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Jeffrey A. Rosenfeld, Ph.D. - Publications

Affiliations: 
2009 Biology New York University, New York, NY, United States 
Area:
evolutionary biology
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47 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
2022 Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, et al. Benchmarking challenging small variants with linked and long reads. Cell Genomics. 2. PMID 36452119 DOI: 10.1016/j.xgen.2022.100128  0.342
2022 Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, ... ... Rosenfeld JA, et al. A complete reference genome improves analysis of human genetic variation. Science (New York, N.Y.). 376: eabl3533. PMID 35357935 DOI: 10.1126/science.abl3533  0.391
2022 Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, ... ... Rosenfeld JA, et al. The complete sequence of a human genome. Science (New York, N.Y.). 376: 44-53. PMID 35357919 DOI: 10.1126/science.abj6987  0.43
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Rosenfeld JA, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8  0.47
2019 Oppenheim S, Cao X, Rueppel O, Krongdang S, Phokasem P, DeSalle R, Goodwin S, Xing J, Chantawannakul P, Rosenfeld J. Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata. Genome Biology and Evolution. PMID 31860080 DOI: 10.1093/Gbe/Evz277  0.789
2017 Das A, Banday M, Fisher MA, Chang YJ, Rosenfeld J, Bellofatto V. An essential domain of an early-diverged RNA polymerase II functions to accurately decode a primitive chromatin landscape. Nucleic Acids Research. PMID 28575287 DOI: 10.1093/Nar/Gkx486  0.309
2017 Oppenheim SJ, Rosenfeld JA, DeSalle R. Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors. Bmc Genomics. 18: 205. PMID 28241792 DOI: 10.1186/S12864-017-3590-0  0.785
2016 Rosenfeld JA, Oppenheim S, DeSalle R. A whole genome gene content phylogenetic analysis of anopheline mosquitoes. Molecular Phylogenetics and Evolution. PMID 27866013 DOI: 10.1016/J.Ympev.2016.11.006  0.769
2016 Kolokotronis SO, Foox J, Rosenfeld JA, Brugler MR, Reeves D, Benoit JB, Booth W, Robison G, Steffen M, Sakas Z, Palli SR, Schal C, Richards S, Narechania A, Baker RH, et al. The mitogenome of the bed bug Cimex lectularius (Hemiptera: Cimicidae). Mitochondrial Dna. Part B, Resources. 1: 425-427. PMID 27617305 DOI: 10.1080/23802359.2016.1180268  0.764
2016 Rosenfeld J, Foox J, DeSalle R. Data for constructing insect genome content matrices for phylogenetic analysis and functional annotation. Data in Brief. 6: 279-81. PMID 26862572 DOI: 10.1016/J.Dib.2015.12.015  0.694
2016 Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, et al. Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nature Communications. 7: 10164. PMID 26836631 DOI: 10.1038/Ncomms10164  0.748
2015 Rosenfeld J, Foox J, DeSalle R. Insect genome content phylogeny and functional annotation of core insect genomes. Molecular Phylogenetics and Evolution. PMID 26549428 DOI: 10.1016/J.Ympev.2015.10.014  0.698
2015 Kumar R, Corbett MA, van Bon BW, Gardner A, Woenig JA, Jolly LA, Douglas E, Friend K, Tan C, Van Esch H, Holvoet M, Raynaud M, Field M, Leffler M, Budny B, ... ... Rosenfeld JA, et al. Increased STAG2 dosage defines a novel cohesinopathy with intellectual disability and behavioural problems. Human Molecular Genetics. PMID 26443594 DOI: 10.1093/hmg/ddv414  0.36
2015 Chhangawala S, Rudy G, Mason CE, Rosenfeld JA. The impact of read length on quantification of differentially expressed genes and splice junction detection. Genome Biology. 16: 131. PMID 26100517 DOI: 10.1186/S13059-015-0697-Y  0.367
2015 Brand H, Collins RL, Hanscom C, Rosenfeld JA, Pillalamarri V, Stone MR, Kelley F, Mason T, Margolin L, Eggert S, Mitchell E, Hodge JC, Gusella JF, Sanders SJ, Talkowski ME. Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation. American Journal of Human Genetics. 97: 170-6. PMID 26094575 DOI: 10.1016/J.Ajhg.2015.05.012  0.334
