Publications

2017


75) Talbott H, Hou X, Qiu F, Zhang P, Guda C, Yu F, Cushman RA, Wood JR, Wang C, Cupp AS, Davis JS.
Transcriptomic and Bioinformatics Analysis of Short Prostaglandin F2 alpha Time-course in Bovine Corpus Luteum.
Data in Brief (2017) 14:695-706.

74) Talbott H, Hou X, Qiu F, Zhang P, Guda C, Yu F, Cushman RA, Wood JR, Wang C, Cupp AS, Davis JS.
Early transcriptome responses of the bovine midcycle corpus luteum to prostaglandin F2α includes cytokine signaling.
Mol Cell Endocrinol (2017) 452:93-109. [PubMed]

73) Negi SK, Guda C.
Global gene expression profiling of healthy human brain and its application in studying neurological disorders, 
Scientific Reports (2017) 7:897 [PubMed]

72) Li Y, Heavican TB, Vellichirammal NN, Iqbad J, Guda C.
ChimeRScope: a novel alignment-free algorithm for fusion gene prediction using paired-end RNA-Seq data,
Nucleic Acids Research (2017) doi: 10.1093/nar/gkx315. [PubMed]

71) Mishra NK, Guda C.
Integrative analysis of genome-wide methylation and expression in pancreatic adenocarcinoma.
Oncotarget (2017) 8:28990-29012. [PubMed]

70) Massilamany C, Nandakumar R, Madayiputhiya, Pandey S, Guda C, Reddy J.
Gender-differences in the expression of proteins in autoreactive T cells specific to central nervous system myelin proteolipid protein.
Journal of Autoimmune Disorders (2017) [Link]

2016


69) Wang X, Guda C.
Integrative Exploration of Genomic Profiles for Triple Negative Breast Cancer Identifies Potential Drug Targets.
Medicine (Baltimore). (2016) Jul;95(30):e4321. [PubMed].

68) Vural S, Wang X, Guda C.
Classification of breast cancer patients using somatic mutation profiles and machine learning approaches. 
BMC Systems Biology (2016) Aug 26;10 Suppl 3:62. [PubMed]

67) Massilamany C, Mohammed A, Loy JD, Purvis T, Krishnan B, Basavalingappa RH, Kelley CM, Guda C, Barletta RG, Moriyama EN, Smith TPL, Reddy J.  
Genome sequence analysis and characterization of Bacillus infantis NRRL B-14911 that can induce myocarditis in A/J mice. 
BMC Genomics. (2016) Aug 22;17 Suppl 7:511. [PubMed]

66) Stauch KL, Villeneuve LM, Purnell, PR, Pandey S, Guda C, and Fox HS.
Genetic ablation of the Parkinson’s disease-related proteins, PINK1, DJ-1, and Parkin, result in common synaptic mitochondrial alterations in the striatum early during disease progression. 
(Submitted).

2015


65) Zhao Z, Jin V, Huang Y, Guda C, Ruan J.
Frontiers in integrative genomics and translational bioinformatics.
BioMed Research International (In press) [PubMed].

64) Shen R, Wang, X, Guda C.
Discovering Distinct Functional Modules of Specific Cancer Types Using Protein-Protein Interaction Networks. 
BioMed Research International, 2015:146365. [PubMed]

63) Cserhati M, Pandey S, Beaudoin J J, Baccaglini L, Guda C, Fox H S. 
The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.
Database (2015) 2015:bav074. [PubMed

62) Lakshmanan I, Seshacharyulu P, Haridas D, Rachagani S, Gupta S, Joshi S, Guda C, Jain M, Ganti AK, Ponnusamy, MP and Batra, SK.
Novel HER3/MUC4 oncogenic signaling aggravates the tumorigenic phenotypes of pancreatic cancer cells.
Oncotarget (2015) 6:21085-21099 [PubMed]

