2021
125) Veerappa A, Pendyala G, Guda C.
A systems omics-based approach to decode substance use disorders and neuroadaptations.
Neuroscience and Biobehavioral Reviews, (2021) (In press)
124) Kim SK, Vishweswaraiah S, Macknis J, Yilmaz A, Lalwani A, Mishra NK, Guda C, Ogunyemi D, Radhakrishan U, Bahado-Singh RO.
New-onset postpartum preeclampsia: Epigenetic mechanism and prediction.
Journal of Maternal-Fetal & Neonatal Medicine, (2021) doi:10.1080/14767058.2021.1946504 [PubMed]
123) Radhakrishna U, Nath SK, Vishweswaraiah S, Uppala LV, Forray A, Muvvala SB, Mishra NK, Siddesh S, Guda C, Govindamangalam H, Vargas D, Gardella WG, Crist RC, Berrettini WH, Metpally RP, Bahado-Singh RO.
Maternal opioid use disorder: Placental transcriptome analysis for neonatal opioid withdrawal syndrome.
Genomics, (2021) doi:10.1016/j.ygeno.2021.08.001 [PubMed]
122) Schissel M, Best R, Liesemeyer S, Tan Y, Avuthu N, Carlson DJ, Shaffer JJ, Guda C, Carlson KA.
Effect of Nora virus infection on native gut bacterial communities and lifespan of Drosophila melanogaster.
AIMS Microbiology, (2021) doi:10.3934/microbiol.2021014 [PubMed]
121) Shakyawar S, Sethi S, Southekal S, Mishra NK, Guda C.
Big data analytics for modelling COVID-19 and comorbidities: An unmet need.
In Computational Intelligence Techniques for Combating COVID-19, Springer Book Chapter, (Eds. Kautish S, Peng S, Obaid A.), (2021) pp.185-201.
120) Rao C, Frodyma DE, Southekal S, Svoboda RA, Guda C, Johnson KR, Fisher KW, Lewis RE.
KSR1- and ERK-dependent Translational Regulation of the Epithelial-to-Mesenchymal Transition.
eLife, (2021) 10:e66608 [PubMed]
119) Hua G, George JW, Clark KL, Southekal S, Guda C, Hou X, Blum HR, Eudy J, Butnev VY, Brown AR, Katta S, May JV, Bousfield GR, Davis JS.
Hypo-glycosylated hFSH drives ovarian follicular development more efficiently than fully glycosylated hFSH: enhanced transcription and PI3K and MAPK signaling.
Human Reproduction, (2021) (in press)
118) Saleem I, Mirza S, Sarkar A, Raza M, Mohapatra B, Mushtaq I, Kim JH, Mishra NK, Alsaleem M, Rakha EA, Qiu F, Guda C, Band H, Band V.
The mammalian ecdysoneless protein interacts with RNA helicase DDX39A to regulate nuclear mRNA export.
Molecular Cell Biology, (2021) MCB.00103-21 [PubMed]
117) Shakyawar SK, Pandey S, Harvey DJ, Bousfield G, Guda C.
FGDB: Database of follicle stimulating hormone glycans.
Comput Struct Biotechnol J., (2021) 19:1635-1640 [PubMed]
116) Southekal S, Mishra NK, Guda C.
Pan-cancer analysis of human kinome gene expression and promoter DNA methylation identifies prognostic biomarkers in multiple cancers.
Cancers, (2021) 13:1189 [PubMed]
115) Uppala R, Vishweswaraiah S, Uppala LV, Crist RC, Mishra NK, Macknis J, Szymanska M, Kumar S, Aydas B, Forray A, Guda C, Carey DJ, Metpally RP, Berrettini WH, Bahado-Singh.
Placental DNA methylation in opioid-exposed pregnancies and associations with the neonatal opioid withdrawal syndrome.
Genomics, (2021) 113:1127-35 [PubMed]
114) Moore R, Puniya BL, Powers R, Guda C, Bayles K, Berkowitz D, Helikar T.
Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome.
Scientific Reports, (2021) 11:5585 [PubMed]
113) Vellichirammal NN, Guda C.
A compiled dataset of molecular pathways associated with fusion genes identified in pediatric cancers.
