| Year |
Citation |
Score |
| 2012 |
Sartor MA, Ade A, Wright Z, States D, Omenn GS, Athey B, Karnovsky A. Metab2MeSH: Annotating compounds with medical subject headings Bioinformatics. 28: 1408-1410. PMID 22492643 DOI: 10.1093/Bioinformatics/Bts156 |
0.311 |
|
| 2011 |
Lee AW, Philips A, Do P, States DJ. Abstract 5119: Quantitative proteomics of myeloid cells reveal upregulation of the Fc receptor and integrin pathways in a mouse ovarian cancer model Cancer Research. 71: 5119-5119. DOI: 10.1158/1538-7445.Am2011-5119 |
0.577 |
|
| 2010 |
Rao A, States DJ, Hero AO, Engel JD. Understanding distal transcriptional regulation from sequence, expression and interactome perspectives. Journal of Bioinformatics and Computational Biology. 8: 219-46. PMID 20401945 DOI: 10.1142/S0219720010004756 |
0.451 |
|
| 2009 |
Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, ... ... States D, et al. Systematic comparison of the human saliva and plasma proteomes. Proteomics. Clinical Applications. 3: 116-134. PMID 19898684 DOI: 10.1002/Prca.200800140 |
0.307 |
|
| 2009 |
Chen Y, Lin G, Huo JS, Barney D, Wang Z, Livshiz T, States DJ, Qin ZS, Schwartz J. Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription. Endocrinology. 150: 3645-54. PMID 19406940 DOI: 10.1210/En.2009-0212 |
0.384 |
|
| 2009 |
Hur J, Schuyler AD, States DJ, Feldman EL. SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics (Oxford, England). 25: 838-40. PMID 19188191 DOI: 10.1093/Bioinformatics/Btp049 |
0.412 |
|
| 2009 |
Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Research. 69: 300-9. PMID 19118015 DOI: 10.1158/0008-5472.Can-08-2145 |
0.354 |
|
| 2009 |
Tarcea VG, Weymouth T, Ade A, Bookvich A, Gao J, Mahavisno V, Wright Z, Chapman A, Jayapandian M, Ozgür A, Tian Y, Cavalcoli J, Mirel B, Patel J, Radev D, ... ... States D, et al. Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Research. 37: D642-6. PMID 18978014 DOI: 10.1093/Nar/Gkn722 |
0.306 |
|
| 2009 |
Gao J, Ade AS, Tarcea VG, Weymouth TE, Mirel BR, Jagadish HV, States DJ. Integrating and annotating the interactome using the MiMI plugin for cytoscape. Bioinformatics (Oxford, England). 25: 137-8. PMID 18812364 DOI: 10.1093/Bioinformatics/Btn501 |
0.33 |
|
| 2008 |
Rao A, Hero AO, States DJ, Engel JD. Using directed information to build biologically relevant influence networks. Journal of Bioinformatics and Computational Biology. 6: 493-519. PMID 18574860 DOI: 10.1142/S0219720008003515 |
0.314 |
|
| 2008 |
Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, ... ... States DJ, et al. A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biology. 9: R93. PMID 18522751 DOI: 10.1186/Gb-2008-9-6-R93 |
0.3 |
|
| 2007 |
Rao A, Hero AO, States DJ, Engel JD. Motif discovery in tissue-specific regulatory sequences using directed information. Eurasip Journal On Bioinformatics & Systems Biology. 13853. PMID 18340376 DOI: 10.1155/2007/13853 |
0.445 |
|
| 2007 |
Rao A, Hero AO, States DJ, Engel JD. Inferring time-varying network topologies from gene expression data. Eurasip Journal On Bioinformatics & Systems Biology. 51947. PMID 18309363 DOI: 10.1155/2007/51947 |
0.314 |
|
| 2007 |
Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, Lee AW, States DJ. Evolutionary-conserved gene expression response profiles across mammalian tissues. Omics : a Journal of Integrative Biology. 11: 96-115. PMID 17411398 DOI: 10.1089/Omi.2006.0007 |
0.647 |
|
| 2007 |
Chen Y, Blackwell TW, Chen J, Gao J, Lee AW, States DJ. Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function. Plos Computational Biology. 3: e63. PMID 17411336 DOI: 10.1371/Journal.Pcbi.0030063 |
0.678 |
|
| 2007 |
Li X, Madison BB, Zacharias W, Kolterud A, States D, Gumucio DL. Deconvoluting the intestine: Molecular evidence for a major role of the mesenchyme in the modulation of signaling cross talk Physiological Genomics. 29: 290-301. PMID 17299133 DOI: 10.1152/Physiolgenomics.00269.2006 |
0.364 |
|
| 2007 |
MacDonald JJ, Lee AW, States DJ. Systematic Definition and Evolutionary Analsis of Macrophage Genes: Evidence for Novel Host Defense Genes. Blood. 110: 3856-3856. DOI: 10.1182/Blood.V110.11.3856.3856 |