61) Li Y, Wang X, Vural S, Mishra N, Cowan KH, Guda C.
Exome analysis reveals differentially mutated gene signatures of stage, grade and subtype in breast cancers.
PLoS ONE (2015): 10:e0119383. [PubMed]

60) Mohammed A, Guda C.
Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism.
BMC Genomics (2015): Suppl 7:S16. doi: 10.1186/1471-2164-16-S7-S16. [PubMed]

59) Cornish A, Guda C.
A comparison of variant calling pipelines using Genome-in-a-Bottle as a reference.
BioMed Research International (2015) 2015:456479. [Hindawi]

58) Negi S, Pandey S, Srinivasan SM, Mohammed A, Guda C.
LocSigDB: A database of experimental and predicted protein localization signals.
Database (2015):2015/bav003. [PubMed]

2014


57) Chaturvedi NK, Mir RA, Band V, Joshi SS, Guda C.
Experimental validation of predicted subcellular localization of human proteins.
BMC Research Notes (2014) 7:912 [PubMed]

56) Shen R, Guda C.
Applied graph-mining algorithms to study biomolecular interaction networks.
BioMed Research International. (2014) 2014:439476. [PubMed]

55) Goonesekhere N, Wang X, Ludwig L, Guda C.
A meta analysis of pancreatic microarray datasets yields new targets as cancer genes and biomarkers.
PLoS ONE (2014) 9:e93046 [PubMed]

54) Wang X, Guda C.
Computational analysis of transcriptional circuitries in human embryonic stem cells reveals multiple and independent networks.
BioMed Research International (2014) 2014:725780. [PubMed]

2013


53) Srinivasan SM, Guda C.
MetaID: A novel method for identification and quantification of metagenomic samples.
BMC Genomics (2013);14 Suppl 8:S4. doi: 10.1186/1471-2164-14-S8-S4. [PubMed]

52) Read BA, Kegel J, . Emiliana huxleyi Annotation Consortium (Guda C.). Grigoriev IV
Pan genome of the phytoplankton Emiliania underpins its global distribution.
Nature (2013) 499, 209-213.[PubMed]

51) Guda C.
Bioinformatic methods and resources for neuroscience research.
In: Current Laboratory Methods in Neuroscience Research, Xiong H and Gendelman HE Eds. Springer publishing (2013)(In press)

50) Ozturk F, Li Y, Zhu X, Guda C, Nawshad A.
Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFbeta3-knockout mice alleles: RNA-Seq analysis of TGFbeta3 Mice.
BMC Genomics (2013) 14:113.[PubMed]

59) Srinivasan SM, Vural S, King BR, Guda C.
Mining for class-specific motifs in protein sequence classification.
BMC Bioinformatics
(2013) 14:96.[PubMed]

2011 - 2012


48) 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
(2012) 5:351.[PubMed]

47) 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.
J. Biol. Chem. (2012) 287:29442-56.[PubMed]

46) Shen R, Gooneshkere NCW, Guda C.
Mining functional subgraphs from cancer protein-protein interaction networks.
BMC Systems Biology, (2012) 6:S2  [PubMed]

45) Gu, SQ, Bakthavachalu B, Han J, Patil D, 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 (2012) 18:1186-1196.[PubMed]

44) Gunda V, Boosani CS, Verma RK, Guda C, Sudhakar, YA.
L-Arginine Mediated Renaturation Enhances Yield of Human, alpha6Type IV Collagen Non-Collagenous Domain from Bacterial Inclusion Bodies.
Protein and Peptide Letters (2012) 19:1112-1121.

