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Publications
2009
40)
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]
39)
Otsuka Y, Chen Y, Guda C and Schoenberg DR
The PMR1 mRNA endonuclease is a product of the peroxidasin gene (Submitted).
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]
2008
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]
2007
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]
2006
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]
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]
2004
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]
2001-2003
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, Elslinger 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)(pdf ),
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.
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