0.657 |
|
| 2007 |
Lee AW, States DJ, Grifka H. Essential Role of Gab2 in CSF-1 Dependent Macrophage Development in the Bone Marrow. Blood. 110: 2197-2197. DOI: 10.1182/Blood.V110.11.2197.2197 |
0.574 |
|
| 2006 |
Carayol N, Chen J, Yang F, Jin T, Jin L, States D, Wang CY. A dominant function of IKK/NF-κB signaling in global lipopolysaccharide-induced gene expression Journal of Biological Chemistry. 281: 31142-31151. PMID 16914552 DOI: 10.1074/Jbc.M603417200 |
0.344 |
|
| 2006 |
Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biology. 7: R35. PMID 16646984 DOI: 10.1186/Gb-2006-7-4-R35 |
0.437 |
|
| 2006 |
States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nature Biotechnology. 24: 333-8. PMID 16525410 DOI: 10.1038/Nbt1183 |
0.33 |
|
| 2006 |
Huo JS, McEachin RC, Cui TX, Duggal NK, Hai T, States DJ, Schwartz J. Profiles of growth hormone (GH)-regulated genes reveal time-dependent responses and identify a mechanism for regulation of activating transcription factor 3 by GH. The Journal of Biological Chemistry. 281: 4132-41. PMID 16326703 DOI: 10.1074/Jbc.M508492200 |
0.381 |
|
| 2006 |
Chen Y, Blackwell TW, Gao J, Hewagama A, Grifka HM, Lee AW, States DJ. Computational Prediction of c-MYC Binding and Action by Integration of Multiple Data Sources. Blood. 108: 4345-4345. DOI: 10.1182/Blood.V108.11.4345.4345 |
0.668 |
|
| 2006 |
Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, States DJ. Identifying Novel Blood Proteins and Protein Isoforms Using Tandem Mass Spectra. Blood. 108: 1616-1616. DOI: 10.1182/Blood.V108.11.1616.1616 |
0.428 |
|
| 2005 |
Ping P, Vondriska TM, Creighton CJ, Gandhi TK, Yang Z, Menon R, Kwon MS, Cho SY, Drwal G, Kellmann M, Peri S, Suresh S, Gronborg M, Molina H, Chaerkady R, ... ... States DJ, et al. A functional annotation of subproteomes in human plasma. Proteomics. 5: 3506-19. PMID 16104058 DOI: 10.1002/Pmic.200500140 |
0.313 |
|
| 2005 |
Martens L, Hermjakob H, Jones P, Adamsk M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R. PRIDE: The proteomics identifications database Proteomics. 5: 3537-3545. PMID 16041671 DOI: 10.1002/Pmic.200401303 |
0.311 |
|
| 2004 |
States DJ, Adamski M, Menon R, Hanash S, Omenn GS. Pilot Phase Results of the Human Proteome Organization Plasma Proteome Project. Blood. 104: 220-220. DOI: 10.1182/Blood.V104.11.220.220 |
0.302 |
|
| 2003 |
Liu R, McEachin RC, States DJ. Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. Genome Research. 13: 654-61. PMID 12654722 DOI: 10.1101/Gr.911803 |
0.748 |
|
| 2002 |
Kan Z, States D, Gish W. Selecting for functional alternative splices in ESTs. Genome Research. 12: 1837-45. PMID 12466287 DOI: 10.1101/Gr.764102 |
0.608 |
|
| 2002 |
Rouchka EC, Gish W, States DJ. Comparison of whole genome assemblies of the human genome. Nucleic Acids Research. 30: 5004-14. PMID 12434005 DOI: 10.1093/Nar/Gkf633 |
0.59 |
|
| 2002 |
Liu R, States DJ. Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling. Genome Research. 12: 462-9. PMID 11875035 DOI: 10.1101/Gr.198002 |
0.764 |
|
| 2001 |
Liu R, Blackwell TW, States DJ. Conformational model for binding site recognition by the E.coli MetJ transcription factor. Bioinformatics (Oxford, England). 17: 622-33. PMID 11448880 DOI: 10.1093/Bioinformatics/17.7.622 |
0.746 |
|
| 2001 |
States DJ. Describing the release of sequence data. Science (New York, N.Y.). 292: 1066-7. PMID 11352052 DOI: 10.1126/Science.292.5519.1066 |
0.322 |
|
| 2001 |
Kan Z, Rouchka EC, Gish WR, States DJ. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Research. 11: 889-900. PMID 11337482 DOI: 10.1101/Gr.155001 |
0.72 |
|
| 2000 |
Kan Z, Gish W, Rouchka E, Glasscock J, States D. UTR reconstruction and analysis using genomically aligned EST sequences. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 218-27. PMID 10977083 |
0.573 |
|
| 2000 |