Data in Brief, (2021) 35:106780 [PubMed]
112) Sagar S, Rathinavel AK, Lutz WE, Struble LR, Khurana S, Schnaubelt AT, Mishra NK, Guda C, Broadhurst MK, Reid SPM, Bayles KW, Borgstahl GEO and Radhakrishnan P.
Bromelain inhibits SARS-CoV-2 infection via targeting ACE-2 and spike protein.
Clinical and Translational Medicine, (2021) 11(2):e281 [PubMed]
111) Gaurav R, Mikuls TR, Thiele GM, Nelson AJ, Niu M, Guda C, Eudy JD, Barry A, Romberger AJ, Duryee MJ, England BR, Poole JA.
High-throughput analysis of lung immune cells in a murine model of rheumatoid arthritis-associated lung disease.
PLOS ONE, (2021) 16(2):e0240707 [PubMed]
110) Odegaard KE, Schaal VL, Clark AR, Koul S, Jagadesan S, Xia Z, Mellon M, Uberti M, Liu Y, Stothert A, Van Hook M, Wang H, Guda C, Lisco SJ, Pendyala G, Yelamanchili S.
A holistic systems approach to characterize the impact of pre- and post-natal oxycodone exposure on neurodevelopment and behavior.
Frontiers in Cell and Developmental Biology, (2021) 8:619199 [PubMed]
2020
109) Wu S, Kumar V, Xiao P, Kuss M, Lim JY, Guda C, Butcher J, Duan B.
Age related extracellular matrix and interstitial cell phenotype in pulmonary valves.
Scientific Reports, (2020) 10(1):21338 [PubMed]
108) Jagadeesan S, Ahmad R, Avuthu N, Singh AP, Guda C.
Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn’s Disease.
Frontiers in Medicine, Gastroenterology, (2020) 7:606298 [PubMed]
107) Vellichirammal NN, Chaturvedi N, Joshi SS, Coulter DW, Guda C
Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy.
Cancer Letters, (2020) 499:24-38 [PubMed]
106) Shakyawar S, Sethi S, Southekal S, Mishra NK, Guda C.
Big data analytics for modelling COVID-19 and comorbidities: An unmet need.
In Computational Intelligence Techniques for Combating COVID-19, Springer Book Chapter, (Eds. Kautish S, Peng S, Obaid A.) (2020) (Accepted)
105) Odegaard KE, Schaal VL, Clark AR, Koul S, Gowen A, Jagadesan S, Xiao P, Guda C, Lisco SJ, Yelamanchili S, Pendyala G.
Characterization of the intergenerational impact of in utero and postnatal oxycodone exposure.
Translational Psychiatry, (2020) 10(1):329 [PubMed]
104) Mishra NK, Meng N, Guda C.
Identification of prognostic markers in cholangiocarcinoma using altered DNA methylation and gene expression profiles.
Frontiers in Genetics, (2020) 11:522125 [PedMed]
103) Cornish A, Roychoudhury S, Sarma K, Pramanik S, Bhakat K, Dudley A, Guda C.
Red Panda: a novel method for detecting variants in single-cell RNA sequencing.
BMC Genomics Supplement, (2020) 21(Suppl 11):830 [PubMed]
102) Chand S, Jo A, Vellichirammal NN, Gowen A, Guda C, Schaal V, Odegaard K, Lee H, Pendyala G, Yelamanchili S
Comprehensive characterization of organ-specific extracellular vesicle protein markers: Implications for preclinical and clinical applications.
ACS Applied Nano Materials, (2020) 3(9):8906-8919 [PubMed]
101) Koul S, Schaal VL, Chand S, Pittenger ST, Vellichirammal NN, Guda C, Bevins RA, Yelamanchili SV, Pendyala G
Role of brain derived extracellular vesicles in decoding sex differences associated with nicotine self-administration.
Cells, (2020) 9(8):1883 [PubMed]
100) Gao L, Kumar V, Vellichirammal NN, Park SY, Rudebush TL, Yu L, Son WM, Pekas EJ, Wafi AM, Hong J, Xiao P, Guda C, Wang HJ, Schultz HD, Zucker IH.
Functional, Proteomic, and Bioinformatic Analyses of Nrf2- and Keap1- Null Skeletal Muscle.
Journal of Physiology, (2020) 598(23):5427-5451 [PubMed]
99) Mishra NK, Southekal S, Guda C
Prognostic value of biomarkers in the tumor microenvironment of pancreatic ductal adenocarcinoma.
