J. Salzman

发表

Projection Pursuit for Discrete Data

P. Diaconis, J. Salzman, 2008, 0805.3043.

Statistical properties of an early stopping rule for resampling-based multiple testing.

J. Salzman, Hui Jiang, 2012, Biometrika.

ESRRA-C11orf20 Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma

Robert J. Marinelli, P. Brown, R. J. Marinelli, 2011, PLoS biology.

Detecting circular RNAs: bioinformatic and experimental challenges

J. Salzman, L. Szabo, 2016, Nature Reviews Genetics.

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

Charles Gawad, Julia Salzman, Patrick O. Brown, 2012, PloS one.

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

Linda Szabo, Julia Salzman, Nathan J. Palpant, 2015, Genome Biology.

Circular RNA Is Expressed across the Eukaryotic Tree of Life

P. Brown, J. Dinneny, Gregory J. Hogan, 2014, PloS one.

Cell-Type Specific Features of Circular RNA Expression

Julia Salzman, Patrick O. Brown, P. Brown, 2013, PLoS genetics.

Circular RNA biogenesis can proceed through an exon-containing lariat precursor

Julia Salzman, J. Salzman, Peter L Wang, 2015, eLife.

Circular RNA Expression: Its Potential Regulation and Function.

Julia Salzman, J. Salzman, 2016, Trends in genetics : TIG.

Circular RNAs: analysis, expression and potential functions

Julia Salzman, J. Salzman, Steven P Barrett, 2016, Development.

Correction: Circular RNA Is Expressed across the Eukaryotic Tree of Life

P. Brown, J. Dinneny, Gregory J. Hogan, 2014, PLoS ONE.

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

O. Delaneau, M. Rivas, A. Raja, 2020, medRxiv.

Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer drivers

E. Lehnert, J. Salzman, Roozbeh Dehghannasiri, 2019, Proceedings of the National Academy of Sciences.

Specific splice junction detection in single cells with SICILIAN

J. Salzman, Roozbeh Dehghannasiri, J. Olivieri, 2020, Genome Biology.

Precise, pan-cancer discovery of gene fusions reveals a signature of selection in primary tumors

E. Lehnert, J. Salzman, J. Howard, 2017, bioRxiv.

Statistical algorithms improve accuracy of gene fusion detection

E. A. Sweet-Cordero, J. Salzman, L. Szabo, 2017, Nucleic acids research.

The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans

Venkata. N. P. Vemuri, Robert C. Jones, N. Neff, 2022, bioRxiv.

Extensive Gene-Specific Translational Reprogramming in a Model of B Cell Differentiation and Abl-Dependent Transformation

Damon H. May, M. McIntosh, Patty B. Garcia, 2012, PLoS ONE.

Conservation of streptococcal CRISPRs on human skin and saliva

Melissa Ly, D. Pride, J. Salzman, 2014, BMC Microbiology.

Activated interstitial macrophages are a predominant target of viral takeover and focus of inflammation in COVID-19 initiation in human lung

Aaron J. Wilk, I. Weissman, S. Quake, 2023, bioRxiv.

Improved Discovery of Molecular Interactions in Genome-Scale Data with Adaptive Model-Based Normalization

P. Brown, J. Salzman, D. Klass, 2013, PloS one.

A statistical, reference-free algorithm subsumes myriad problems in genome science and enables novel discovery

Tavor Z. Baharav, J. Salzman, Kaitlin Chaung, 2022 .

Automated assays for superoxide dismutase, catalase, glutathione peroxidase, and glutathione reductase activity.

J. Salzman, S. Omaye, N. Elsayed, 1990, Analytical biochemistry.

Supplementary Materials for A statistical reference-free genomic algorithm subsumes common workflows and enables novel discovery

Tavor Z. Baharav, J. Salzman, Kaitlin Chaung, 2022 .