Lee AW, States DJ. Both src-dependent and -independent mechanisms mediate phosphatidylinositol 3-kinase regulation of colony-stimulating factor 1-activated mitogen-activated protein kinases in myeloid progenitors. Molecular and Cellular Biology. 20: 6779-98. PMID 10958675 DOI: 10.1128/Mcb.20.18.6779-6798.2000 |
0.566 |
|
| 1998 |
Rouchka EC, States DJ. Sequence assembly validation by multiple restriction digest fragment coverage analysis. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 6: 140-7. PMID 9783219 |
0.544 |
|
| 1998 |
Agarwal P, States DJ. Comparative accuracy of methods for protein sequence similarity search. Bioinformatics (Oxford, England). 14: 40-7. PMID 9520500 DOI: 10.1093/Bioinformatics/14.1.40 |
0.581 |
|
| 1996 |
Agarwal P, States DJ. A Bayesian evolutionary distance for parametrically aligned sequences. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 3: 1-17. PMID 8697232 DOI: 10.1089/Cmb.1996.3.1 |
0.539 |
|
| 1994 |
States DJ, Gish W. Combined use of sequence similarity and codon bias for coding region identification. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 1: 39-50. PMID 8790452 DOI: 10.1089/Cmb.1994.1.39 |
0.342 |
|
| 1993 |
Gish W, States DJ. Identification of protein coding regions by database similarity search. Nature Genetics. 3: 266-72. PMID 8485583 DOI: 10.1038/Ng0393-266 |
0.38 |
|
| 1993 |
Green P, Lipman D, Hillier L, Waterston R, States D, Claverie JM. Ancient conserved regions in new gene sequences and the protein databases Science. 259: 1711-1716. PMID 8456298 DOI: 10.1126/Science.8456298 |
0.445 |
|
| 1993 |
Claverie JM, States DJ. Information enhancement methods for large scale sequence analysis Computers and Chemistry. 17: 191-201. DOI: 10.1016/0097-8485(93)85010-A |
0.374 |
|
| 1992 |
States DJ. Molecular sequence accuracy: analysing imperfect data. Trends in Genetics : Tig. 8: 52-5. PMID 1566371 DOI: 10.1016/0168-9525(92)90349-9 |
0.342 |
|
| 1991 |
States DJ, Botstein D. Molecular sequence accuracy and the analysis of protein coding regions. Proceedings of the National Academy of Sciences of the United States of America. 88: 5518-22. PMID 2062834 DOI: 10.1073/Pnas.88.13.5518 |
0.327 |
|
| 1991 |
Stote R, States D, Karplus M. On the treatment of electrostatic interactions in biomolecular simulation Journal De Chimie Physique. 88: 2419-2433. DOI: 10.1063/1.41345 |
0.619 |
|
| 1991 |
States DJ, Gish W, Altschul SF. Improved sensitivity of nucleic acid database searches using application-specific scoring matrices Methods. 3: 66-70. DOI: 10.1016/S1046-2023(05)80165-3 |
0.324 |
|
| 1988 |
Takahashi H, Nukiwa T, Yoshimura K, Quick CD, States DJ, Holmes MD, Whang-Peng J, Knutsen T, Crystal RG. Structure of the human neutrophil elastase gene. The Journal of Biological Chemistry. 263: 14739-47. PMID 2902087 |
0.312 |
|
| 1987 |
Delepierre M, Dobson CM, Karplus M, Poulsen FM, States DJ, Wedin RE. Electrostatic effects and hydrogen exchange behaviour in proteins. The pH dependence of exchange rates in lysozyme. Journal of Molecular Biology. 197: 111-30. PMID 2824793 DOI: 10.1016/0022-2836(87)90613-9 |
0.442 |
|
| 1987 |
States DJ, Creighton TE, Dobson CM, Karplus M. Conformations of intermediates in the folding of the pancreatic trypsin inhibitor. Journal of Molecular Biology. 195: 731-9. PMID 2443711 DOI: 10.1016/0022-2836(87)90192-6 |
0.445 |
|
| 1987 |
States DJ, Karplus M. A model for electrostatic effects in proteins Journal of Molecular Biology. 197: 122-130. DOI: 10.1016/0022-2836(87)90614-0 |
0.332 |
|
| 1984 |
States DJ, Dobson CM, Karplus M. A new two-disulphide intermediate in the refolding of reduced bovine pancreatic trypsin inhibitor. Journal of Molecular Biology. 174: 411-8. PMID 6201619 DOI: 10.1016/0022-2836(84)90345-0 |
0.432 |
|
| 1983 |
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations Journal of Computational Chemistry. 4: 187-217. DOI: 10.1002/Jcc.540040211 |
0.501 |
|
| 1980 |
States DJ, Dobson CM, Karplus M, Creighton TE. A conformational isomer of bovine pancreatic trypsin inhibitor protein produced by refolding. Nature. 286: 630-2. PMID 7402343 DOI: 10.1038/286630A0 |
0.453 |
|
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