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Julia Salzman - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
Biochemistry
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38 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
2024 Kokot M, Dehghannasiri R, Baharav T, Salzman J, Deorowicz S. Scalable and unsupervised discovery from raw sequencing reads using SPLASH2. Nature Biotechnology. PMID 39313645 DOI: 10.1038/s41587-024-02381-2  0.358
2023 Olivieri J, Salzman J. Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation. Biorxiv : the Preprint Server For Biology. PMID 36993757 DOI: 10.1101/2023.03.13.532412  0.319
2023 Kokot M, Dehghannasiri R, Baharav T, Salzman J, Deorowicz S. NOMAD2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads. Biorxiv : the Preprint Server For Biology. PMID 36993432 DOI: 10.1101/2023.03.17.533189  0.341
2023 Chen LL, Bindereif A, Bozzoni I, Chang HY, Matera AG, Gorospe M, Hansen TB, Kjems J, Ma XK, Pek JW, Rajewsky N, Salzman J, Wilusz JE, Yang L, Zhao F. A guide to naming eukaryotic circular RNAs. Nature Cell Biology. PMID 36658223 DOI: 10.1038/s41556-022-01066-9  0.318
2022 Meyer E, Chaung K, Dehghannasiri R, Salzman J. ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq. Genome Biology. 23: 226. PMID 36284317 DOI: 10.1186/s13059-022-02795-8  0.361
2022 Olivieri JE, Dehghannasiri R, Salzman J. The SpliZ generalizes 'percent spliced in' to reveal regulated splicing at single-cell resolution. Nature Methods. PMID 35241832 DOI: 10.1038/s41592-022-01400-x  0.304
2021 Olivieri JE, Dehghannasiri R, Wang PL, Jang S, de Morree A, Tan SY, Ming J, Ruohao Wu A, Quake SR, Krasnow MA, Salzman J. RNA splicing programs define tissue compartments and cell types at single cell resolution. Elife. 10. PMID 34515025 DOI: 10.7554/eLife.70692  0.321
2019 Horn C, Salzman J. Molecular sampling at logarithmic rates for next-generation sequencing. Plos Computational Biology. 15: e1007537. PMID 31830035 DOI: 10.1371/Journal.Pcbi.1007537  0.306
2019 Dehghannasiri R, Freeman DE, Jordanski M, Hsieh GL, Damljanovic A, Lehnert E, Salzman J. Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer drivers. Proceedings of the National Academy of Sciences of the United States of America. PMID 31308241 DOI: 10.1073/Pnas.1900391116  0.401
2019 Patel BB, Lebensohn AM, Pusapati GV, Carette JE, Salzman J, Rohatgi R. Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens. Plos One. 14: e0198463. PMID 30695034 DOI: 10.1371/Journal.Pone.0198463  0.329
2019 Dehghannasiri R, Szabo L, Salzman J. Ambiguous splice sites distinguish circRNA and linear splicing in the human genome. Bioinformatics. 35: 1263-1268. PMID 30192918 DOI: 10.1093/Bioinformatics/Bty785  0.427
2019 Dehghannasiri R, Jordanski M, Freeman DE, Hsieh GL, Howard JM, Lehnert E, Salzman J. Abstract 2468: Towards precise and cost-effective fusion discovery: A landscape of druggable gene fusions across TCGA cancers Cancer Research. 79: 2468-2468. DOI: 10.1158/1538-7445.Am2019-2468  0.322
2017 Barrett SP, Parker KR, Horn C, Mata M, Salzman J. ciRS-7 exonic sequence is embedded in a long non-coding RNA locus. Plos Genetics. 13: e1007114. PMID 29236709 DOI: 10.1371/Journal.Pgen.1007114  0.451
2017 Hsieh G, Bierman R, Szabo L, Lee AG, Freeman DE, Watson N, Sweet-Cordero EA, Salzman J. Statistical algorithms improve accuracy of gene fusion detection. Nucleic Acids Research. PMID 28541529 DOI: 10.1093/Nar/Gkx453  0.352
2017 Lehnert ED, Freeman E, Salzman J. Abstract LB-005: Precise and rapid detection of gene fusions and microbial pathogens in next-generation sequencing data with sequence bloom trees Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-005  0.317
2016 Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J. Erratum to: Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biology. 17: 263. PMID 27993159 DOI: 10.1186/S13059-016-1123-9  0.309
2016 Szabo L, Salzman J. Detecting circular RNAs: bioinformatic and experimental challenges Nature Reviews Genetics. 17: 679-692. PMID 27739534 DOI: 10.1038/Nrg.2016.114  0.453
