| Year |
Citation |
Score |
| 2014 |
Mariotti M, Smith TF, Sudmant PH, Goldberger G. Pseudogenization of testis-specific Lfg5 predates human/Neanderthal divergence. Journal of Human Genetics. 59: 288-91. PMID 24599118 DOI: 10.1038/Jhg.2014.6 |
0.67 |
|
| 2012 |
Schneider S, Smith T, Hansen U. SCOREM: statistical consolidation of redundant expression measures. Nucleic Acids Research. 40: e46. PMID 22210887 DOI: 10.1093/Nar/Gkr1270 |
0.581 |
|
| 2010 |
Cui J, Das S, Smith TF, Samuelson J. Trichomonas transmembrane cyclases result from massive gene duplication and concomitant development of pseudogenes. Plos Neglected Tropical Diseases. 4: e782. PMID 20689771 DOI: 10.1371/Journal.Pntd.0000782 |
0.385 |
|
| 2010 |
Reznik GO, Vishwanath P, Pynn MA, Sitnik JM, Todd JJ, Wu J, Jiang Y, Keenan BG, Castle AB, Haskell RF, Smith TF, Somasundaran P, Jarrell KA. Use of sustainable chemistry to produce an acyl amino acid surfactant. Applied Microbiology and Biotechnology. 86: 1387-97. PMID 20094712 DOI: 10.1007/S00253-009-2431-8 |
0.583 |
|
| 2008 |
Smith TF. Diversity of WD-repeat proteins. Sub-Cellular Biochemistry. 48: 20-30. PMID 18925368 DOI: 10.1007/978-0-387-09595-0_3 |
0.316 |
|
| 2008 |
Schaeffer SW, Bhutkar A, McAllister BF, Matsuda M, Matzkin LM, O'Grady PM, Rohde C, Valente VL, Aguadé M, Anderson WW, Edwards K, Garcia AC, Goodman J, Hartigan J, Kataoka E, ... ... Smith TF, et al. Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. Genetics. 179: 1601-55. PMID 18622037 DOI: 10.1534/Genetics.107.086074 |
0.625 |
|
| 2008 |
Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM. Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes. Genetics. 179: 1657-80. PMID 18622036 DOI: 10.1534/Genetics.107.086108 |
0.654 |
|
| 2007 |
Cui J, Smith TF, Samuelson J. Gene expansion in Trichomonas vaginalis: a case study on transmembrane cyclases. Genome Informatics. International Conference On Genome Informatics. 18: 35-43. PMID 18546472 DOI: 10.11234/Gi1990.18.35 |
0.4 |
|
| 2007 |
Bhutkar A, Gelbart WM, Smith TF. Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study. Genome Biology. 8: R236. PMID 17996033 DOI: 10.1186/Gb-2007-8-11-R236 |
0.627 |
|
| 2007 |
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Smith TF, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.776 |
|
| 2007 |
Bhutkar A, Russo SM, Smith TF, Gelbart WM. Genome-scale analysis of positionally relocated genes. Genome Research. 17: 1880-7. PMID 17989252 DOI: 10.1101/Gr.7062307 |
0.644 |
|
| 2007 |
Hu L, Segrè D, Smith TF. Evolutionary changes in gene regulation from a comparative analysis of multiple Drosophila species. Genome Informatics. 18: 12-21. DOI: 10.11234/Gi1990.18.12 |
0.343 |
|
| 2006 |
Bhutkar A, Russo S, Smith TF, Gelbart WM. Techniques for multi-genome synteny analysis to overcome assembly limitations. Genome Informatics. International Conference On Genome Informatics. 17: 152-61. PMID 17503388 DOI: 10.11234/Gi1990.17.2_152 |
0.671 |
|
| 2006 |
Hartman H, Favaretto P, Smith TF. The archaeal origins of the eukaryotic translational system. Archaea (Vancouver, B.C.). 2: 1-9. PMID 16877317 DOI: 10.1155/2006/431618 |
0.786 |
