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For: Wu CH, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu ZZ, Ledley RS, Lewis KC, Mewes HW, Orcutt BC, Suzek BE, Tsugita A, Vinayaka CR, Yeh LSL, Zhang J, Barker WC. The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res 2002;30:35-7. [PMID: 11752247 PMCID: PMC99125 DOI: 10.1093/nar/30.1.35] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Meng Y, Zhang Z, Zhou C, Tang X, Hu X, Tian G, Yang J, Yao Y. Protein structure prediction via deep learning: an in-depth review. Front Pharmacol 2025;16:1498662. [PMID: 40248099 PMCID: PMC12003282 DOI: 10.3389/fphar.2025.1498662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 02/28/2025] [Indexed: 04/19/2025]  Open
2
Islamaj R, Wei CH, Lai PT, Huston M, Coss C, Kochar PG, Miliaras N, Mork JG, Rodionov O, Sekiya K, Trinh D, Whitman D, Wallin C, Lu Z. Assessing Artificial Intelligence (AI) Implementation for Assisting Gene Linking (at the National Library of Medicine). JAMIA Open 2025;8:ooae129. [PMID: 39776621 PMCID: PMC11706533 DOI: 10.1093/jamiaopen/ooae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 10/18/2024] [Accepted: 11/16/2024] [Indexed: 01/11/2025]  Open
3
Iyyappan Y, Dhayabaran V, Elayappan M, Chaudhary SK, Palaniappan C, Kanagaraj S. Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus. Proteins 2023;91:1427-1436. [PMID: 37254593 DOI: 10.1002/prot.26530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/06/2023] [Accepted: 04/19/2023] [Indexed: 06/01/2023]
4
Pan G, Sun C, Liao Z, Tang J. Machine and Deep Learning for Prediction of Subcellular Localization. Methods Mol Biol 2022;2361:249-261. [PMID: 34236666 DOI: 10.1007/978-1-0716-1641-3_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
5
Widowati W, Handono K, Marlina M, Sholihah IA, Jasaputra DK, Wargasetia TL, Subangkit M, Faried A, Girsang E, Lister IN, Ginting CN, Nainggolan IM, Rizal R, Kusuma H, Chiuman L. In Silico Approach for Pro-inflammatory Protein Interleukin 1β and Interleukin-1 Receptor Antagonist Protein Docking as Potential Therapy for COVID-19 Disease. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.7405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]  Open
6
Shrestha R, Fajardo E, Gil N, Fidelis K, Kryshtafovych A, Monastyrskyy B, Fiser A. Assessing the accuracy of contact predictions in CASP13. Proteins 2019;87:1058-1068. [PMID: 31587357 PMCID: PMC6851495 DOI: 10.1002/prot.25819] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 01/07/2023]
7
Saidi R, Boudellioua I, Martin MJ, Solovyev V. Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways. Methods Mol Biol 2017;1613:311-331. [PMID: 28849566 DOI: 10.1007/978-1-4939-7027-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
8
Singhal A, Leaman R, Catlett N, Lemberger T, McEntyre J, Polson S, Xenarios I, Arighi C, Lu Z. Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. Database (Oxford) 2016;2016:baw161. [PMID: 28025348 PMCID: PMC5199160 DOI: 10.1093/database/baw161] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 12/24/2022]
9
Boudellioua I, Saidi R, Hoehndorf R, Martin MJ, Solovyev V. Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining. PLoS One 2016;11:e0158896. [PMID: 27390860 PMCID: PMC4938425 DOI: 10.1371/journal.pone.0158896] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/23/2016] [Indexed: 11/21/2022]  Open
10
Pullan ST, Allnutt JC, Devine R, Hatch KA, Jeeves RE, Hendon-Dunn CL, Marsh PD, Bacon J. The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity? BMC Infect Dis 2016;16:205. [PMID: 27184366 PMCID: PMC4869200 DOI: 10.1186/s12879-016-1533-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/29/2016] [Indexed: 11/24/2022]  Open
11
Wu TJ, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014;2014:bau022. [PMID: 24667251 PMCID: PMC3965850 DOI: 10.1093/database/bau022] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
12
Mavridis L, Nath N, Mitchell JBO. PFClust: a novel parameter free clustering algorithm. BMC Bioinformatics 2013;14:213. [PMID: 23819480 PMCID: PMC3747858 DOI: 10.1186/1471-2105-14-213] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 07/01/2013] [Indexed: 12/02/2022]  Open
