| Year |
Citation |
Score |
| 2020 |
Goncearenco A, LaBarre BA, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Turner SD, Hayes VM, Elnitski L. DNA methylation profiles unique to Kalahari KhoeSan individuals. Epigenetics. 1-17. PMID 32892676 DOI: 10.1080/15592294.2020.1809852 |
0.393 |
|
| 2019 |
Chen YC, Elnitski L. Aberrant DNA methylation defines isoform usage in cancer, with functional implications. Plos Computational Biology. 15: e1007095. PMID 31329578 DOI: 10.1371/Journal.Pcbi.1007095 |
0.315 |
|
| 2019 |
Gotea V, Margolin G, Elnitski L. CAGI experiments: modeling sequence variant impact on gene splicing using predictions from computational tools. Human Mutation. PMID 31066132 DOI: 10.1002/Humu.23782 |
0.566 |
|
| 2019 |
Huang D, Petrykowska HM, Miller BF, Elnitski L, Ovcharenko I. Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression. Genome Research. PMID 30886051 DOI: 10.1101/Gr.247007.118 |
0.43 |
|
| 2017 |
Chen YC, Gotea V, Margolin G, Elnitski L. Significant associations between driver gene mutations and DNA methylation alterations across many cancer types. Plos Computational Biology. 13: e1005840. PMID 29125844 DOI: 10.1371/Journal.Pcbi.1005840 |
0.363 |
|
| 2017 |
Lichtenberg J, Elnitski L, Bodine DM. SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures. Bioinformatics (Oxford, England). PMID 28449120 DOI: 10.1093/Bioinformatics/Btx276 |
0.44 |
|
| 2017 |
Sánchez-Vega F, Gotea V, Chen YC, Elnitski L. CpG island methylator phenotype in adenocarcinomas from the digestive tract: Methods, conclusions, and controversies. World Journal of Gastrointestinal Oncology. 9: 105-120. PMID 28344746 DOI: 10.4251/Wjgo.V9.I3.105 |
0.335 |
|
| 2015 |
Al-Ouran R, Schmidt R, Naik A, Jones J, Drews F, Juedes D, Elnitski L, Welch L. Discovering Gene Regulatory Elements Using Coverage-based Heuristics. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 26540692 DOI: 10.1109/Tcbb.2015.2496261 |
0.461 |
|
| 2015 |
Gotea V, Gartner JJ, Qutob N, Elnitski L, Samuels Y. The functional relevance of somatic synonymous mutations in melanoma and other cancers. Pigment Cell & Melanoma Research. 28: 673-84. PMID 26300548 DOI: 10.1111/Pcmr.12413 |
0.357 |
|
| 2015 |
Sánchez-Vega F, Gotea V, Margolin G, Elnitski L. Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype. Epigenetics & Chromatin. 8: 14. PMID 25960768 DOI: 10.1186/S13072-015-0007-7 |
0.333 |
|
| 2014 |
Yang M, Elnitski L. Orthology-driven mapping of bidirectional promoters in human and mouse genomes. Bmc Bioinformatics. 15: S1. PMID 25559261 DOI: 10.1186/1471-2105-15-S17-S1 |
0.515 |
|
| 2014 |
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/Pnas.1410434111 |
0.539 |
|
| 2014 |
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111 |
0.671 |
|
| 2014 |
Gotea V, Elnitski L. Ascertaining regions affected by GC-biased gene conversion through weak-to-strong mutational hotspots. Genomics. 103: 349-56. PMID 24727706 DOI: 10.1016/J.Ygeno.2014.04.001 |
0.357 |
|
| 2014 |
Ye Z, Chen Z, Lan X, Hara S, Sunkel B, Huang TH, Elnitski L, Wang Q, Jin VX. Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. Nucleic Acids Research. 42: 2856-69. PMID 24369421 DOI: 10.1093/Nar/Gkt1338 |
0.383 |
|
| 2013 |
Sánchez-Vega F, Gotea V, Petrykowska HM, Margolin G, Krivak TC, DeLoia JA, Bell DW, Elnitski L. Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines. Epigenetics. 8: 1355-72. PMID 24149212 DOI: 10.4161/Epi.26701 |
0.361 |
|
| 2013 |
Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, ... ... Elnitski LL, et al. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proceedings of the National Academy of Sciences of the United States of America. 110: 13481-6. PMID 23901115 DOI: 10.1073/Pnas.1304227110 |
0.315 |
|
| 2013 |
Gotea V, Petrykowska HM, Elnitski L. Bidirectional promoters as important drivers for the emergence of species-specific transcripts. Plos One. 8: e57323. PMID 23460838 DOI: 10.1371/Journal.Pone.0057323 |
0.468 |
|
| 2012 |
Roessler E, Hu P, Hong SK, Srivastava K, Carrington B, Sood R, Petrykowska H, Elnitski L, Ribeiro LA, Richieri-Costa A, Feldman B, Odenwald WF, Muenke M. Unique alterations of an ultraconserved non-coding element in the 3'UTR of ZIC2 in holoprosencephaly. Plos One. 7: e39026. PMID 22859937 DOI: 10.1371/Journal.Pone.0039026 |
0.412 |
|
| 2011 |
Yang MQ, Laflamme K, Gotea V, Joiner CH, Seidel NE, Wong C, Petrykowska HM, Lichtenberg J, Lee S, Welch L, Gallagher PG, Bodine DM, Elnitski L. Genome-wide detection of a TFIID localization element from an initial human disease mutation. Nucleic Acids Research. 39: 2175-87. PMID 21071415 DOI: 10.1093/Nar/Gkq1035 |
0.47 |
|
| 2010 |
Lichtenberg J, Kurz K, Liang X, Al-ouran R, Neiman L, Nau LJ, Welch JD, Jacox E, Bitterman T, Ecker K, Elnitski L, Drews F, Lee SS, Welch LR. WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. Bmc Bioinformatics. 11: S6. PMID 21210985 DOI: 10.1186/1471-2105-11-S12-S6 |
0.543 |
|
| 2010 |
Jacox E, Gotea V, Ovcharenko I, Elnitski L. Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes. Plos One. 5: e12274. PMID 20806066 DOI: 10.1371/Journal.Pone.0012274 |
0.352 |
|
| 2010 |
Elnitski L, Burhans R, Riemer C, Hardison R, Miller W. MultiPipMaker: a comparative alignment server for multiple DNA sequences. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit10.4. PMID 20521245 DOI: 10.1002/0471250953.bi1004s30 |
0.815 |
|
| 2010 |
Laflamme K, Owen AN, Devlin EE, Yang MQ, Wong C, Steiner LA, Garrett LJ, Elnitski L, Gallagher PG, Bodine DM. Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter. Molecular and Cellular Biology. 30: 3493-502. PMID 20479128 DOI: 10.1128/Mcb.00119-10 |
0.521 |
|
| 2010 |
Woolfe A, Mullikin JC, Elnitski L. Genomic features defining exonic variants that modulate splicing. Genome Biology. 11: R20. PMID 20158892 DOI: 10.1186/Gb-2010-11-2-R20 |
0.51 |
|
| 2009 |
Lichtenberg J, Jacox E, Welch JD, Kurz K, Liang X, Yang MQ, Drews F, Ecker K, Lee SS, Elnitski L, Welch LR. Word-based characterization of promoters involved in human DNA repair pathways. Bmc Genomics. 10: S18. PMID 19594877 DOI: 10.1186/1471-2164-10-S1-S18 |
0.437 |
|
| 2009 |
Piontkivska H, Yang MQ, Larkin DM, Lewin HA, Reecy J, Elnitski L. Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. Bmc Genomics. 10: 189. PMID 19393065 DOI: 10.1186/1471-2164-10-189 |
0.472 |
|
| 2009 |
Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (New York, N.Y.). 324: 522-8. PMID 19390049 DOI: 10.1126/Science.1169588 |
0.592 |
|
| 2008 |
Jacox E, Elnitski L. Finding Occurrences of Relevant Functional Elements in Genomic Signatures. International Journal of Computational Science. 2: 599-606. PMID 20046539 |
0.472 |
|
| 2008 |
Yang MQ, Taylor J, Elnitski L. Comparative analyses of bidirectional promoters in vertebrates Bmc Bioinformatics. 9. PMID 18541062 DOI: 10.1186/1471-2105-9-S6-S9 |
0.388 |
|
| 2008 |
Petrykowska HM, Vockley CM, Elnitski L. Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus. Genome Research. 18: 1238-46. PMID 18436892 DOI: 10.1101/Gr.073817.107 |
