ponnala, Klaas J. Van Wijk. The nuclear proteome of sink and source regions of developing maize leaves: a quantitative analysis based on spectral counting. ASMS Conference on Mass Spectrometry and Allied Topics, June 5 - 9, 2011, Colorado Convention Center, Denver, CO
  4. Klaas J. Van Wijk, Paul Dominic B. Olinares, Jitae Kim, Anton Poliakov, Lalit Ponnala, Giulia Friso. Structural organization and function of the oligomeric Clp protease in plants determined by QConCAT and spectral counting-based quantitative proteomics. ASMS Conference on Mass Spectrometry and Allied Topics, June 5 - 9, 2011, Colorado Convention Center, Denver, CO
  5. Pinghua Li, Lalit Ponnala, Neeru Gandotra, Lin Wang, Yaqing Si, Lori Tausta, Tesfamichael Kebrom, Nicholas Provart, Rohan Patel, Christopher Myers, Edwin Reidel, Robert Turgeon, Peng Liu, Qi Sun, Timothy Nelson, Thomas P Brutnell. The developmental dynamics of the maize leaf transcriptome as revealed through ultra high throughput sequencing. 53rd Annual Maize Genetics Conference, March 17-20, 2011, St. Charles, Illinois USA
  6. Mingshu Huang, Wojciech Majeran, Giulia Friso, Lalit Ponnala, Brian Connolly, Edwin Reidel, Cankui Zhang, Yukari Asakura, Nazmul H Bhuiyan, Qi Sun, Robert Turgeon, Klaas J van Wijk. Structural and metabolic transitions of C3 rice and C4 maize leaf development and differentiation determined by a systems biology approach. 53rd Annual Maize Genetics Conference, March 17-20, 2011, St. Charles, Illinois USA
  7. Anton Poliakov, Lalit Ponnala, Paul Dominic Olinares, Yukari Asakura and Klaas van Wijk. A Statistical Solution for Pair-Wise Comparative Proteome Analysis using Large Scale Label-Free Spectral Counting. Sanibel Conference "From Fragmentation Mechanisms to Sequencing: Tandem Mass Spectrometry Based Peptide and Protein Identification", St. Pete Beach, Florida, January 21 - 24, 2011
  8. Paul Dominic B. Olinares, Lalit Ponnala, Klaas J. Van Wijk. Probing the oligomeric state of chloroplast proteome in Arabidopsis thaliana by mass spectrometry: megadalton-sized complexes and the Clp protease machinery. 58th ASMS Conference on Mass Spectrometry, Salt Lake City, Utah, May 23 - 27, 2010
  9. Lalit Ponnala. RNA-Seq: High-throughput transcriptomics. Next Generation Sequencing Workshop, Cornell University, March 31, 2010
  10. Pinghua Li, Lalit Ponnala, Neeru Gandotra, Lori Tausta, Lin Wang, Yaqing Si, Nicholas Provart, Rohan Patel, Chris Myers, Edwin Reidel, Robert Turgeon, Peng Liu, Qi Sun, Tim Nelson, Thomas P. Brutnell. Characterization of the maize leaf transcriptome through ultra high-throughput sequencing. 52nd Annual Maize Genetics Conference, March 18 - 21, 2010, Riva del Garda, Italy
  11. Lalit Ponnala, Stefan Stefanov, Matha Hamblin, Stephen Kresovich, Lance Cadle-Davidson, Michael Milgroom, Marsha Wallace, John Schimenti, Wei Wang, Peter Schweitzer and Qi Sun. Genome Complexity Reduction for NGS and a Pipeline for identifying and integrating Genetic Variations across Multiple Samples. Cambridge Healthtech Institute (CHI) meeting "Next-Generation Sequencing Data Analysis" Sept 21-23, 2009, Providence RI
  12. Pinghua Li, Thomas Brutnell, Peng Liu, Qi Sun and Lalit Ponnala. Software Tools for Analyzing the Maize Leaf Transcriptome. Cambridge Healthtech Institute (CHI) meeting "Next-Generation Sequencing Data Analysis" Sept 21-23, 2009, Providence RI
  13. P. Li, W. Majeran, L. Ponnala, L. Tausta, E. Reidel, A. Nunes-Nesi, G. Friso, B.M. Connolly, N. Gandotra, T. Kebrom, L. Wang, A. Fernie, C. Myers, P. Liu, R. Turgeon, Q. Sun, T. Nelson, K. van Wijk and T.P. Brutnell. A systems approach to understanding C4 photosynthetic differentiation in maize. "Plant Biology 2009": Joint Annual Meetings of the American Society of Plant Biologists and the Phycological Society of America, July 18-22, 2009, Honolulu, Hawaii
  14. N. Gandotra, L. Tausta, P. Li, E. Reidel, T. Kebrom, L. Ponnala, W. Majeran, Q. Sun, P. Liu, T. Brutnell, K. van Wijk, R. Turgeon and T. Nelson. Comparative Analysis Of C3 And C4 Leaf Development In Rice, Sorghum And Maize. "Plant Biology 2009": Joint Annual Meetings of the American Society of Plant Biologists and the Phycological Society of America, July 18-22, 2009, Honolulu, Hawaii
  15. Pinghua Li, Tesfamichael Kebrom, Lalit Ponnala, Edwin Reidel, Qi Sun, Robert Turgeon, Thomas P. Brutnell. A Systems Biology Approach To Understanding C4 Photosynthetic Development In Maize. Plant & Animal Genomes XVII Conference, San Diego, CA, January 10-14, 2009
