Chittibabu Guda - Publications

Affiliations: 
Computer Science State University of New York, Albany, Albany, NY, United States 
Area:
Bioinformatics Biology, Computer Science

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Vural S, Wang X, Guda C. Classification of breast cancer patients using somatic mutation profiles and machine learning approaches. Bmc Systems Biology. 10: 62. PMID 27587275 DOI: 10.1186/s12918-016-0306-z  0.52
2016 Massilamany C, Mohammed A, Loy JD, Purvis T, Krishnan B, Basavalingappa RH, Kelley CM, Guda C, Barletta RG, Moriyama EN, Smith TP, Reddy J. Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe. Bmc Genomics. 17: 511. PMID 27557119 DOI: 10.1186/s12864-016-2900-2  0.96
2016 Wang X, Guda C. Integrative exploration of genomic profiles for triple negative breast cancer identifies potential drug targets. Medicine. 95: e4321. PMID 27472710 DOI: 10.1097/MD.0000000000004321  0.96
2015 Zhao Z, Jin VX, Huang Y, Guda C, Ruan J. Frontiers in Integrative Genomics and Translational Bioinformatics. Biomed Research International. 2015: 725491. PMID 26605336 DOI: 10.1155/2015/725491  0.96
2015 Cornish A, Guda C. A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference. Biomed Research International. 2015: 456479. PMID 26539496 DOI: 10.1155/2015/456479  0.96
2015 Shen R, Wang X, Guda C. Discovering Distinct Functional Modules of Specific Cancer Types Using Protein-Protein Interaction Networks. Biomed Research International. 2015: 146365. PMID 26495282 DOI: 10.1155/2015/146365  0.96
2015 Cserhati MF, Pandey S, Beaudoin JJ, Baccaglini L, Guda C, Fox HS. The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies. Database : the Journal of Biological Databases and Curation. 2015: bav074. PMID 26228431 DOI: 10.1093/database/bav074  0.96
2015 Mohammed A, Guda C. Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism. Bmc Genomics. 16: S16. PMID 26099921 DOI: 10.1186/1471-2164-16-S7-S16  0.96
2015 Lakshmanan I, Seshacharyulu P, Haridas D, Rachagani S, Gupta S, Joshi S, Guda C, Yan Y, Jain M, Ganti AK, Ponnusamy MP, Batra SK. Novel HER3/MUC4 oncogenic signaling aggravates the tumorigenic phenotypes of pancreatic cancer cells. Oncotarget. PMID 26035354  0.96
2015 Li Y, Wang X, Vural S, Mishra NK, Cowan KH, Guda C. Exome analysis reveals differentially mutated gene signatures of stage, grade and subtype in breast cancers. Plos One. 10: e0119383. PMID 25803781 DOI: 10.1371/journal.pone.0119383  0.96
2015 Negi S, Pandey S, Srinivasan SM, Mohammed A, Guda C. LocSigDB: a database of protein localization signals. Database : the Journal of Biological Databases and Curation. 2015. PMID 25725059 DOI: 10.1093/database/bav003  0.96
2014 Chaturvedi NK, Mir RA, Band V, Joshi SS, Guda C. Experimental validation of predicted subcellular localizations of human proteins. Bmc Research Notes. 7: 912. PMID 25510246 DOI: 10.1186/1756-0500-7-912  0.96
2014 Shen R, Guda C. Applied graph-mining algorithms to study biomolecular interaction networks. Biomed Research International. 2014: 439476. PMID 24800226 DOI: 10.1155/2014/439476  0.96
2014 Goonesekere NC, Wang X, Ludwig L, Guda C. A meta analysis of pancreatic microarray datasets yields new targets as cancer genes and biomarkers. Plos One. 9: e93046. PMID 24740004 DOI: 10.1371/journal.pone.0093046  0.96
2014 Wang X, Guda C. Computational analysis of transcriptional circuitries in human embryonic stem cells reveals multiple and independent networks. Biomed Research International. 2014: 725780. PMID 24511543 DOI: 10.1155/2014/725780  0.96
2013 Srinivasan SM, Guda C. MetaID: a novel method for identification and quantification of metagenomic samples. Bmc Genomics. 14: S4. PMID 24564518 DOI: 10.1186/1471-2164-14-S8-S4  0.96
2013 Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, Young J, Aguilar M, Claverie JM, Frickenhaus S, Gonzalez K, et al. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature. 499: 209-13. PMID 23760476 DOI: 10.1038/nature12221  0.96
2013 Srinivasan SM, Vural S, King BR, Guda C. Mining for class-specific motifs in protein sequence classification. Bmc Bioinformatics. 14: 96. PMID 23496846 DOI: 10.1186/1471-2105-14-96  0.96
2013 Ozturk F, Li Y, Zhu X, Guda C, Nawshad A. Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFβ3-knockout mice alleles: RNA-Seq analysis of TGFβ3 Mice. Bmc Genomics. 14: 113. PMID 23421592 DOI: 10.1186/1471-2164-14-113  0.96