13
Garaguso I, Borlak J. A rapid screening assay to search for phosphorylated proteins in tissue extracts. PLoS One 2012;7:e50025. [PMID: 23166814 PMCID: PMC3499474 DOI: 10.1371/journal.pone.0050025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/19/2012] [Indexed: 11/19/2022]  Open
14
Vollan HS, Tannaes T, Yamaoka Y, Bukholm G. In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA). BMC Microbiol 2012;12:206. [PMID: 22974200 PMCID: PMC3490997 DOI: 10.1186/1471-2180-12-206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 08/31/2012] [Indexed: 01/19/2023]  Open
15
Brown AM, Zondlo NJ. A propensity scale for type II polyproline helices (PPII): aromatic amino acids in proline-rich sequences strongly disfavor PPII due to proline-aromatic interactions. Biochemistry 2012;51:5041-51. [PMID: 22667692 DOI: 10.1021/bi3002924] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
16
Tebaldi T, Re A, Viero G, Pegoretti I, Passerini A, Blanzieri E, Quattrone A. Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. BMC Genomics 2012;13:220. [PMID: 22672192 PMCID: PMC3441405 DOI: 10.1186/1471-2164-13-220] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/06/2012] [Indexed: 11/10/2022]  Open
17
Yu GX. RULEMINER: A KNOWLEDGE SYSTEM FOR SUPPORTING HIGH-THROUGHPUT PROTEIN FUNCTION ANNOTATIONS. J Bioinform Comput Biol 2011;2:615-37. [PMID: 15617156 DOI: 10.1142/s0219720004000752] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Revised: 03/23/2004] [Accepted: 03/24/2004] [Indexed: 11/18/2022]
18
Madhavan S, Gusev Y, Harris M, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet LA, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, Weiner LM. G-DOC: a systems medicine platform for personalized oncology. Neoplasia 2011;13:771-83. [PMID: 21969811 PMCID: PMC3182270 DOI: 10.1593/neo.11806] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/28/2011] [Accepted: 08/01/2011] [Indexed: 01/05/2023]
19
Cueva JP, Gallardo-Godoy A, Juncosa JI, Vidi PA, Lill MA, Watts VJ, Nichols DE. Probing the steric space at the floor of the D1 dopamine receptor orthosteric binding domain: 7α-, 7β-, 8α-, and 8β-methyl substituted dihydrexidine analogues. J Med Chem 2011;54:5508-21. [PMID: 21714510 PMCID: PMC3150624 DOI: 10.1021/jm200334c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
20
Bonner LA, Laban U, Chemel BR, Juncosa JI, Lill MA, Watts VJ, Nichols DE. Mapping the catechol binding site in dopamine D₁ receptors: synthesis and evaluation of two parallel series of bicyclic dopamine analogues. ChemMedChem 2011;6:1024-40. [PMID: 21538900 DOI: 10.1002/cmdc.201100010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/19/2011] [Indexed: 11/08/2022]
21
Hung CL, Lee C, Lin CY, Chang CH, Chung YC, Yi Tang C. Feature amplified voting algorithm for functional analysis of protein superfamily. BMC Genomics 2010;11 Suppl 3:S14. [PMID: 21143781 PMCID: PMC2999344 DOI: 10.1186/1471-2164-11-s3-s14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
22
Capone G, Novello G, Fasano C, Trost B, Bickis M, Kusalik A, Kanduc D. The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand. BMC Bioinformatics 2010;11:383. [PMID: 20646284 PMCID: PMC2919516 DOI: 10.1186/1471-2105-11-383] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 07/20/2010] [Indexed: 11/10/2022]  Open
23
Greaves LC, Barron MJ, Plusa S, Kirkwood TB, Mathers JC, Taylor RW, Turnbull DM. Defects in multiple complexes of the respiratory chain are present in ageing human colonic crypts. Exp Gerontol 2010;45:573-9. [PMID: 20096767 PMCID: PMC2887930 DOI: 10.1016/j.exger.2010.01.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/12/2010] [Accepted: 01/14/2010] [Indexed: 01/21/2023]
24
Kimura A, Tyacke RJ, Robinson JJ, Husbands SM, Minchin MC, Nutt DJ, Hudson AL. Identification of an imidazoline binding protein: creatine kinase and an imidazoline-2 binding site. Brain Res 2009;1279:21-8. [PMID: 19410564 PMCID: PMC2722693 DOI: 10.1016/j.brainres.2009.04.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2009] [Revised: 03/28/2009] [Accepted: 04/22/2009] [Indexed: 12/11/2022]
25
