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Jeremy Leipzig - Publications

Affiliations: 
Drexel University, Philadelphia, PA, United States 
Area:
Bioinformatics
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24 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
2021 Leipzig J, Nüst D, Hoyt CT, Ram K, Greenberg J. The role of metadata in reproducible computational research. Patterns (New York, N.Y.). 2: 100322. PMID 34553169 DOI: 10.1016/j.patter.2021.100322  0.574
2019 Raman P, Zimmerman S, Rathi KS, de Torrenté L, Sarmady M, Wu C, Leipzig J, Taylor DM, Tozeren A, Mar JC. A comparison of survival analysis methods for cancer gene expression RNA-Sequencing data. Cancer Genetics. 235: 1-12. PMID 31296308 DOI: 10.1016/J.Cancergen.2019.04.004  0.344
2018 McManus MJ, Picard M, Chen HW, De Haas HJ, Potluri P, Leipzig J, Towheed A, Angelin A, Sengupta P, Morrow RM, Kauffman BA, Vermulst M, Narula J, Wallace DC. Mitochondrial DNA Variation Dictates Expressivity and Progression of Nuclear DNA Mutations Causing Cardiomyopathy. Cell Metabolism. PMID 30174309 DOI: 10.1016/J.Cmet.2018.08.002  0.318
2017 Sonney S, Leipzig J, Lott MT, Zhang S, Procaccio V, Wallace DC, Sondheimer N. Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP. Plos Computational Biology. 13: e1005867. PMID 29227991 DOI: 10.1371/Journal.Pcbi.1005867  0.333
2016 Shen L, Diroma MA, Gonzalez M, Navarro-Gomez D, Leipzig J, Lott MT, van Oven M, Wallace DC, Muraresku CC, Zolkipli-Cunningham Z, Chinnery PF, Attimonelli M, Zuchner S, Falk MJ, Gai X. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease. Human Mutation. PMID 26919060 DOI: 10.1002/Humu.22974  0.405
2015 Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, et al. Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities. Molecular Genetics and Metabolism. 114: 388-96. PMID 25542617 DOI: 10.1016/J.Ymgme.2014.11.016  0.394
2015 Navarro-Gomez D, Leipzig J, Shen L, Lott M, Stassen AP, Wallace DC, Wiggs JL, Falk MJ, van Oven M, Gai X. Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier. Bioinformatics (Oxford, England). 31: 1310-2. PMID 25505086 DOI: 10.1093/Bioinformatics/Btu825  0.355
2015 Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, et al. MSeqDR: Making genomics accessible to the mitochondrial disease community Mitochondrion. 24: S2-S3. DOI: 10.1016/J.Mito.2015.07.013  0.301
2013 Zhang Z, Leipzig J, Sasson A, Yu AM, Perin JC, Xie HM, Sarmady M, Warren PV, White PS. Efficient digest of high-throughput sequencing data in a reproducible report. Bmc Bioinformatics. 14: S3. PMID 24564231 DOI: 10.1186/1471-2105-14-S11-S3  0.317
2013 Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YH, Deanfield J, DePalma S, Fakhro KA, ... ... Leipzig J, et al. De novo mutations in histone-modifying genes in congenital heart disease. Nature. 498: 220-3. PMID 23665959 DOI: 10.1038/Nature12141  0.31
2012 Barrantes I, Leipzig J, Marwan W. A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level. Gene Regulation and Systems Biology. 6: 127-37. PMID 23071390 DOI: 10.4137/Grsb.S10224  0.342
2011 Shi L, Perin JC, Leipzig J, Zhang Z, Sullivan KE. Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes Gene. 487: 21-28. PMID 21803131 DOI: 10.1016/J.Gene.2011.07.004  0.381
2008 Wang GP, Garrigue A, Ciuffi A, Ronen K, Leipzig J, Berry C, Lagresle-Peyrou C, Benjelloun F, Hacein-Bey-Abina S, Fischer A, Cavazzana-Calvo M, Bushman FD. DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Research. 36: e49. PMID 18411205 DOI: 10.1093/Nar/Gkn125  0.582
2008 Meekings KN, Leipzig J, Bushman FD, Taylor GP, Bangham CR. HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP. Plos Pathogens. 4: e1000027. PMID 18369476 DOI: 10.1371/Journal.Ppat.1000027  0.539
2007 Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, Bushman FD. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Research. 35: e91. PMID 17576693 DOI: 10.1093/Nar/Gkm435  0.474
2007 Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Research. 17: 1186-94. PMID 17545577 DOI: 10.1101/Gr.6286907  0.592
2006 Berry C, Hannenhalli S, Leipzig J, Bushman FD. Selection of target sites for mobile DNA integration in the human genome. Plos Computational Biology. 2: e157. PMID 17166054 DOI: 10.1371/Journal.Pcbi.0020157  0.593
2006 Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: viral and cellular determinants of target-site selection. Plos Pathogens. 2: e60. PMID 16789841 DOI: 10.1371/Journal.Ppat.0020060  0.582
2006 Barr SD, Ciuffi A, Leipzig J, Shinn P, Ecker JR, Bushman FD. HIV Integration Site Selection: Targeting in Macrophages and the Effects of Different Routes of Viral Entry Molecular Therapy. 14: 218-225. PMID 16647883 DOI: 10.1016/J.Ymthe.2006.03.012  0.576
2006 Ciuffi A, Mitchell RS, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman FD. Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts. Molecular Therapy : the Journal of the American Society of Gene Therapy. 13: 366-73. PMID 16325473 DOI: 10.1016/J.Ymthe.2005.10.009  0.594
2005 Ciuffi A, Llano M, Poeschla E, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman F. A role for LEDGF/p75 in targeting HIV DNA integration Nature Medicine. 11: 1287-1289. PMID 16311605 DOI: 10.1038/Nm1329  0.549
2005 Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C. Genome-wide analysis of retroviral DNA integration. Nature Reviews. Microbiology. 3: 848-58. PMID 16175173 DOI: 10.1038/Nrmicro1263  0.58
2005 Barr SD, Leipzig J, Shinn P, Ecker JR, Bushman FD. Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome Journal of Virology. 79: 12035-12044. PMID 16140779 DOI: 10.1128/Jvi.79.18.12035-12044.2005  0.598
2004 Leipzig J, Pevzner P, Heber S. The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Research. 32: 3977-83. PMID 15292448 DOI: 10.1093/Nar/Gkh731  0.648
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