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Items: 1 to 20 of 32


Toward Personalized Network Biomarkers in Alzheimer's Disease: Computing Individualized Genomic and Protein Crosstalk Maps.

Padmanabhan K, Shpanskaya K, Bello G, Doraiswamy PM, Samatova NF.

Front Aging Neurosci. 2017 Sep 26;9:315. doi: 10.3389/fnagi.2017.00315. eCollection 2017. No abstract available.


The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

Chen W, Hendrix W, Samatova NF.

J Comput Biol. 2017 Dec;24(12):1195-1211. doi: 10.1089/cmb.2017.0064. Epub 2017 Sep 11.


An efficient algorithm for pairwise local alignment of protein interaction networks.

Chen W, Schmidt M, Tian W, Samatova NF, Zhang S.

J Bioinform Comput Biol. 2015 Apr;13(2):1550003. doi: 10.1142/S0219720015500031. Epub 2014 Dec 5.


Complex biomarker discovery in neuroimaging data: Finding a needle in a haystack.

Atluri G, Padmanabhan K, Fang G, Steinbach M, Petrella JR, Lim K, Macdonald A 3rd, Samatova NF, Doraiswamy PM, Kumar V.

Neuroimage Clin. 2013 Aug 7;3:123-31. doi: 10.1016/j.nicl.2013.07.004. Review.


Global alignment of pairwise protein interaction networks for maximal common conserved patterns.

Tian W, Samatova NF.

Int J Genomics. 2013;2013:670623. doi: 10.1155/2013/670623. Epub 2013 Mar 27.


In-silico identification of phenotype-biased functional modules.

Padmanabhan K, Wilson K, Rocha AM, Wang K, Mihelcic JR, Samatova NF.

Proteome Sci. 2012 Jun 21;10 Suppl 1:S2. doi: 10.1186/1477-5956-10-S1-S2.


NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems.

Schmidt MC, Rocha AM, Padmanabhan K, Shpanskaya Y, Banfield J, Scott K, Mihelcic JR, Samatova NF.

PLoS Comput Biol. 2012;8(5):e1002490. doi: 10.1371/journal.pcbi.1002490. Epub 2012 May 10.


SPICE: discovery of phenotype-determining component interplays.

Chen Z, Padmanabhan K, Rocha AM, Shpanskaya Y, Mihelcic JR, Scott K, Samatova NF.

BMC Syst Biol. 2012 May 14;6:40. doi: 10.1186/1752-0509-6-40.


Functional annotation of hierarchical modularity.

Padmanabhan K, Wang K, Samatova NF.

PLoS One. 2012;7(4):e33744. doi: 10.1371/journal.pone.0033744. Epub 2012 Apr 4.


Efficient α, β-motif finder for identification of phenotype-related functional modules.

Schmidt MC, Rocha AM, Padmanabhan K, Chen Z, Scott K, Mihelcic JR, Samatova NF.

BMC Bioinformatics. 2011 Nov 11;12:440. doi: 10.1186/1471-2105-12-440.


DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules.

Hendrix W, Rocha AM, Padmanabhan K, Choudhary A, Scott K, Mihelcic JR, Samatova NF.

BMC Syst Biol. 2011 Oct 24;5:172. doi: 10.1186/1752-0509-5-172.


Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions.

Belnap CP, Pan C, Denef VJ, Samatova NF, Hettich RL, Banfield JF.

ISME J. 2011 Jul;5(7):1152-61. doi: 10.1038/ismej.2010.200. Epub 2011 Jan 13.


Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions.

Karpinets TV, Romine MF, Schmoyer DD, Kora GH, Syed MH, Leuze MR, Serres MH, Park BH, Samatova NF, Uberbacher EC.

Database (Oxford). 2010 Jul 6;2010:baq012. doi: 10.1093/database/baq012.


A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.

Pan C, Park BH, McDonald WH, Carey PA, Banfield JF, VerBerkmoes NC, Hettich RL, Samatova NF.

BMC Bioinformatics. 2010 Mar 5;11:118. doi: 10.1186/1471-2105-11-118.


Cultivation and quantitative proteomic analyses of acidophilic microbial communities.

Belnap CP, Pan C, VerBerkmoes NC, Power ME, Samatova NF, Carver RL, Hettich RL, Banfield JF.

ISME J. 2010 Apr;4(4):520-30. doi: 10.1038/ismej.2009.139. Epub 2009 Dec 24.


BioDEAL: community generation of biological annotations.

Breimyer P, Green N, Kumar V, Samatova NF.

BMC Med Inform Decis Mak. 2009 Nov 3;9 Suppl 1:S5. doi: 10.1186/1472-6947-9-S1-S5.


Improved genome annotation for Zymomonas mobilis.

Yang S, Pappas KM, Hauser LJ, Land ML, Chen GL, Hurst GB, Pan C, Kouvelis VN, Typas MA, Pelletier DA, Klingeman DM, Chang YJ, Samatova NF, Brown SD.

Nat Biotechnol. 2009 Oct;27(10):893-4. doi: 10.1038/nbt1009-893. No abstract available.


Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis.

Raman B, Pan C, Hurst GB, Rodriguez M Jr, McKeown CK, Lankford PK, Samatova NF, Mielenz JR.

PLoS One. 2009;4(4):e5271. doi: 10.1371/journal.pone.0005271. Epub 2009 Apr 22.


Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris.

Karpinets TV, Pelletier DA, Pan C, Uberbacher EC, Melnichenko GV, Hettich RL, Samatova NF.

PLoS One. 2009;4(2):e4615. doi: 10.1371/journal.pone.0004615. Epub 2009 Feb 26.


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