Annals of Translational Medicine, (2020) 8(10):615 [PubMed]
98) Tan Y, Xiao P, Guda C
In-depth Mendelian randomization analysis of causal factors for coronary artery disease.
Scientific Reports, (2020) 10(1):9208. [PubMed]
97) Kumar SRP, Wang X, Avuthu N, Bertolini TB, Terhorst C, Guda C, Daniell H, Herzog RW.
Role of small intestine and gut microbiome in plant-based oral tolerance for hemophilia.
Frontiers in Immunology, (2020) 11:844. [PubMed]
96) Zhang W, Klinkebiel D, Barger CJ, Pandey S, Guda C, Miller A, Akers S, Odunsi K, Karpf AR
Global DNA hypomethylation in epithelial ovarian cancer: passive demethylation and association with genomic instability.
Cancers, (2020) 12(3):764. [PubMed]
95) Bahado-Singh R, Vishweswaraiah S, Veerappa AM, Aydas B, Yilmaz A, Saiyed NM, Mishra NK, Guda C, Radhakrishna U.
Precision Cardiovascular Medicine: Artificial Intelligence and Epigenetics for the Pathogenesis and Prediction of Coarctation in Neonates.
Journal of Maternal-Fetal & Neonatal Medicine, (2020) doi:10.1080/14767058.2020.1722995 [PubMed]
94) Vellichirammal NN, Albahrani A, Banwait JK, Mishra NK, Li Y, Roychoudhury S, King MJ, Mirza S, Bhakat KK, Band V, Joshi SS, Guda C
Pan-cancer analysis reveals the diverse landscape of novel sense and antisense fusion transcripts.
Molecular Therapy Nucleic Acids, (2020) 19:1379-1398. [PubMed]
93) Tom E, Mushtaq I, Mohapatra B, Luan H, Zutshi N, Bhat A, Goetz B, Arya P, Bielecki T, Iseka F, Bhattacharyya S, Cypher L, Negi S, Storck M, Rana S, Barnekow A, Singh P, Ying G, Guda C, Natarajan A, V Band, H Band.
EHD1 and RUSC2 Control Basal EGFR Cell Surface Expression and Recycling.
Molecular and Cellular Biology, (2020) 40(7):e00434-19. [PubMed]
92) Jang HS, Noh MR, Jung EM, Kim WY, Guda C, Foster KW, Oupicky D, Ferrer FA, Padanilam BJ.
Proximal tubule cyclophilin D regulates fatty acid oxidation in cisplatin-induced acute kidney injury.
Kidney International, (2020) doi:10.1016/j.kint.2019.08.019. [PubMed]
91) Vellichirammal NN, Albahrani A, Li Y, Guda C
Identification of fusion transcripts from unaligned RNA-seq reads using ChimeRScope.
Methods in Molecular Biology, (2020) doi:10.1007/978-1-4939-9904-0_2. [PubMed]
2019
90) Cserhati M, Peng X, Guda C.
K-mer based motif analysis in insect species across Anopheles, Drosophila and Glossina genera and its application to species classification.
Computational and Mathematical Models in Medicine, (2019) doi:10.1155/2019/4259479. [PubMed]
89) Bahado-Singh R, Vishweswaraiah S, Aydas B, Mishra NK, Yilmaz A, Guda C, Radhakrishna U.
Artificial intelligence analysis of Newborn Leucocyte epigenomic markers for the Prediction of Autism.
Brain Research, (2019) 1724:146457. [PubMed]
88) Mishra NK, Siddesh S, Guda C.
Survival analysis of multi-omics data identifies potential prognostic markers of pancreatic ductal adenocarcinoma.
Frontiers in Genetics, (2019) doi:10.3389/fgene.2019.00624. [PubMed]
87) Bahado-Singh R, Vishweswaraiah S, Aydas B, Mishra NK, Guda C, Radhakrishna U.
Deep Learning/ Artificial Intelligence and the Epigenomic Prediction of Cerebral Palsy.
Int. J. Molecular Sciences, (2019) 20:E2075. [PubMed]
86) Moore D, Meays BM, Madduri LSV, Shahjin F, Chand S, Niu M, Albahrani A, Guda C, Pendyala G, Fox HS, and Yelamanchili SV.
Downregulation of an evolutionary young miR-1290 in an iPSC derived neural stem cell model of autism spectrum disorder.
