Laura Elnitski - Publications

Affiliations: 
1998 Molecular and Cell Biology Pennsylvania State University, State College, PA, United States 

39/70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Margolin G, Petrykowska HM, Jameel N, Bell DW, Young AC, Elnitski L. Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development. The Journal of Molecular Diagnostics : Jmd. 18: 283-98. PMID 26857064 DOI: 10.1016/j.jmoldx.2015.11.004  0.52
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  0.52
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  0.52
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  0.52
2012 Kolbe DL, DeLoia JA, Porter-Gill P, Strange M, Petrykowska HM, Guirguis A, Krivak TC, Brody LC, Elnitski L. Differential analysis of ovarian and endometrial cancers identifies a methylator phenotype. Plos One. 7: e32941. PMID 22403726 DOI: 10.1371/journal.pone.0032941  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
2008 Yang MQ, Elnitski LL. Diversity of core promoter elements comprising human bidirectional promoters Bmc Genomics. 9. PMID 18831794 DOI: 10.1186/1471-2164-9-S2-S3  0.52
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  0.52
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  0.52
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  0.48
2007 Yang MQ, Koehly LM, Elnitski LL. Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. Plos Computational Biology. 3: e72. PMID 17447839 DOI: 10.1371/journal.pcbi.0030072  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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
2005 Wu J, Iwata F, Grass JA, Osborne CS, Elnitski L, Fraser P, Ohneda O, Yamamoto M, Bresnick EH. Molecular determinants of NOTCH4 transcription in vascular endothelium. Molecular and Cellular Biology. 25: 1458-74. PMID 15684396 DOI: 10.1128/Mcb.25.4.1458-1474.2005  0.52
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  0.52
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  0.48
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  0.52
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  0.52
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  0.52
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  0.52
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  0.48
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
Low-probability matches
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  0.16
2016 Yang MQ, Elnitski L. A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. Plos One. 11: e0163353. PMID 27788148 DOI: 10.1371/journal.pone.0163353  0.12
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  0.12
2017 Chen YC, Sudre G, Sharp W, Donovan F, Chandrasekharappa SC, Hansen N, Elnitski L, Shaw P. Neuroanatomic, epigenetic and genetic differences in monozygotic twins discordant for attention deficit hyperactivity disorder. Molecular Psychiatry. PMID 28322272 DOI: 10.1038/mp.2017.45  0.08
2018 Elnitski L, Ovcharenko I. The hypothesis of ultraconserved enhancer dispensability overturned. Genome Biology. 19: 57. PMID 29739466 DOI: 10.1186/s13059-018-1433-1  0.04
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  0.04
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  0.04
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  0.04
2012 Scott A, Petrykowska HM, Hefferon T, Gotea V, Elnitski L. Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene. Journal of Cystic Fibrosis : Official Journal of the European Cystic Fibrosis Society. 11: 511-7. PMID 22591852 DOI: 10.1016/j.jcf.2012.04.009  0.04
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  0.04
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  0.04
2021 Miller BF, Petrykowska HM, Elnitski L. Assessing ZNF154 methylation in patient plasma as a multicancer marker in liquid biopsies from colon, liver, ovarian and pancreatic cancer patients. Scientific Reports. 11: 221. PMID 33420235 DOI: 10.1038/s41598-020-80345-7  0.01
2020 Miller BF, Pisanic Ii TR, Margolin G, Petrykowska HM, Athamanolap P, Goncearenco A, Osei-Tutu A, Annunziata CM, Wang TH, Elnitski L. Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers. Clinical Epigenetics. 12: 154. PMID 33081832 DOI: 10.1186/s13148-020-00939-w  0.01
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  0.01
2019 LaBarre BA, Goncearenco A, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Hayes VM, Elnitski L. MethylToSNP: identifying SNPs in Illumina DNA methylation array data. Epigenetics & Chromatin. 12: 79. PMID 31861999 DOI: 10.1186/s13072-019-0321-6  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
2016 Miller BF, Sánchez-Vega F, Elnitski L. The Emergence of Pan-Cancer CIMP and Its Elusive Interpretation. Biomolecules. 6. PMID 27879658 DOI: 10.3390/biom6040045  0.01
2016 Gallego-Bustos F, Gotea V, Ramos-Amador JT, Rodríguez-Pena R, Gil-Herrera J, Sastre A, Delmiro A, Rai G, Elnitski L, González-Granado LI, Allende LM. A Case of IL-7R Deficiency Caused by a Novel Synonymous Mutation and Implications for Mutation Screening in SCID Diagnosis. Frontiers in Immunology. 7: 443. PMID 27833609 DOI: 10.3389/fimmu.2016.00443  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
2008 Jacox E, Elnitski L. Finding Occurrences of Relevant Functional Elements in Genomic Signatures. International Journal of Computational Science. 2: 599-606. PMID 20046539  0.01
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  0.01
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  0.01
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