Lucchese A, Serpico R, Crincoli V, Shoenfeld Y, Kanduc D. Sequence Uniqueness as a Molecular Signature of HIV-1-Derived B-Cell Epitopes. Int J Immunopathol Pharmacol 2009;22:639-46. [DOI: 10.1177/039463200902200309] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
26
Song CM, Lim SJ, Tong JC. Recent advances in computer-aided drug design. Brief Bioinform 2009;10:579-91. [PMID: 19433475 DOI: 10.1093/bib/bbp023] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
27
Stufano A, Kanduc D. Proteome-based epitopic peptide scanning along PSA. Exp Mol Pathol 2009;86:36-40. [DOI: 10.1016/j.yexmp.2008.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 11/26/2008] [Indexed: 12/18/2022]
28
Peng Y, Reyes JL, Wei H, Yang Y, Karlson D, Covarrubias AA, Krebs SL, Fessehaie A, Arora R. RcDhn5, a cold acclimation-responsive dehydrin from Rhododendron catawbiense rescues enzyme activity from dehydration effects in vitro and enhances freezing tolerance in RcDhn5-overexpressing Arabidopsis plants. PHYSIOLOGIA PLANTARUM 2008;134:583-97. [PMID: 19000195 DOI: 10.1111/j.1399-3054.2008.01164.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
29
Chiang HI, Swaggerty CL, Kogut MH, Dowd SE, Li X, Pevzner IY, Zhou H. Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44 K Agilent microarray. BMC Genomics 2008;9:526. [PMID: 18990222 PMCID: PMC2588606 DOI: 10.1186/1471-2164-9-526] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 11/06/2008] [Indexed: 06/04/2025]  Open
30
Dai Q, Wang T. Comparison study on k-word statistical measures for protein: from sequence to 'sequence space'. BMC Bioinformatics 2008;9:394. [PMID: 18811946 PMCID: PMC2571980 DOI: 10.1186/1471-2105-9-394] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 09/23/2008] [Indexed: 11/30/2022]  Open
31
Dowd SE, Killinger-Mann K, Brashears M, Fralick J. Evaluation of gene expression in a single antibiotic exposure-derived isolate of Salmonella enterica typhimurium 14028 possessing resistance to multiple antibiotics. Foodborne Pathog Dis 2008;5:205-21. [PMID: 18407759 DOI: 10.1089/fpd.2007.0062] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
32
Kojetin DJ, Sullivan DM, Thompson RJ, Cavanagh J. Classification of response regulators based on their surface properties. Methods Enzymol 2008;422:141-69. [PMID: 17628138 DOI: 10.1016/s0076-6879(06)22007-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
33
Ladunga I. Finding homologs in amino acid sequences using network BLAST searches. CURRENT PROTOCOLS IN BIOINFORMATICS 2008;Chapter 3:Unit 3.4. [PMID: 18428697 DOI: 10.1002/0471250953.bi0304s00] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
34
Sulakhe D, Rodriguez A, Wilde M, Foster I, Maltsev N. Interoperability of GADU in Using Heterogeneous Grid Resources for Bioinformatics Applications. ACTA ACUST UNITED AC 2008;12:241-6. [DOI: 10.1109/titb.2007.897783] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
35
Parrish JR, Yu J, Liu G, Hines JA, Chan JE, Mangiola BA, Zhang H, Pacifico S, Fotouhi F, DiRita VJ, Ideker T, Andrews P, Finley RL. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol 2008;8:R130. [PMID: 17615063 PMCID: PMC2323224 DOI: 10.1186/gb-2007-8-7-r130] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 05/14/2007] [Accepted: 07/05/2007] [Indexed: 11/12/2022]  Open
36
Correlating low-similarity peptide sequences and HIV B-cell epitopes. Autoimmun Rev 2008;7:291-6. [DOI: 10.1016/j.autrev.2007.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 11/06/2007] [Indexed: 11/20/2022]
37
Li X, Chiang HI, Zhu J, Dowd SE, Zhou H. Characterization of a newly developed chicken 44K Agilent microarray. BMC Genomics 2008;9:60. [PMID: 18237426 PMCID: PMC2262898 DOI: 10.1186/1471-2164-9-60] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 01/31/2008] [Indexed: 12/05/2022]  Open
38
Baerson SR, Dayan FE, Rimando AM, Nanayakkara NPD, Liu CJ, Schröder J, Fishbein M, Pan Z, Kagan IA, Pratt LH, Cordonnier-Pratt MM, Duke SO. A functional genomics investigation of allelochemical biosynthesis in Sorghum bicolor root hairs. J Biol Chem 2007;283:3231-3247. [PMID: 17998204 DOI: 10.1074/jbc.m706587200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