Stem Cells Int., (2019) doi: 10.1155/2019/8710180. eCollection 2019. [PubMed]
85) Vishweswaraiah S, Swierkowska J, Ratnamala U, Mishra NK, Guda C, Johar KR, Mrugacz M, Karolak JA, Gajecka M, Radhakrishna U.
Epigenetically dysregulated genes and pathways implicated in the pathogenesis of non-syndromic high myopia.
Scientific Reports, (2019) 9:4145, PMID: 30858441. [PubMed]
84) Bahado-Singh R, Vishweswaraiah S, Veerappa AM, Mishra NK, Guda C, Radhakrishna U.
Placental DNA methylation changes for the detection of Tetralogy of Fallot (TOF)
Ultrasound in Obstetrics and Gynecology, (2019) doi: 10.1002/uog.20292. [PubMed]
83) Bahado-Singh R, Albayrak S Zafra R, Baraa A, Veerappa AV, Mahishi D, Saiyed NM, *Mishra NK, Guda C, Ali-Fehmi R, Radhakrishna U.
Placental epigenetics for evaluation of fetal congenital heart defects: Ventricular septal defect (VSD).
PLoS One, (2019) 14:e0200229, PMID: 30897084 [PubMed]
82) Heithoff AJ, Totusek SA, Le D, Barwick L, Gensler G, Franklin DR, Dye AC, Pandey S, Sherman S, Guda C, Fox HS.
The integrated national neuroAIDS tissue consortium (NNTC) database: A rich platform for neuroHIV research.
Database, (2019) doi: 10.1093/database/bay134. PMID: 30624650. [PubMed]
2018
81) Radhakrishna U, Veerappa AV, Vishweswaraiah S, Zafra R, Albayrak S, Sitharam PH, Saiyed NM, Mishra NK, Guda C, Bahado-Singh R.
Cord blood DNA epigenetic variations and signaling pathway genes associated 1 with Tetralogy of Fallot (TOF).
PLoS One, (2018) 13:e0203893 [PubMed]
80) Roy S, Bag AK, Dutta S, Polavaram NS, Islam R, Schellenburg S, Banwait JK, Guda C, Ran S, Hollingsworth MA, Singh RK, Talmadge JE, Muders MH, Batra SK, Datta K.
Macrophage-derived Neuropilin-2 exhibits novel tumor-promoting functions.
Cancer Research, (2018) 78:5600-5617 [PubMed]
79) Wipfler K, Cornish A, Guda C.
Comparative molecular characterization of typical and exceptional responders in Glioblastoma.
Oncotarget, (2018) 9:28421-28433 [PubMed]
78) Cserhati M, Mooter ME, Peterson L, Wicks B, Pauley M and Guda C.
Motifome comparison between modern human, Neanderthal and Denisova.
BMC Genomics, (2018) 19:472 [PubMed]
77) Luan H, Mohapatra B, Bielecki T, Mushtaq I, Mirza S, Bailey T, Clubb R, An W, Ahmed D, Ansari R, Storck M, Mishra NK, Guda C, Sheinin Y, Meza J, Raja S, Rakha E, Band V, Band H.
Loss of the nuclear pool of ubiquitin ligase CHIP/STUB1 in breast cancer unleashes the MZF1-cathepsin pro-oncogenic program.
Cancer Research, (2018) 78:2524-2535 [PubMed]
76) Lopez W, Page AM, Carlson DJ, Ericson BL, Cserhati MF, Guda C, Carlson KA.
Analysis of immune-related genes during Nora virus infection of Drosophila melanogaster using next-generation sequencing.
AIMS Microbiology, (2018) 4:123-139[PubMed]
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. [PubMed]
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) [PubMed]
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.
SWATH-MS proteome profiling data comparison of DJ-1, Parkin, and PINK1 knockout rat striatal mitochondria.
Data in Brief. (2016) 9:589-593 [PubMed]
2011-2015
65) Zhao Z, Jin V, Huang Y, Guda C, Ruan J.
Frontiers in integrative genomics and translational bioinformatics.
BioMed Research International. 2015 doi: 10.1155/2015/725491. [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. [PubMed]
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]
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]
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)
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]
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). 10.2174/092986612802762750. [Link]
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) doi: 10.1016/S1672-0229(08)60030-3 [PubMed]
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.