|
| 2006 |
Wang K, Vishwanath P, Eichler GS, Al-Sebaei MO, Edgar CM, Einhorn TA, Smith TF, Gerstenfeld LC. Analysis of fracture healing by large-scale transcriptional profile identified temporal relationships between metalloproteinase and ADAMTS mRNA expression. Matrix Biology : Journal of the International Society For Matrix Biology. 25: 271-81. PMID 16584876 DOI: 10.1016/J.Matbio.2006.02.001 |
0.589 |
|
| 2006 |
Wang Y, Berg EA, Feng X, Shen L, Smith T, Costello CE, Zhang YX. Identification of surface-exposed components of MOMP of Chlamydia trachomatis serovar F Protein Science. 15: 122-134. PMID 16322562 DOI: 10.1110/Ps.051616206 |
0.311 |
|
| 2005 |
Favaretto P, Bhutkar A, Smith TF. Constraining ribosomal RNA conformational space. Nucleic Acids Research. 33: 5106-11. PMID 16155182 DOI: 10.1093/Nar/Gki805 |
0.775 |
|
| 2004 |
Vishwanath P, Favaretto P, Hartman H, Mohr SC, Smith TF. Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes. Molecular Phylogenetics and Evolution. 33: 615-25. PMID 15522791 DOI: 10.1016/J.Ympev.2004.07.003 |
0.79 |
|
| 2003 |
Bienkowska JR, Hartman H, Smith TF. A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells? Protein Engineering. 16: 897-904. PMID 14983069 DOI: 10.1093/Protein/Gzg130 |
0.498 |
|
| 2003 |
Venkatesan K, McManus HR, Mello CC, Smith TF, Hansen U. Functional conservation between members of an ancient duplicated transcription factor family, LSF/Grainyhead. Nucleic Acids Research. 31: 4304-16. PMID 12888489 DOI: 10.1093/Nar/Gkg644 |
0.555 |
|
| 2002 |
He H, McAllister G, Smith TF. Triage protein fold prediction. Proteins. 48: 654-63. PMID 12211033 DOI: 10.1002/Prot.10194 |
0.591 |
|
| 2002 |
Graber JH, McAllister GD, Smith TF. Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites. Nucleic Acids Research. 30: 1851-8. PMID 11937640 DOI: 10.1093/Nar/30.8.1851 |
0.304 |
|
| 2001 |
Plasterer TN, Smith TF, Mohr SC. Survey of human mitochondrial diseases using new genomic/proteomic tools. Genome Biology. 2: RESEARCH0021. PMID 11423010 DOI: 10.1186/Gb-2001-2-6-Research0021 |
0.753 |
|
| 2001 |
Moreno-Hagelsieb G, Treviño V, Pérez-Rueda E, Smith TF, Collado-Vides J. Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends in Genetics : Tig. 17: 175-7. PMID 11275307 DOI: 10.1016/S0168-9525(01)02241-7 |
0.346 |
|
| 2001 |
Hisbergues M, Gaitatzes CG, Joset F, Bedu S, Smith TF. A noncanonical WD-repeat protein from the cyanobacterium Synechocystis PCC6803: structural and functional study. Protein Science : a Publication of the Protein Society. 10: 293-300. PMID 11266615 DOI: 10.1110/Ps.22701 |
0.79 |
|
| 2000 |
Yu L, Gaitatzes C, Neer E, Smith TF. Thirty-plus functional families from a single motif. Protein Science : a Publication of the Protein Society. 9: 2470-6. PMID 11206068 DOI: 10.1110/Ps.9.12.2470 |
0.811 |
|
| 2000 |
Nagl SB, Das S, Smith TF. Prediction of interaction partners for orphan nuclear receptors by prior-based protein sequence profiles. Journal of Molecular Recognition. 13: 117-126. PMID 10867707 DOI: 10.1002/1099-1352(200005/06)13:3<117::Aid-Jmr494>3.0.Co;2-D |
0.347 |
|
| 2000 |