  16. Manish Kohli, Paul G. Rothberg, Peter Schweitzer, Qi Sun, Lalit Ponnala, George Grills, Deepak Sahasrabudhe, Edward Messing, Jean Joseph, Wei Wang. Genetic polymorphism association with hot flashes in prostate cancer patients initiated on androgen deprivation therapy (ADT). ASCO-NCI-EORTC Annual Meeting on Molecular Markers in Cancer, Hollywood, Florida, Oct 30-Nov 1, 2008
  17. Lalit Ponnala, Qi Sun. Data mining pipelines for next generation sequencing platforms. 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada, July 17-23, 2008
  18. Manish Kohli, Paul G. Rothberg, Peter Schweitzer, Qi Sun, Lalit Ponnala, George Grills, Deepak Sahasrabudhe, Edward Messing, Jean Joseph, Wei Wang. The Prognostic Influence of Inherited Polymorphisms on Prostate Cancer Outcomes. AACR Special Conference in Cancer Research "Candidate Pathways, Whole Genome Scans: Reconciling Results, Looking into the Future", May 20-23, 2008, Carefree, Arizona
  19. Lalit Ponnala, Qi Sun, Data Processing Pipelines for Next Generation Sequencing Platforms. Life Sciences Research Resources Expo. Cornell University, Ithaca NY, May 14-15, 2008
  20. Lalit Ponnala, Genomic Signal Processing. Invited talk given at the Information Systems and Networks seminar, Department of Electrical and Computer Engineering, Cornell University, Feb 27, 2008
  21. Schweitzer P, Sun Q, Wang W, Ponnala L, Zhao J, Hover B, Spisak J, Stelick T, VanEe J, Grills G. Implementation of next generation sequencing technologies as core facility resources. Association of Biomolecular Resource Facilities (ABRF), Salt Lake City, Utah, Feb 9-12, 2008
  22. Grills G, Schweitzer P, Sun Q, Ponnala L, Wang W, Stelick T, Bukowski R, VanEe J. Application of Massively Parallel Sequencing Technologies as Shared Research Resources. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, Feb 6-9, 2008
  23. Pillardy J, Sun Q, Ripoll D, Bukowski R, Myers C, Ponnala L. Computational Biology Service Unit : Microsoft High-Performance Computing Institute. Northeast Regional Life Sciences Core Directors Meeting, Cornell University, Ithaca NY, Nov 7-9, 2007
  24. Qi Sun and Lalit Ponnala. Data Integration for Genome-wide Association Studies of Human Diseases. Microsoft eScience meeting at RENCI, UNC Chapel Hill, North Carolina (Oct 21-23, 2007)
  25. L Ponnala, R Bukowski, J VanEe, P Schweitzer, K Simpson and Q Sun. Data processing strategies for bacterial genome re-sequencing projects using Illumina Solexa technology. Exploring Next Generation Sequencing: Applications and Case Studies, Cambridge Healthtech Institute (CHI) Meeting (Oct 17-18, 2007)
  26. Guohong Cai, Lalit Ponnala, Qi Sun, Jarek Pillardy and Bill Fry. Bioinformatic and experimental identification of microRNA in Phytophthora infestans. Phytophopthora Infestans Genome meeting, Broad Institute of MIT and Harvard (Sept 18-19, 2007)
  27. L. Ponnala and A. Stomp. A computational model for reading frame maintenance. NC State RNA Biology Group Meeting (March 6, 2007)
  28. L. Ponnala. Steps in frame: decoding the motion of the ribosome. NC State RNA Biology Group Meeting (Oct 3, 2006)
  29. L. Ponnala. Mechanism of frameshifting in bacteria. First Annual Duke Systems Biology Symposium, Duke University, Durham, NC (Sept 14-15, 2006)
  30. Lalit Ponnala. Computational Model for Reading Frame Maintenance. presentation at BioMeet RTP 2006, organized by the International Society for Computational Biology (ISCB) Student Council, Research Triangle Park, NC (Apr 13, 2006)
  31. L. Ponnala. Ribosome-mRNA interaction. Symposium on RNA Biology VI "RNA, Tool and Target: Small RNAs and RNPs", Research Triangle Park, NC (Oct 21-22, 2005)
  32. L. Ponnala and A. Stomp. mRNA Signal Processing. NC State RNA Biology Group Meeting (Sept 8, 2005)
  33. L. Ponnala. Frequency-domain analysis of prokaryotic translation. RNA Society of North Carolina Seminar Series, North Carolina Biotechnology Center, RTP, NC (Aug 23 2005)
  34. L. Ponnala and T.M.Barnes. Genetic Algorithms for finding the optimal ribosome. Annual Biomedical Engineering Research Review, UNC-CH, Chapel Hill, NC (Apr 16, 2004)

Software

  1. GLEE: differential protein expression analysis | Python version : [github] | R package : [github] | Shiny app : [live]

  2. Protein expression gradient viewer | written in Microsoft Visual C# [screenshot]

  3. RNA-Seq analysis pipeline | developed using PERL [website] [screenshot]

  4. Genome browser for maize transcriptome visualization | developed using GBrowse [screenshot]

  5. Survey data uploader for Excel, using a web service | developed using VSTO 2005 [screenshot]

  6. Free-energy signal analysis toolbox | developed in MATLAB [github]