0.548 |
|
| 2008 |
Yang MQ, Elnitski LL. Prediction-based approaches to characterize bidirectional promoters in the mammalian genome Bmc Genomics. 9. PMID 18366609 DOI: 10.1186/1471-2164-9-S1-S2 |
0.462 |
|
| 2007 |
Elnitski LL, Shah P, Moreland RT, Umayam L, Wolfsberg TG, Baxevanis AD. The ENCODEdb portal: simplified access to ENCODE Consortium data. Genome Research. 17: 954-9. PMID 17568011 DOI: 10.1101/gr.5582207 |
0.52 |
|
| 2007 |
Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, et al. PhenCode: connecting ENCODE data with mutations and phenotype. Human Mutation. 28: 554-62. PMID 17326095 DOI: 10.1002/Humu.20484 |
0.793 |
|
| 2007 |
Elnitski L, Welch LR. New Frontiers in Computational Genomics: Identification of Novel Functional Elements and Genome-scale Pattern Analysis Scalable Computing: Practice and Experience. 8. DOI: 10.12694/Scpe.V8I3.413 |
0.491 |
|
| 2006 |
Elnitski L, Jin VX, Farnham PJ, Jones SJ. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Research. 16: 1455-64. PMID 17053094 DOI: 10.1101/Gr.4140006 |
0.406 |
|
| 2006 |
Elnitski L, King D, Hardison RC. Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA. Methods in Molecular Biology (Clifton, N.J.). 338: 91-103. PMID 16888352 DOI: 10.1385/1-59745-097-9:91 |
0.787 |
|
| 2006 |
Owen AN, Wolfsberg T, Laflamme K, Wong C, Maksimova Y, Elnitski L, Gallagher PG, Bodine DM. A 200 kb Survey of Chromatin in the ANK-1 Locus Demonstrates an Erythroid-Specific Chromatin Hub That Activates the Erythrocyte Ankyrin (ANK-1E) Promoter. Blood. 108: 536-536. DOI: 10.1182/Blood.V108.11.536.536 |
0.38 |
|
| 2006 |
Laflamme K, Elnitski L, Owen AN, Gallagher PG, Bodine DM. Identification of a Novel Core Promoter Element That Enhances Transcription: Application to Ankyrin Promoters for Globin Gene Therapy. Blood. 108: 3261-3261. DOI: 10.1182/Blood.V108.11.3261.3261 |
0.468 |
|
| 2005 |
Elnitski L, Riemer C, Burhans R, Hardison R, Miller W. MultiPipMaker: comparative alignment server for multiple DNA sequences. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit10.4. PMID 18428743 DOI: 10.1002/0471250953.Bi1004S9 |
0.821 |
|
| 2005 |
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Research. 15: 1451-5. PMID 16169926 DOI: 10.1101/Gr.4086505 |
0.774 |
|
| 2005 |
King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Research. 15: 1051-60. PMID 16024817 DOI: 10.1101/Gr.3642605 |
0.784 |
|
| 2005 |
Elnitski L, Giardine B, Shah P, Zhang Y, Riemer C, Weirauch M, Burhans R, Miller W, Hardison RC. Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Research. 33: D466-70. PMID 15608239 DOI: 10.1093/Nar/Gki045 |
0.814 |
|
| 2004 |
Piontkivska H, Zhang Y, Green ED, Elnitski L. Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions. Bmc Genomics. 5: 31. PMID 15149554 DOI: 10.1186/1471-2164-5-31 |
0.532 |
|
| 2004 |
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research. 14: 708-15. PMID 15060014 DOI: 10.1101/Gr.1933104 |
0.788 |
|
| 2004 |
Kolbe D, Taylor J, Elnitski L, Eswara P, Li J, Miller W, Hardison R, Chiaromonte F. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Research. 14: 700-7. PMID 15060013 DOI: 10.1101/Gr.1976004 |
0.636 |
|
| 2004 |
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Elnitski L, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426 |
0.822 |
|
| 2003 |