Bienkowska JR, Yu L, Zarakhovich S, Rogers RG, Smith TF. Protein fold recognition by total alignment probability Proteins. 40: 451-462. PMID 10861936 DOI: 10.1002/1097-0134(20000815)40:3<451::Aid-Prot110>3.0.Co;2-J |
0.44 |
|
| 2000 |
Cosenza L, Rosenbach A, White JV, Murphy JR, Smith T. Comparative model building of interleukin-7 using interleukin-4 as a template: a structural hypothesis that displays atypical surface chemistry in helix D important for receptor activation. Protein Science : a Publication of the Protein Society. 9: 916-26. PMID 10850801 DOI: 10.1110/Ps.9.5.916 |
0.316 |
|
| 2000 |
Das S, Smith TF. Identifying nature's protein lego set Advances in Protein Chemistry. 54: 159-183. PMID 10829228 DOI: 10.1016/S0065-3233(00)54006-6 |
0.356 |
|
| 2000 |
Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J. Operons in Escherichia coli: genomic analyses and predictions. Proceedings of the National Academy of Sciences of the United States of America. 97: 6652-6657. PMID 10823905 DOI: 10.1073/Pnas.110147297 |
0.349 |
|
| 1999 |
Mohr S, Freeman J, Plasterer T, Smith T. Patterns of Mitochondrial DNA Strand Asymmetry Correlate With Phylogeny. The Biological Bulletin. 196: 411-412. PMID 28296485 DOI: 10.2307/1542983 |
0.75 |
|
| 1999 |
Bienkowska JR, Rogers RG, Smith TF. Filtered neighbors threading. Proteins. 37: 346-359. PMID 10591096 DOI: 10.1002/(Sici)1097-0134(19991115)37:3<346::Aid-Prot4>3.0.Co;2-1 |
0.37 |
|
| 1999 |
Bieńkowska JR, Rogers RG, Smith TF. Performance of threading scoring functions designed using new optimization method. Journal of Computational Biology. 6: 299-311. PMID 10582568 DOI: 10.1089/106652799318283 |
0.304 |
|
| 1999 |
Graber JH, Cantor CR, Mohr SC, Smith TF. In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species. Proceedings of the National Academy of Sciences of the United States of America. 96: 14055-60. PMID 10570197 DOI: 10.1073/Pnas.96.24.14055 |
0.314 |
|
| 1999 |
Yu L, Smith TF. Positional statistical significance in sequence alignment. Journal of Computational Biology. 6: 253-259. PMID 10421526 DOI: 10.1089/Cmb.1999.6.253 |
0.353 |
|
| 1999 |
Smith TF. The art of matchmaking: Sequence alignment methods and their structural implications Structure. 7. PMID 10368278 DOI: 10.1016/S0969-2126(99)80003-3 |
0.32 |
|
| 1999 |
Smith TF, Gaitatzes C, Saxena K, Neer EJ. The WD repeat: a common architecture for diverse functions. Trends in Biochemical Sciences. 24: 181-5. PMID 10322433 DOI: 10.1016/S0968-0004(99)01384-5 |
0.793 |
|
| 1999 |
Graber JH, Cantor CR, Mohr SC, Smith TF. Genomic detection of new yeast pre-mRNA 3'-end-processing signals. Nucleic Acids Research. 27: 888-94. PMID 9889288 DOI: 10.1093/Nar/27.3.888 |
0.335 |
|
| 1998 |
Yu L, White JV, Smith TF. A homology identification method that combines protein sequence and structure information. Protein Science : a Publication of the Protein Society. 7: 2499-510. PMID 9865944 DOI: 10.1002/Pro.5560071203 |
0.437 |
|
| 1998 |
Maalouf GJ, Xu W, Smith TF, Mohr SC. Homology model for the ligand-binding domain of the human estrogen receptor. Journal of Biomolecular Structure & Dynamics. 15: 841-51. PMID 9619507 DOI: 10.1080/07391102.1998.10508206 |