2016 Barrett SP, Salzman J. Circular RNAs: analysis, expression and potential functions. Development (Cambridge, England). 143: 1838-47. PMID 27246710 DOI: 10.1242/Dev.128074  0.459
2016 Salzman J. Circular RNA Expression: Its Potential Regulation and Function. Trends in Genetics. 32: 309-316. PMID 27050930 DOI: 10.1016/J.Tig.2016.03.002  0.453
2016 Hsieh G, Szabo L, Salzman J. A novel statistical methodology to detect gene fusions in RNA-Seq data. Journal of Clinical Oncology. 34: 11575-11575. DOI: 10.1200/Jco.2016.34.15_Suppl.11575  0.378
2015 Jiang H, Salzman J. A penalized likelihood approach for robust estimation of isoform expression. Statistics and Its Interface. 8: 437-445. PMID 27239250 DOI: 10.4310/Sii.2015.V8.N4.A3  0.364
2015 Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J. Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biology. 16: 126. PMID 26076956 DOI: 10.1186/S13059-015-0690-5  0.471
2015 Barrett SP, Wang PL, Salzman J. Circular RNA biogenesis can proceed through an exon-containing lariat precursor. Elife. 4. PMID 26057830 DOI: 10.7554/Elife.07540  0.431
2015 Barrett SP, Wang PL, Salzman J. Author response: Circular RNA biogenesis can proceed through an exon-containing lariat precursor Elife. DOI: 10.7554/Elife.07540.025  0.396
2014 Wang PL, Bao Y, Yee MC, Barrett SP, Hogan GJ, Olsen MN, Dinneny JR, Brown PO, Salzman J. Circular RNA is expressed across the eukaryotic tree of life. Plos One. 9: e90859. PMID 24609083 DOI: 10.1371/Journal.Pone.0090859  0.456
2013 Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. Plos Genetics. 9: e1003777. PMID 24039610 DOI: 10.1371/Journal.Pgen.1003777  0.468
2013 Robles-Sikisaka R, Ly M, Boehm T, Naidu M, Salzman J, Pride DT. Association between living environment and human oral viral ecology. The Isme Journal. 7: 1710-24. PMID 23598790 DOI: 10.1038/Ismej.2013.63  0.303
2013 Salzman J, Klass DM, Brown PO. Improved discovery of molecular interactions in genome-scale data with adaptive model-based normalization. Plos One. 8: e53930. PMID 23349766 DOI: 10.1371/Journal.Pone.0053930  0.435
2013 Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Correction: Cell-Type Specific Features of Circular RNA Expression Plos Genetics. 9. DOI: 10.1371/Annotation/F782282B-Eefa-4C8D-985C-B1484E845855  0.361
2012 Bates JG, Salzman J, May D, Garcia PB, Hogan GJ, McIntosh M, Schlissel MS, Brown PO. Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation. Plos One. 7: e37108. PMID 22693568 DOI: 10.1371/Journal.Pone.0037108  0.303
2012 Pride DT, Salzman J, Relman DA. Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environmental Microbiology. 14: 2564-76. PMID 22583485 DOI: 10.1111/J.1462-2920.2012.02775.X  0.309
2012 Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. Plos One. 7: e30733. PMID 22319583 DOI: 10.1371/Journal.Pone.0030733  0.481
2012 Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA, Loomer P, Armitage GC, Relman DA. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. The Isme Journal. 6: 915-26. PMID 22158393 DOI: 10.1038/Ismej.2011.169  0.323
2012 Nieves BI, Niu S, Vaka D, Salzman J, Brown P, Sweet-Cordero AI. Abstract 204: Molecular function of the RNA binding protein EWS in RNA processing Cancer Research. 72: 204-204. DOI: 10.1158/1538-7445.Am2012-204  0.397
2011 Salzman J, Jiang H, Wong WH. Statistical Modeling of RNA-Seq Data. Statistical Science : a Review Journal of the Institute of Mathematical Statistics. 26. PMID 24307754 DOI: 10.1214/10-Sts343  0.463
2011 Salzman J, Marinelli RJ, Wang PL, Green AE, Nielsen JS, Nelson BH, Drescher CW, Brown PO. ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma. Plos Biology. 9: e1001156. PMID 21949640 DOI: 10.1371/Journal.Pbio.1001156  0.333
2011 Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA. Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Research. 21: 126-36. PMID 21149389 DOI: 10.1101/Gr.111732.110  0.321
2010 Tsvetanova NG, Klass DM, Salzman J, Brown PO. Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. Plos One. 5. PMID 20844764 DOI: 10.1371/Journal.Pone.0012671  0.415
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