2012 Shen R, Goonesekere NC, Guda C. Mining functional subgraphs from cancer protein-protein interaction networks. Bmc Systems Biology. 6: S2. PMID 23282132 DOI: 10.1186/1752-0509-6-S3-S2  0.96
2012 King BR, Vural S, Pandey S, Barteau A, Guda C. ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes. Bmc Research Notes. 5: 351. PMID 22780965 DOI: 10.1186/1756-0500-5-351  0.96
2012 Mohibi S, Gurumurthy CB, Nag A, Wang J, Mirza S, Mian Y, Quinn M, Katafiasz B, Eudy J, Pandey S, Guda C, Naramura M, Band H, Band V. Mammalian alteration/deficiency in activation 3 (Ada3) is essential for embryonic development and cell cycle progression. The Journal of Biological Chemistry. 287: 29442-56. PMID 22736770 DOI: 10.1074/jbc.M112.378901  0.96
2012 Gu SQ, Bakthavachalu B, Han J, Patil DP, Otsuka Y, Guda C, Schoenberg DR. Identification of the human PMR1 mRNA endonuclease as an alternatively processed product of the gene for peroxidasin-like protein. Rna (New York, N.Y.). 18: 1186-96. PMID 22543864 DOI: 10.1261/rna.031369.111  0.96
2012 Zhu X, Ozturk F, Pandey S, Guda CB, Nawshad A. Implications of TGFβ on Transcriptome and Cellular Biofunctions of Palatal Mesenchyme. Frontiers in Physiology. 3: 85. PMID 22514539 DOI: 10.3389/fphys.2012.00085  0.96
2012 Gunda V, Boosani CS, Verma RK, Guda C, Sudhakar YA. L-arginine mediated renaturation enhances yield of human, α6 Type IV collagen non-collagenous domain from bacterial inclusion bodies. Protein and Peptide Letters. 19: 1112-21. PMID 22512648 DOI: 10.2174/092986612802762750  0.96
2012 Mukherjee A, Reisdorph N, Guda C, Pandey S, Roy SK. Changes in ovarian protein expression during primordial follicle formation in the hamster. Molecular and Cellular Endocrinology. 348: 87-94. PMID 21821096 DOI: 10.1016/j.mce.2011.07.043  0.96
2011 Mohammed A, Guda C. Computational Approaches for Automated Classification of Enzyme Sequences. Journal of Proteomics & Bioinformatics. 4: 147-152. PMID 22114367 DOI: 10.4172/jpb.1000183  0.96
2009 Guda P, Chittur SV, Guda C. Comparative analysis of protein-protein interactions in cancer-associated genes. Genomics, Proteomics & Bioinformatics. 7: 25-36. PMID 19591789 DOI: 10.1016/S1672-0229(08)60030-3  0.96
2009 Guda C, King BR, Pal LR, Guda P. A top-down approach to infer and compare domain-domain interactions across eight model organisms. Plos One. 4: e5096. PMID 19333396 DOI: 10.1371/journal.pone.0005096  0.96
2008 Meller N, Westbrook MJ, Shannon JD, Guda C, Schwartz MA. Function of the N-terminus of zizimin1: autoinhibition and membrane targeting. The Biochemical Journal. 409: 525-33. PMID 17935486 DOI: 10.1042/BJ20071263  0.96
2008 King BR, Guda C. Semi-supervised learning for classification of protein sequence data Scientific Programming. 16: 5-29.  0.96
2007 Guda P, Guda C, Subramaniam S. Reconstruction of pathways associated with amino acid metabolism in human mitochondria. Genomics, Proteomics & Bioinformatics. 5: 166-76. PMID 18267298 DOI: 10.1016/S1672-0229(08)60004-2  0.96
2007 Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK, Luo H, Tomkins J, Rognli OA, Daniell H, Clarke JL. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 115: 571-90. PMID 17534593 DOI: 10.1007/s00122-007-0567-4  0.96
2007 King BR, Guda C. ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes. Genome Biology. 8: R68. PMID 17472741 DOI: 10.1186/gb-2007-8-5-r68  0.96
2007 Guda P, Subramaniam S, Guda C. Mitoproteome: human heart mitochondrial protein sequence database. Methods in Molecular Biology (Clifton, N.J.). 357: 375-83. PMID 17172703 DOI: 10.1385/1-59745-214-9:375  0.96
2007 Guda P, Bourne PE, Guda C. Conserved motifs in voltage-sensing and pore-forming modules of voltage-gated ion channel proteins. Biochemical and Biophysical Research Communications. 352: 292-8. PMID 17126810 DOI: 10.1016/j.bbrc.2006.10.190  0.96
2006 Pal LR, Guda C. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. Bmc Evolutionary Biology. 6: 91. PMID 17090320 DOI: 10.1186/1471-2148-6-91  0.96
2006 Acquaah-Mensah GK, Leach SM, Guda C. Predicting the subcellular localization of human proteins using machine learning and exploratory data analysis. Genomics, Proteomics & Bioinformatics. 4: 120-33. PMID 16970551 DOI: 10.1016/S1672-0229(06)60023-5  0.96
2006 Guda C. pTARGET: a web server for predicting protein subcellular localization. Nucleic Acids Research. 34: W210-3. PMID 16844995 DOI: 10.1093/nar/gkl093  0.96