0.306 |
|
| 1998 |
Garcia-Higuera I, Gaitatzes C, Smith TF, Neer EJ. Folding a WD repeat propeller. Role of highly conserved aspartic acid residues in the G protein beta subunit and Sec13. The Journal of Biological Chemistry. 273: 9041-9. PMID 9535892 DOI: 10.1074/jbc.273.15.9041 |
0.792 |
|
| 1998 |
Lathrop RH, Rogers RG, Bienkowska J, Bryant BKM, Buturović LJ, Gaitatzes C, Nambudripad R, White JV, Smith TF. Chapter 12 Analysis and algorithms for protein sequence-structure alignment New Comprehensive Biochemistry. 32: 227-283. DOI: 10.1016/S0167-7306(08)60469-X |
0.803 |
|
| 1998 |
Lathrop RH, Rogers RG, Smith TF, White JV. A Bayes-optimal Sequence-structure Theory that Unifies Protein Sequence-structure Recognition and Alignment Bulletin of Mathematical Biology. 60: 1039-1071. DOI: 10.1016/S0092-8240(98)90002-7 |
0.399 |
|
| 1997 |
Conte LL, Smith TF. Visible volume: A robust measure for protein structure characterization Journal of Molecular Biology. 273: 338-348. PMID 9367766 DOI: 10.1006/Jmbi.1997.1298 |
0.436 |
|
| 1997 |
Smith TF, Zhang X. The challenges of genome sequence annotation or "the devil is in the details" Nature Biotechnology. 15: 1222-1223. PMID 9359093 DOI: 10.1038/Nbt1197-1222 |
0.362 |
|
| 1997 |
Smith TF. Current limitations to protein threading approaches Journal of Computational Biology. 4: 217-225. PMID 9278056 DOI: 10.1089/Cmb.1997.4.217 |
0.342 |
|
| 1997 |
Das S, Yu L, Gaitatzes C, Rogers R, Freeman J, Bienkowska J, Adams RM, Smith TF, Lindelien J. Biology's new Rosetta stone. Nature. 385: 29-30. PMID 8985242 DOI: 10.1038/385029A0 |
0.733 |
|
| 1996 |
Saxena K, Gaitatzes C, Walsh MT, Eck M, Neer EJ, Smith TF. Analysis of the physical properties and molecular modeling of Sec13: A WD repeat protein involved in vesicular traffic. Biochemistry. 35: 15215-21. PMID 8952469 DOI: 10.1021/Bi961616X |
0.787 |
|
| 1996 |
Garcia-Higuera I, Fenoglio J, Li Y, Lewis C, Panchenko MP, Reiner O, Smith TF, Neer EJ. Folding of proteins with WD-repeats: comparison of six members of the WD-repeat superfamily to the G protein beta subunit. Biochemistry. 35: 13985-94. PMID 8909296 DOI: 10.1021/Bi9612879 |
0.419 |
|
| 1996 |
Guigo R, Muchnik I, Smith TF. Reconstruction of Ancient Molecular Phylogeny Molecular Phylogenetics and Evolution. 6: 189-213. PMID 8899723 DOI: 10.1006/Mpev.1996.0071 |
0.356 |
|
| 1996 |
Adams RM, Das S, Smith TF. Multiple domain protein diagnostic patterns. Protein Science : a Publication of the Protein Society. 5: 1240-9. PMID 8819157 DOI: 10.1002/Pro.5560050703 |
0.377 |
|
| 1996 |
Lathrop RH, Smith TF. Global optimum protein threading with gapped alignment and empirical pair score functions Journal of Molecular Biology. 255: 641-665. PMID 8568903 DOI: 10.1006/Jmbi.1996.0053 |
0.425 |
|
| 1996 |
Neer EJ, Smith TF. G protein heterodimers: New structures propel new questions Cell. 84: 175-178. PMID 8565060 DOI: 10.1016/S0092-8674(00)80969-1 |
0.359 |
|
| 1995 |
Mirkin BG, Muchnik IB, Smith TF. A Biologically Consistent Model for Comparing Molecular Phylogenies Journal of Computational Biology. 2: 493-507. PMID 8634901 DOI: 10.1089/Cmb.1995.2.493 |
0.319 |
|
| 1994 |