2015 Brand H, Collins RL, Hanscom C, Rosenfeld JA, Pillalamarri V, Stone MR, Kelley F, Mason T, Margolin L, Eggert S, Mitchell E, Hodge JC, Gusella JF, Sanders SJ, Talkowski ME. Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation American Journal of Human Genetics. 97: 170-176. DOI: 10.1016/j.ajhg.2015.05.012  0.335
2014 Brand H, Pillalamarri V, Collins RL, Eggert S, O'Dushlaine C, Braaten EB, Stone MR, Chambert K, Doty ND, Hanscom C, Rosenfeld JA, Ditmars H, Blais J, Mills R, Lee C, et al. Cryptic and complex chromosomal aberrations in early-onset neuropsychiatric disorders. American Journal of Human Genetics. 95: 454-61. PMID 25279985 DOI: 10.1016/J.Ajhg.2014.09.005  0.356
2014 Campbell IM, Gambin T, Dittwald P, Beck CR, Shuvarikov A, Hixson P, Patel A, Gambin A, Shaw CA, Rosenfeld JA, Stankiewicz P. Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination. Bmc Biology. 12: 74. PMID 25246103 DOI: 10.1186/S12915-014-0074-4  0.35
2014 Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C, Buono S, Vissers LE, Schuurs-Hoeijmakers JH, Hoischen A, Pfundt R, Krumm N, Carvill GL, et al. Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nature Genetics. 46: 1063-71. PMID 25217958 DOI: 10.1038/Ng.3092  0.309
2014 Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, ... ... Rosenfeld J, ... ... Rosenfeld J, et al. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nature Biotechnology. 32: 915-25. PMID 25150835 DOI: 10.1038/Nbt.2972  0.352
2014 Rosenfeld J, Mason C. Response to 'pervasive sequence patents cover the entire human genome' - authors' reply. Genome Medicine. 6: 15. PMID 24764495 DOI: 10.1186/Gm532  0.429
2013 Lencz T, Guha S, Liu C, Rosenfeld J, Mukherjee S, DeRosse P, John M, Cheng L, Zhang C, Badner JA, Ikeda M, Iwata N, Cichon S, Rietschel M, Nöthen MM, et al. Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder. Nature Communications. 4: 2739. PMID 24253340 DOI: 10.1038/Ncomms3739  0.316
2013 Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, ... ... Rosenfeld JA, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science (New York, N.Y.). 342: 1235587. PMID 24092746 DOI: 10.1126/Science.1235587  0.428
2013 Repnikova EA, Rosenfeld JA, Bailes A, Weber C, Erdman L, McKinney A, Ramsey S, Hashimoto S, Lamb Thrush D, Astbury C, Reshmi SC, Shaffer LG, Gastier-Foster JM, Pyatt RE. Characterization of copy number variation in genomic regions containing STR loci using array comparative genomic hybridization. Forensic Science International. Genetics. 7: 475-81. PMID 23948316 DOI: 10.1016/J.Fsigen.2013.05.008  0.368
2013 Dittwald P, Gambin T, Szafranski P, Li J, Amato S, Divon MY, Rodríguez Rojas LX, Elton LE, Scott DA, Schaaf CP, Torres-Martinez W, Stevens AK, Rosenfeld JA, Agadi S, Francis D, et al. NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits. Genome Research. 23: 1395-409. PMID 23657883 DOI: 10.1101/Gr.152454.112  0.365
2013 Rosenfeld JA, Mason CE. Pervasive sequence patents cover the entire human genome. Genome Medicine. 5: 27. PMID 23522065 DOI: 10.1186/Gm431  0.572
2013 Nguyen LS, Kim HG, Rosenfeld JA, Shen Y, Gusella JF, Lacassie Y, Layman LC, Shaffer LG, Gécz J. Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders. Human Molecular Genetics. 22: 1816-25. PMID 23376982 DOI: 10.1093/Hmg/Ddt035  0.316
2012 Talkowski ME, Ordulu Z, Pillalamarri V, Benson CB, Blumenthal I, Connolly S, Hanscom C, Hussain N, Pereira S, Picker J, Rosenfeld JA, Shaffer LG, Wilkins-Haug LE, Gusella JF, Morton CC. Clinical diagnosis by whole-genome sequencing of a prenatal sample. The New England Journal of Medicine. 367: 2226-32. PMID 23215558 DOI: 10.1056/Nejmoa1208594  0.345
2012 Rosenfeld JA, Mason CE, Smith TM. Limitations of the human reference genome for personalized genomics. Plos One. 7: e40294. PMID 22811759 DOI: 10.1371/Journal.Pone.0040294  0.488
2012 Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, Curry CJ, Shafer S, Shaffer LG, de Jong PJ, Wilson RK, et al. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell. 149: 912-22. PMID 22559943 DOI: 10.1016/J.Cell.2012.03.033  0.39