DIVE: a reference-free statistical approach to diversity-generating & mobile genetic element discovery

J. Salzman, Peter L. Wang, J. Abante, 2023, bioRxiv.

The SZS is an efficient statistical method to identify regulated splicing events in droplet-based RNA sequencing

J. Salzman, Roozbeh Dehghannasiri, J. Olivieri, 2020, bioRxiv.

Independent regulation of prostaglandin production and the stress response in human fibroblasts

J. Salzman, P. Bowman, 1992, Journal of Cellular Physiology.

TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron-dependent neurological phenotypes in vivo and prevents neurodegeneration

B. Wirth, S. Artandi, L. Pellizzoni, 2022, Nucleic acids research.

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

L. Laurent, Robert E Morey, M. Parast, 2015, Genome Biology.

ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq

J. Salzman, Roozbeh Dehghannasiri, Kaitlin Chaung, 2022, bioRxiv.

Statistical analysis supports pervasive RNA subcellular localization and alternative 3’ UTR regulation

J. Salzman, D. Greif, Rob Bierman, 2023, bioRxiv.

Limits on the ability of quantum states to convey classical messages

Ashwin Nayak, Julia Salzman, A. Nayak, 2006, JACM.

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

D. Relman, M. Haynes, F. Rohwer, 2011, The ISME Journal.

Hyperammonemia after capecitabine associated with occult impairment of the urea cycle

J. Salzman, Gilbert Chu, 2019, Cancer medicine.

Cell types of origin of the cell-free transcriptome

Venkata. N. P. Vemuri, Robert C. Jones, N. Neff, 2022, Nature Biotechnology.

Correction: Cell-Type Specific Features of Circular RNA Expression

P. Brown, Raymond E. Chen, J. Salzman, 2013, PLoS Genetics.

Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells

Tavor Z. Baharav, J. Salzman, Roozbeh Dehghannasiri, 2022, bioRxiv.

Statistical Modeling of RNA-Seq Data.

Hui Jiang, Julia Salzman, Wing Hung Wong, 2011, Statistical science : a review journal of the Institute of Mathematical Statistics.

The SpliZ generalizes ‘percent spliced in’ to reveal regulated splicing at single-cell resolution

J. Salzman, Roozbeh Dehghannasiri, J. Olivieri, 2022, Nature Methods.

RNA splicing programs define tissue compartments and cell types at single cell resolution

S. Quake, M. Krasnow, Serena Y Tan, 2021, bioRxiv.

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time.

Christine L. Sun, J. Banfield, D. Relman, 2011, Genome research.

DIVE: a reference-free statistical approach to diversity-generating & mobile genetic element discovery

J. Salzman, J. Abante, P.L. Wang, 2023, bioRxiv.

ReadZS detects developmentally regulated RNA processing programs in single cell RNA-seq and defines subpopulations independent of gene expression

J. Salzman, Roozbeh Dehghannasiri, Kaitlin Chaung, 2021 .

TGS1 controls snRNA 3’ end processing, prevents neurodegeneration and ameliorates SMN-dependent neurological phenotypes in vivo

B. Wirth, S. Artandi, L. Pellizzoni, 2020, bioRxiv.

Best permutation analysis

Julia Salzman, Bala Rajaratnam, B. Rajaratnam, 2013, J. Multivar. Anal..

RNA splicing programs define tissue compartments and cell types at single-cell resolution

S. Quake, M. Krasnow, Serena Y Tan, 2021, eLife.

Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

D. Herschlag, F. Sunden, A. Peck, 2015, eLife.

Association between living environment and human oral viral ecology

Melissa Ly, D. Pride, J. Salzman, 2013, The ISME Journal.

Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae

Julia Salzman, Patrick O. Brown, P. Brown, 2010, PloS one.

ciRS-7 exonic sequence is embedded in a long non-coding RNA locus

Kevin R. Parker, J. Salzman, Steven P. Barrett, 2017, bioRxiv.