Elnitski L, Riemer C, Schwartz S, Hardison R, Miller W. PipMaker: a World Wide Web server for genomic sequence alignments. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 10.2. PMID 18428692 DOI: 10.1002/0471250953.Bi1002S00 |
0.823 |
|
| 2003 |
Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin KM, Weber RJ, Diekhans M, et al. Global predictions and tests of erythroid regulatory regions. Cold Spring Harbor Symposia On Quantitative Biology. 68: 335-44. PMID 15338635 DOI: 10.1101/Sqb.2003.68.335 |
0.729 |
|
| 2003 |
Rijnkels M, Elnitski L, Miller W, Rosen JM. Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins. Genomics. 82: 417-32. PMID 13679022 DOI: 10.1016/S0888-7543(03)00114-9 |
0.486 |
|
| 2003 |
Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, ... ... Elnitski L, et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 424: 788-93. PMID 12917688 DOI: 10.1038/Nature01858 |
0.631 |
|
| 2003 |
Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A, Green ED, Hardison RC, Miller W. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Research. 31: 3518-24. PMID 12824357 DOI: 10.1093/Nar/Gkg579 |
0.826 |
|
| 2003 |
Giardine B, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W, Hardison RC. GALA, a database for genomic sequence alignments and annotations. Genome Research. 13: 732-41. PMID 12671007 DOI: 10.1101/Gr.603103 |
0.827 |
|
| 2003 |
Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, Chiaromonte F. Distinguishing regulatory DNA from neutral sites. Genome Research. 13: 64-72. PMID 12529307 DOI: 10.1101/Gr.817703 |
0.772 |
|
| 2003 |
Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13: 13-26. PMID 12529302 DOI: 10.1101/Gr.844103 |
0.737 |
|
| 2003 |
Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC. Cross-species sequence comparisons: a review of methods and available resources. Genome Research. 13: 1-12. PMID 12529301 DOI: 10.1101/Gr.222003 |
0.677 |
|
| 2002 |
Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics. 80: 681-90. PMID 12504859 DOI: 10.1006/Geno.2002.7018 |
0.822 |
|
| 2002 |
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Elnitski L, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262 |
0.779 |
|
| 2002 |
DeSilva U, Elnitski L, Idol JR, Doyle JL, Gan W, Thomas JW, Schwartz S, Dietrich NL, Beckstrom-Sternberg SM, McDowell JC, Blakesley RW, Bouffard GG, Thomas PJ, Touchman JW, Miller W, et al. Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome. Genome Research. 12: 3-15. PMID 11779826 DOI: 10.1101/Gr.214802 |
0.576 |
|
| 2001 |
Chiaromonte F, Yang S, Elnitski L, Yap VB, Miller W, Hardison RC. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA Proceedings of the National Academy of Sciences of the United States of America. 98: 14503-14508. PMID 11717405 DOI: 10.1073/Pnas.251423898 |
0.73 |
|
| 2000 |
Elnitski L, Li J, Noguchi CT, Miller W, Hardison R. A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control region. The Journal of Biological Chemistry. 276: 6289-98. PMID 11092897 DOI: 10.1074/Jbc.M009624200 |
0.576 |
|
| 2000 |
Elnitski L, Hardison R. Efficient and reliable transfection of mouse erythroleukemia cells using cationic lipids. Blood Cells, Molecules & Diseases. 25: 299-304. PMID 10744425 DOI: 10.1006/Bcmd.1999.0257 |
0.492 |
|
| 1997 |
Elnitski L, Miller W, Hardison R. Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region. Role of basic helix-loop-helix proteins. The Journal of Biological Chemistry. 272: 369-78. PMID 8995271 DOI: 10.1074/Jbc.272.1.369 |
0.545 |
|
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