2006 Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, Jansen RK. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 112: 1503-18. PMID 16575560 DOI: 10.1007/s00122-006-0254-x  0.96
2006 Cotter D, Maer A, Guda C, Saunders B, Subramaniam S. LMPD: LIPID MAPS proteome database. Nucleic Acids Research. 34: D507-10. PMID 16381922 DOI: 10.1093/nar/gkj122  0.96
2006 Guda C, Pal LR, Shindyalov IN. DMAPS: a database of multiple alignments for protein structures. Nucleic Acids Research. 34: D273-6. PMID 16381863 DOI: 10.1093/nar/gkj018  0.96
2005 Meller N, Merlot S, Guda C. CZH proteins: a new family of Rho-GEFs. Journal of Cell Science. 118: 4937-46. PMID 16254241 DOI: 10.1242/jcs.02671  0.96
2005 Guda C, Subramaniam S. pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics (Oxford, England). 21: 3963-9. PMID 16144808 DOI: 10.1093/bioinformatics/bti650  0.96
2004 Chukkapalli G, Guda C, Subramaniam S. SledgeHMMER: a web server for batch searching the Pfam database. Nucleic Acids Research. 32: W542-4. PMID 15215445 DOI: 10.1093/nar/gkh395  0.96
2004 Guda C, Guda P, Fahy E, Subramaniam S. MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Research. 32: W372-4. PMID 15215413 DOI: 10.1093/nar/gkh374  0.96
2004 Guda C, Lu S, Scheeff ED, Bourne PE, Shindyalov IN. CE-MC: a multiple protein structure alignment server. Nucleic Acids Research. 32: W100-3. PMID 15215359 DOI: 10.1093/nar/gkh464  0.96
2004 Heine A, Canaves JM, von Delft F, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, et al. Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution. Proteins. 56: 387-91. PMID 15211522 DOI: 10.1002/prot.20003  0.96
2004 Guda C, Fahy E, Subramaniam S. MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics (Oxford, England). 20: 1785-94. PMID 15037509 DOI: 10.1093/bioinformatics/bth171  0.96
2004 Schwarzenbacher R, von Delft F, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, et al. Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution. Proteins. 54: 174-7. PMID 14705036 DOI: 10.1002/prot.10594  0.96
2003 Schwarzenbacher R, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, et al. Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution. Proteins. 53: 142-5. PMID 12945057 DOI: 10.1002/prot.10462  0.96
2003 Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, et al. Crystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 A resolution. Proteins. 50: 371-4. PMID 12486729 DOI: 10.1002/prot.10302  0.96
2002 Kuhn P, Lesley SA, Mathews II, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Hodgson KO, et al. Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution. Proteins. 49: 142-5. PMID 12211025 DOI: 10.1002/prot.10202  0.96
2002 Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, ... ... Guda C, et al. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proceedings of the National Academy of Sciences of the United States of America. 99: 11664-9. PMID 12193646 DOI: 10.1073/pnas.142413399  0.96
2001 Guda C, Scheeff ED, Bourne PE, Shindyalov IN. A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 275-86. PMID 11262947  0.96
2000 Guda C, Lee SB, Daniell H. Stable expression of a biodegradable protein-based polymer in tobacco chloroplasts Plant Cell Reports. 19: 257-262.  0.96
1997 Daniell H, Guda C, McPherson DT, Zhang X, Xu J, Urry DW. Hyperexpression of a synthetic protein-based polymer gene. Methods in Molecular Biology (Clifton, N.J.). 63: 359-71. PMID 9113662 DOI: 10.1385/0-89603-481-X:359  0.96
1997 Brixey PJ, Guda C, Daniell H. The chloroplast psbA promoter is more efficient in Escherichia coli than the T7 promoter for hyperexpression of a foreign protein Biotechnology Letters. 19: 395-399. DOI: 10.1023/A:1018371405675  0.96
1997 Daniell H, Guda C. Biopolymer production in microorganisms and plants Chemistry and Industry (London). 555-558.  0.96
1995 Zhang X, Guda C, Datta R, Dute R, Urry DW, Daniell H. Nuclear expression of an environmentally friendly synthetic protein based polymer gene in tobacco cells Biotechnology Letters. 17: 1279-1284. DOI: 10.1007/BF00189210  0.96
1995 Guda C, Zhang X, McPherson DT, Xu J, Cherry JH, Urry DW, Daniell H. Hyper expression of an environmentally friendly synthetic polymer gene Biotechnology Letters. 17: 745-750. DOI: 10.1007/BF00130362  0.96
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