43) Zhu X, Ozturk F, Pandey S, Guda C, Nowshad A.
Implications of TGF-B on transcriptome and cellular biofunctions of palatal mesenchyme.
Frontiers in Craniofacial Biology (2012) 3:1-22 . [PubMed]

42) Mohammed A, Guda C.
Computational approaches for automated classification of enzyme sequences.
Journal of Proteomics and Bioinformatics (2011) 4:147-152.[PubMed]

41) 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 (2012) 348:87-94 .[PubMed]


2006 -2010


40) Guda C.
Towards cataloguing the subcellular proteomes of eukaryotic organisms.
In: Sequence and Genome Analysis (Zhao, Z. ed),iConcepts press. (2010)

39) 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 (2009) 4:e5096 [PubMed]

38) Guda P, Chittur VS, Guda C
Comparative analysis of protein-protein interactions in cancer-associated genes.
Genomics, Proteomics & Bioinformatics (2009) 7:25-36

37) King BR, Latham L Guda C
Estimation of subcellular proteins in bacterial species
The Open and Applied informatics Journal (2009) 3:1-11 [PDF]

36) King BR, Guda C
Semi-supervised learning for classification of protein sequence data
Scientific Programming (2008) 16:5-29 [Abstract]

35) Meller N, Westbrook JM, Shannon JD, Guda C, Schwartz MA
Function of the N-terminus of zizimin1: autoinhibition and membrane targeting.
Biochemical Journal (2008) 409:525-533 [PubMed]

34) King BR, Guda C
ngLOC:An n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes
Genome Biology (2007) 8:R68 [PubMed]

33) Guda P, Bourne PE, Guda C
Conserved motifs in voltage-sensing and pore-forming modules of voltage-gated ion channel proteins
Biochem. Biophys. Res. Commun. (2007) 352:292-298 [PubMed]

32) Guda P, Subramaniam S, Guda C
MitoProteome: Human heart mitochondrial protein sequence database In: Cardiovascular Proteomics, Methods and Protocols.
Methods in Molecular Biology (2007) 357:375-384 [PubMed]

31) Guda P, Guda C, Subramaniam S
Reconstruction of pathways associated with amino acid metabolism in human mitochondria
Genomics, Proteomics & Bioinformatics (2007) 5:166-176 [PubMed]

30) Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK, 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.
Theoretical and Applied Genetics (2007) 115:571-590 [PubMed]

29) Guda C
pTARGET: A web server for predicting protein subcellular localization
Nucleic Acids Research (2006) 35:W210-213 [PubMed]

28) Guda C, Pal LR, Shindyalov IN.
DMAPS: A Database of Multiple Alignments for Protein Structures
Nucleic Acids Research (2006) 34: D273-276 [PubMed]

27) 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 (2006) 6:91 [PubMed]

26) Acquaah-Mensah GK, Leach SM, Guda C
Predicting the subcellular localization of human proteins using machine learning and exploratory data analysis.
Genomics, Proteomics & Bioinformatics (2006) 4:120-133 [PubMed]

25) Daniell H, Lee SB, Grevich J, Saski C, Guda C, Tomkins J, Jansen RK.
Complete chloroplast genome sequence of Solanum tuberosum, Lycopersicon esculentum and comparative analyses with other Solanaceous genomes.
Theoretical and Applied Genetics (2006) 112:1503-1518 [PubMed]

24) Cotter D, Maer A, Guda C, Saunders B, Subramaniam S.
LIPID MAPS: Lipid Proteome Database
Nucleic Acids Research (2006) 34: D507-510 [PubMed]


2001 -2005


23) Guda C, Subramaniam S.
pTARGET: A new method for predicting protein sub-cellular localization in eukaryotes
Bioinformatics (2005) 21: 3963-3969 [PubMed]

22) Meller N, Merlot S, Guda C
CZH proteins-New family of Rho GEFs
Journal of Cell Science (2005) 118: 4937-4946 [PubMed]

21) Guda C, Guda P, Fahy E, Subramaniam S.
MITOPRED: a web server for genome-scale prediction of mitochondrial proteins.
Nucleic Acids Research (2004) 32: W372-W374 [PubMed]

20) Guda C, Lu S, Scheeff E, Bourne PE, Shindyalov IN.
CE-MC: A Multiple Protein Structure Alignment Server.
Nucleic Acids Research (2004) 32: W100-W103 [PubMed]