A guide to naming eukaryotic circular RNAs

Howard Y. Chang, M. Gorospe, N. Rajewsky, 2023, Nature Cell Biology.

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

Osagie G. Izuogu, P. Flicek, P. Stadler, 2022, bioRxiv.

Erratum to: Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

L. Laurent, M. Parast, C. Murry, 2016, Genome Biology.

Widespread mRNA Association with Cytoskeletal Motor Proteins and Identification and Dynamics of Myosin-Associated mRNAs in S. cerevisiae

W. E. Moerner, Julia Salzman, Patrick O. Brown, 2012, PloS one.

A statistical reference-free algorithm subsumes and generalizes common genomic sequence analysis and uncovers novel biological regulation

Tavor Z. Baharav, J. Salzman, Peter L Wang, 2023 .

Comparisons of CRISPRs and viromes in human saliva reveal bacterial adaptations to salivary viruses

D. Relman, D. Pride, J. Salzman, 2012 .

Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses.

D. Relman, D. Pride, J. Salzman, 2012, Environmental microbiology.

Human oral viruses are personal, persistent and gender-consistent

Julia Salzman, Refugio Robles-Sikisaka, Melissa Ly, 2014, The ISME Journal.

Conservation of streptococcal CRISPRs on human skin and saliva

Melissa Ly, D. Pride, J. Salzman, 2014, BMC Microbiology.

Ambiguous splice sites distinguish circRNA and linear splicing in the human genome

Roozbeh Dehghannasiri, Linda Szabo, Julia Salzman, 2018, Bioinform..

An interpretable, finite sample valid alternative to Pearson’s X2 for scientific discovery

Tavor Z. Baharav, David Tse, J. Salzman, 2023, bioRxiv.

Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation

J. Salzman, J. Olivieri, 2023, bioRxiv.

1 ciRS-7 exonic sequence is embedded in a long non-coding RNA locus 1 2

Kevin R. Parker, J. Salzman, Steven P. Barrett, 2017 .

Erratum to: Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

L. Laurent, M. Parast, C. Murry, 2016, Genome Biology.

NOMAD2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads

Tavor Z. Baharav, S. Deorowicz, J. Salzman, 2023, bioRxiv.

Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens

J. Carette, J. Salzman, R. Rohatgi, 2018, bioRxiv.

DIVE: a reference-free statistical approach to diversity-generating & mobile genetic element discovery

J. Salzman, J. Abante, P. Wang, 2023, bioRxiv.

Reliable concurrent calling of multiple genetic alleles and 24-chromosome ploidy without embryo freezing using parental support™ technology (PS)

M. Rabinowitz, C. Cinnioğlu, J. Salzman, 2008 .

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

Osagie G. Izuogu, P. Flicek, P. Stadler, 2023, bioRxiv.

SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

Tavor Z. Baharav, J. Salzman, Peter L Wang, 2022, Cell.

SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads

Tavor Z. Baharav, S. Deorowicz, J. Salzman, 2023, bioRxiv.

A penalized likelihood approach for robust estimation of isoform expression.

Julia Salzman, Hui Jiang, J. Salzman, 2013, Statistics and its interface.

Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens

J. Carette, J. Salzman, R. Rohatgi, 2018, bioRxiv.

On communication over an entanglement-assisted quantum channel

Ashwin Nayak, Julia Salzman, A. Nayak, 2002, Proceedings 17th IEEE Annual Conference on Computational Complexity.

RNA Isoform Discovery Through Goodness of Fit Diagnostics

Julia Salzman, J. Salzman, 2014 .

Author response: Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

D. Herschlag, F. Sunden, A. Peck, 2015 .

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

L. Laurent, M. Parast, C. Murry, 2015, Genome Biology.

The Plateau Problem in the Heteroskedastic Probit Model

David K. Park, L. Keele, J. Salzman, 2015, 1508.03262.