2012 Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren AM, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris DJ, et al. Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell. 149: 525-37. PMID 22521361 DOI: 10.1016/J.Cell.2012.03.028  0.315
2012 Rosenfeld JA, Payne A, DeSalle R. Random roots and lineage sorting. Molecular Phylogenetics and Evolution. 64: 12-20. PMID 22445448 DOI: 10.1016/J.Ympev.2012.02.029  0.624
2012 MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, ... ... Rosenfeld JA, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science (New York, N.Y.). 335: 823-8. PMID 22344438 DOI: 10.1126/Science.1215040  0.537
2012 Rosenfeld JA, DeSalle R. E value cutoff and eukaryotic genome content phylogenetics. Molecular Phylogenetics and Evolution. 63: 342-50. PMID 22306824 DOI: 10.1016/J.Ympev.2012.01.003  0.654
2012 Samoshkin A, Dulev S, Loukinov D, Rosenfeld JA, Strunnikov AV. Condensin dysfunction in human cells induces nonrandom chromosomal breaks in anaphase, with distinct patterns for both unique and repeated genomic regions. Chromosoma. 121: 191-9. PMID 22179743 DOI: 10.1007/S00412-011-0353-6  0.434
2012 Lazzarini LC, Rosenfeld J, Huard RC, Hill V, Lapa e Silva JR, DeSalle R, Rastogi N, Ho JL. Mycobacterium tuberculosis spoligotypes that may derive from mixed strain infections are revealed by a novel computational approach. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 12: 798-806. PMID 21920466 DOI: 10.1016/J.Meegid.2011.08.028  0.479
2011 Kurt Lienau E, DeSalle R, Allard M, Brown EW, Swofford D, Rosenfeld JA, Sarkar IN, Planet PJ. The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life. Cladistics : the International Journal of the Willi Hennig Society. 27: 417-427. PMID 34875790 DOI: 10.1111/j.1096-0031.2010.00337.x  0.653
2011 Kurt Lienau E, DeSalle R, Allard M, Brown EW, Swofford D, Rosenfeld JA, Sarkar IN, Planet PJ. The mega-matrix tree of life: Using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life Cladistics. 27: 417-427. DOI: 10.1111/J.1096-0031.2010.00337.X  0.686
2010 Rosenfeld JA, Malhotra AK, Lencz T. Novel multi-nucleotide polymorphisms in the human genome characterized by whole genome and exome sequencing. Nucleic Acids Research. 38: 6102-11. PMID 20488869 DOI: 10.1093/Nar/Gkq408  0.435
2009 Rosenfeld JA, Xuan Z, DeSalle R. Investigating repetitively matching short sequencing reads: the enigmatic nature of H3K9me3. Epigenetics : Official Journal of the Dna Methylation Society. 4: 476-86. PMID 19786836 DOI: 10.4161/Epi.4.7.9809  0.667
2009 Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. Determination of enriched histone modifications in non-genic portions of the human genome. Bmc Genomics. 10: 143. PMID 19335899 DOI: 10.1186/1471-2164-10-143  0.569
2009 Lemke MJ, Lienau EK, Rothe J, Pagioro TA, Rosenfeld J, Desalle R. Description of freshwater bacterial assemblages from the upper paraná river floodpulse system, Brazil. Microbial Ecology. 57: 94-103. PMID 18587611 DOI: 10.1007/S00248-008-9398-3  0.714
2008 Rosenfeld JA, DeSalle R, Lee EK, O'Grady P. Using whole genome presence/absence data to untangle function in 12 Drosophila genomes. Fly. 2: 291-9. PMID 19139635 DOI: 10.4161/Fly.7481  0.749
2008 Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics. 40: 897-903. PMID 18552846 DOI: 10.1038/Ng.154  0.355
2006 Lienau EK, DeSalle R, Rosenfeld JA, Planet PJ. Reciprocal illumination in the gene content tree of life. Systematic Biology. 55: 441-53. PMID 16861208 DOI: 10.1080/10635150600697416  0.762
2004 Rosenfeld JA, Sarkar IN, Planet PJ, Figurski DH, DeSalle R. ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms. Bioinformatics (Oxford, England). 20: 3462-5. PMID 15271781 DOI: 10.1093/Bioinformatics/Bth427  0.623
2001 Kaneshiro ES, Rosenfeld JA, Basselin M, Bradshaw S, Stringer JR, Smulian AG, Giner JL. Pneumocystis carinii erg6 gene: sequencing and expression of recombinant SAM:sterol methyltransferase in heterologous systems. The Journal of Eukaryotic Microbiology. 144S-146S. PMID 11906033 DOI: 10.1111/J.1550-7408.2001.Tb00491.X  0.309
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