White JV, Stultz CM, Smith TF. Protein classification by stochastic modeling and optimal filtering of amino-acid sequences Mathematical Biosciences. 119: 35-75. PMID 8111135 DOI: 10.1016/0025-5564(94)90004-3 |
0.423 |
|
| 1994 |
Neer EJ, Schmidt CJ, Nambudripad R, Smith TF. The ancient regulatory-protein family of WD-repeat proteins Nature. 371: 297-300. PMID 8090199 DOI: 10.1038/371297A0 |
0.418 |
|
| 1994 |
White JV, Muchnik I, Smith TF. Modeling protein cores with Markov random fields. Mathematical Biosciences. 124: 149-79. PMID 7833593 DOI: 10.1016/0025-5564(94)90041-8 |
0.449 |
|
| 1994 |
Neer EJ, Schmidt CJ, Nambudripad R, Smith TF. Erratum: The ancient regulatory-protein family of WD-repeat proteins Nature. 371: 812-812. DOI: 10.1038/371812B0 |
0.391 |
|
| 1994 |
Buturovic LJ, Smith TF, Vajda S. Finite-state and reduced-parameter representations of protein backbone conformations Journal of Computational Chemistry. 15: 300-312. DOI: 10.1002/Jcc.540150305 |
0.347 |
|
| 1993 |
Rao S, Zhu QL, Vajda S, Smith T. The local information content of the protein structural database Febs Letters. 322: 143-146. PMID 8482381 DOI: 10.1016/0014-5793(93)81555-E |
0.408 |
|
| 1993 |
Stultz CM, White JV, Smith TF. Structural analysis based on state-space modeling Protein Science. 2: 305-314. PMID 8453370 DOI: 10.1002/Pro.5560020302 |
0.426 |
|
| 1993 |
Figge J, Breese K, Vajda S, Zhu QL, Eisele L, Andersen TT, MacColl R, Friedrich T, Smith TF. The binding domain structure of retinoblastoma-binding proteins Protein Science. 2: 155-164. PMID 8382993 DOI: 10.1002/Pro.5560020204 |
0.365 |
|
| 1993 |
Kister A, Muchnik I, Bouzida D, Reinherz EL, Smith T. Efficient pattern comparative method for selecting functionally important motifs in protein sequences: Application to zinc enzymes Biosystems. 30: 233-240. PMID 8374078 DOI: 10.1016/0303-2647(93)90073-L |
0.421 |
|
| 1993 |
Lawler J, Duquette M, Urry L, McHenry K, Smith TF. The evolution of the thrombospondin gene family Journal of Molecular Evolution. 36: 509-516. PMID 8350346 DOI: 10.1007/Bf00556355 |
0.343 |
|
| 1992 |
Smith RF, Smith TF. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Engineering. 5: 35-41. PMID 1631044 DOI: 10.1093/protein/5.1.35 |
0.301 |
|
| 1990 |
Smith RF, Smith TF. Automatic generation of primary sequence patterns from sets of related protein sequences Proceedings of the National Academy of Sciences of the United States of America. 87: 118-122. PMID 2296575 DOI: 10.1073/Pnas.87.1.118 |
0.398 |
|
| 1990 |
Fischel-Ghodsian F, Mathiowitz G, Smith TF. Alignment of protein sequences using secondary structure: a modified dynamic programming method. Protein Engineering. 3: 577-581. PMID 2217132 DOI: 10.1093/Protein/3.7.577 |
0.444 |
|
| 1989 |
Webster TA, Patarca R, Lathrop RH, Smith TF. Potential structural motifs for reverse transcriptases Molecular Biology and Evolution. 6: 317-320. PMID 2482917 DOI: 10.1093/Oxfordjournals.Molbev.A040543 |
0.319 |
|
| 1987 |
Gruskin KD, Smith TF, Goodman M. Possible origin of a calmodulin gene that lacks intervening sequences. Proceedings of the National Academy of Sciences of the United States of America. 84: 1605-8. PMID 3470746 DOI: 10.1073/Pnas.84.6.1605 |