19) Guda C, Fahy E, Subramaniam S.
MITOPRED: A genome-scale method for prediction of nuclear-encoded mitochondrial proteins.
Bioinformatics (2004) 20:1785-1794 [PubMed]

18) Chukkapalli G, Guda C, Subramaniam S.
SledgeHMMER: A web server for batch searching of Pfam database
Nucleic Acids Research (2004) 32: W542-W544 [PubMed]

17) 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, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Rodrigues K, Schwarzenbacher R, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA.
Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 Å  resolution,
Proteins (2004) 56:387-391 [PubMed]

16) 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, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA.
Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 Å  resolution,
Proteins (2004) 54:174-177 [PubMed]

15) 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, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA.
Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 Å  resolution,
Proteins (2003) 52:142-145 [PubMed]

14) 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, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Taylor SS, Hodgson KO, Wooley J, Wilson IA.
Crystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 Å resolution.
Proteins (2003) 50:371-374 [PubMed]

13) 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, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, McMullan D, McPhillips TM, Miller MA,Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K,Selby TL, Spraggon G, Stevens RC, Taylor SS, Van Den Bedem H,Velasquez J, Vincent J, Wang X, West B, Wolf G, Wooley J, Wilson IA.
Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 Å resolution.
Proteins (2002) 49:142-145 [PubMed]

12)  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, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC.  
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline.
Proceedings of the National Academy of Sciences, USA (2002) 99:11664-11669 [PubMed]

11)  Guda C, Scheeff ED, Bourne PE, Shindyalov IN
Comparative Analysis of Protein Structure: New Concepts and Approaches for Multiple Structure Alignment.
In: Protein Structure Prediction: Bioinformatics Approach (2002) pp.451-459

10)  Guda C, Scheeff ED, Bourne PE, Shindyalov IN.
A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization.
Proceedings of the Pacific Symposium on Biocomputing (2001), pp. 275-286 [PubMed]


1994 -2000


9)  Guda C, Lee SB, Daniell H.
Stable transformation of chloroplasts using a universal integration vector.
Plant Cell Reports (2000) 19:257-262 [Abstract]

8)  Daniell H, Guda C.
Biopolymer production in microorganisms and plants (Review Article).
Chemistry and Industry (1997) 14: 555-558

7)  Brixey J, Guda C, Daniell H.
The chloroplast psbA promoter is more efficient in E. coli than the T7 promoter for hyperexpression of a foreign protein.
Biotechnology Letters (1997) 19: 395-399 [Abstract]

6)  Daniell H, Guda C, McPherson DT, Zhang X, Urry DW.
Hyper expression of a synthetic protein based polymer gene.
Methods in Molecular Biology (1997) 63: 359-371 [PubMed]
(Appeared on the cover page)

5)  Urry DW, McPherson DT, Xu J, Daniell H, Guda C, Gowda DC, Jing N, Parker TM.
Protein- Based Polymeric Materials: Syntheses and Properties.
In: The Polymeric Materials Encyclopedia: Synthesis, Properties and Applications (1996) pp. 2645-2699, CRC Press,Boca Raton

4)  Guda C, Zhang X, McPherson DT, Xu J, Cherry JH, Urry DW, Daniell H.
Hyperexpression of an environmentally friendly synthetic polymer gene.
Biotechnology Letters (1995) 17: 745-750

3)  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 (1995) 17:1279-1284

2)  Daniell H, Zhang X, Guda C., Urry DW.
Plastics from Plants.
Highlights of Agricultural Research (1995) 42: 18-19

1)  Daniell H, Guda C, Singh NK, Weete JD, Cherry JH.
Photosynthesis, epicuticular wax and lipid changes in cowpea cultivars grown under hyperthermic conditions. In: Biochemical and Cellular Mechanisms of Stress Tolerance in Plants (J.H. Cherry ed.)
NATO ASI Series (1994) Vol. H 86: 213-227,Springer-Verlag,Heidelberg.