39
Dowd SE, Killinger-Mann K, Blanton J, San Francisco M, Brashears M. Positive adaptive state: microarray evaluation of gene expression in Salmonella enterica Typhimurium exposed to nalidixic acid. Foodborne Pathog Dis 2007;4:187-200. [PMID: 17600486 DOI: 10.1089/fpd.2006.0075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
40
Ferrè F, Ponty Y, Lorenz WA, Clote P. DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res 2007;35:W659-68. [PMID: 17567620 PMCID: PMC1933154 DOI: 10.1093/nar/gkm334] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]  Open
41
Biro JC, Biro JMK. The BlastNP: a novel, sensitive sequence similarity searching method using overlappingly translated sequences. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2007;2004:2777-80. [PMID: 17270853 DOI: 10.1109/iembs.2004.1403794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
42
Polimeno L, Mittelman A, Gennero L, Ponzetto A, Lucchese G, Stufano A, Kusalik A, Kanduc D. Sub-epitopic dissection of HCV E1315-328HRMAWDMMMNWSPT sequence by similarity analysis. Amino Acids 2007;34:479-84. [PMID: 17458624 DOI: 10.1007/s00726-007-0539-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 02/23/2007] [Indexed: 11/24/2022]
43
Evans EE, Henn AD, Jonason A, Paris MJ, Schiffhauer LM, Borrello MA, Smith ES, Sahasrabudhe DM, Zauderer M. C35 (C17orf37) is a novel tumor biomarker abundantly expressed in breast cancer. Mol Cancer Ther 2007;5:2919-30. [PMID: 17121940 DOI: 10.1158/1535-7163.mct-06-0389] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chen Y, Reilly KD, Sprague AP, Guan Z. SEQOPTICS: a protein sequence clustering system. BMC Bioinformatics 2006;7 Suppl 4:S10. [PMID: 17217502 PMCID: PMC1780130 DOI: 10.1186/1471-2105-7-s4-s10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
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Zhang W, Culley DE, Gritsenko MA, Moore RJ, Nie L, Scholten JCM, Petritis K, Strittmatter EF, Camp DG, Smith RD, Brockman FJ. LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris. Biochem Biophys Res Commun 2006;349:1412-9. [PMID: 16982031 DOI: 10.1016/j.bbrc.2006.09.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 09/07/2006] [Indexed: 11/26/2022]
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Lucchese A, Mittelman A, Tessitore L, Serpico R, Sinha AA, Kanduc D. Proteomic definition of a desmoglein linear determinant common to Pemphigus vulgaris and Pemphigus foliaceous. J Transl Med 2006;4:37. [PMID: 16925820 PMCID: PMC1590053 DOI: 10.1186/1479-5876-4-37] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 08/22/2006] [Indexed: 11/25/2022]  Open
47
Sulakhe D, Rodriguez A, D'Souza M, Wilde M, Nefedova V, Foster I, Maltsev N. GNARE: automated system for high-throughput genome analysis with grid computational backend. J Clin Monit Comput 2006;19:361-9. [PMID: 16328950 DOI: 10.1007/s10877-005-3463-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Accepted: 06/30/2005] [Indexed: 10/25/2022]
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Güldener U, Münsterkötter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stümpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res 2006;34:D436-41. [PMID: 16381906 PMCID: PMC1347366 DOI: 10.1093/nar/gkj003] [Citation(s) in RCA: 234] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
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Hazai E, Visy J, Fitos I, Bikádi Z, Simonyi M. Selective binding of coumarin enantiomers to human alpha1-acid glycoprotein genetic variants. Bioorg Med Chem 2005;14:1959-65. [PMID: 16290938 DOI: 10.1016/j.bmc.2005.10.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 10/19/2005] [Accepted: 10/25/2005] [Indexed: 11/23/2022]
50
Lucchese A, Willers J, Mittelman A, Kanduc D, Dummer R. Proteomic Scan for Tyrosinase Peptide Antigenic Pattern in Vitiligo and Melanoma: Role of Sequence Similarity and HLA-DR1 Affinity. THE JOURNAL OF IMMUNOLOGY 2005;175:7009-20. [PMID: 16272362 DOI: 10.4049/jimmunol.175.10.7009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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