0.372 |
|
| 1987 |
Webster TA, Lathrop RH, Smith TF. Prediction of a common structural domain in aminoacyl-tRNA synthetases through use of a new pattern-directed inference system Biochemistry. 26: 6950-6957. PMID 3322392 DOI: 10.1021/Bi00396A014 |
0.423 |
|
| 1987 |
Bradley MK, Smith TF, Lathrop RH, Livingston DM, Webster TA. Consensus topography in the ATP binding site of the simian virus 40 and polyomavirus large tumor antigens Proceedings of the National Academy of Sciences of the United States of America. 84: 4026-4030. PMID 3035562 DOI: 10.1073/Pnas.84.12.4026 |
0.319 |
|
| 1987 |
Lathrop RH, Webster TA, Smith TF. ARIADNE: pattern-directed inference and hierarchical abstraction in protein structure recognition Communications of the Acm. 30: 909-921. DOI: 10.1145/32206.32207 |
0.321 |
|
| 1986 |
Fitch WM, Smith T, Breslow JL. Detecting internally repeated sequences and inferring the history of duplication Methods in Enzymology. 773-787. PMID 3088394 DOI: 10.1016/0076-6879(86)28105-7 |
0.398 |
|
| 1984 |
Lipman DJ, Wilbur WJ, Smith TF, Waterman MS. On the statistical significance of nucleic add similarities Nucleic Acids Research. 12: 215-226. PMID 6694902 DOI: 10.1093/Nar/12.1Part1.215 |
0.321 |
|
| 1983 |
Fitch WM, Smith TF. Optimal sequence alignments Proceedings of the National Academy of Sciences of the United States of America. 80: 1382-1386. PMID 16593289 DOI: 10.1073/Pnas.80.5.1382 |
0.304 |
|
| 1983 |
Smith TF, Waterman MS, Sadler JR. Statistical characterization of nucleic acid sequence functional domains Nucleic Acids Research. 11: 2205-2220. PMID 6835847 DOI: 10.1093/Nar/11.7.2205 |
0.389 |
|
| 1982 |
Lipman DJ, Smith TF, Beckman RJ, Waterman MS. Hierarchical analysis of influenza A hemagglutinin gene sequences Nucleic Acids Research. 10: 5375-5389. PMID 7145705 DOI: 10.1093/Nar/10.17.5375 |
0.381 |
|
| 1982 |
Smith TF, Waterman MS, Fitch WM. Comparative biosequence metrics Journal of Molecular Evolution. 18: 423. DOI: 10.1007/Bf01733210 |
0.345 |
|
| 1981 |
Smith TF, Waterman MS. Comparison of biosequences Advances in Applied Mathematics. 2: 482-489. DOI: 10.1016/0196-8858(81)90046-4 |
0.352 |
|
| 1980 |
Smith TF, Waterman MS. New Stratigraphic Correlation Techniques The Journal of Geology. 88: 451-457. DOI: 10.1086/628528 |
0.335 |
|
| 1980 |
Smith TF, Waterman MS. Protein constraints induced by multiframe encoding Mathematical Biosciences. 49: 17-26. DOI: 10.1016/0025-5564(80)90108-X |
0.441 |
|
| 1977 |
Smith TF, Sadler JR, Goad W. Statistical-mechanical modeling of a regulatory protein: the lactose repressor Bellman Prize in Mathematical Biosciences. 36: 61-86. DOI: 10.1016/0025-5564(77)90016-5 |
0.309 |
|
| 1976 |
Waterman MS, Smith TF, Beyer WA. Some Biological Sequence Metrics Advances in Mathematics. 20: 367-387. DOI: 10.1016/0001-8708(76)90202-4 |
0.364 |
|
| 1974 |
Beyer WA, Stein ML, Smith TF, Ulam SM. A molecular sequence metric and evolutionary trees Bellman Prize in Mathematical Biosciences. 19: 9-25. DOI: 10.1016/0025-5564(74)90028-5 |
0.401 |
|
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