How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data

Detection of aberrant gene expression events in RNA sequencing data

(2021) Vicente A. Yépez et al.   Nature Protocols

Detection of aberrant splicing events in RNA-seq data using FRASER

(2021) Christian Mertes et al.   Nature Communications

A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

(2021) Sijin Cheng et al.   CELL

Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics

(2021) Lars Velten et al.   Nature Communications

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Beyond mass spectrometry, the next step in proteomics

(2020) Winston Timp et al.   Science Advances

LeafCutterMD: an algorithm for outlier splicing detection in rare diseases

(2020) Garrett Jenkinson et al.   BIOINFORMATICS

Single-Cell RNA Sequencing and Its Combination with Protein and DNA Analyses

(2020) Jane Ru Choi et al.   Cells

The emergence and promise of single-cell temporal-omics approaches

(2020) Alex R Lederer et al.   CURRENT OPINION IN BIOTECHNOLOGY

Methodologies for Transcript Profiling Using Long-Read Technologies

(2020) Spyros Oikonomopoulos et al.   Frontiers in Genetics

Genetics of mitochondrial diseases: Identifying mutations to help diagnosis

(2020) Sarah L. Stenton et al.   EBioMedicine

Transcriptomic signatures across human tissues identify functional rare genetic variation

(2020) Nicole M. Ferraro et al.   SCIENCE

Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing

(2020) David R. Murdock et al.   JOURNAL OF CLINICAL INVESTIGATION

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome

(2019) Nurun Nahar Borna et al.   NEUROGENETICS

Altered human oligodendrocyte heterogeneity in multiple sclerosis

(2019) Sarah Jäkel et al.   NATURE

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

(2019) Deanne M. Taylor et al.   DEVELOPMENTAL CELL

Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease

(2019) Hernan D. Gonorazky et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The diagnosis of inborn errors of metabolism by an integrative “multi‐omics” approach: a perspective encompassing genomics, transcriptomics and proteomics

(2019) Sarah Louise Stenton et al.   JOURNAL OF INHERITED METABOLIC DISEASE

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

(2019) Fan Zhang et al.   NATURE IMMUNOLOGY

Long-Read Sequencing Emerging in Medical Genetics

(2019) Tuomo Mantere et al.   Frontiers in Genetics

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts

(2019) Laure Frésard et al.   NATURE MEDICINE

Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database

(2019) Stéphanie Nguengang Wakap et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Long-read sequencing for rare human genetic diseases

(2019) Satomi Mitsuhashi et al.   JOURNAL OF HUMAN GENETICS

A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease

(2019) Gavin R. Oliver et al.   PLoS One

Genetic regulatory variation in populations informs transcriptome analysis in rare disease

(2019) Pejman Mohammadi et al.   SCIENCE

Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome

(2018) Nicole J. Lake et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Expanding Landscape of Alternative Splicing Variation in Human Populations

(2018) Eddie Park et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fusion genes: A promising tool combating against cancer

(2018) Xiaofeng Dai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly

(2018) Tatsiana Aneichyk et al.   CELL

Rare genetic diseases: update on diagnosis, treatment and online resources

(2018) Robert E. Pogue et al.   DRUG DISCOVERY TODAY

Modeling rare diseases with induced pluripotent stem cell technology

(2018) Ruthellen H. Anderson et al.   MOLECULAR AND CELLULAR PROBES

Points of Significance: Statistics versus machine learning

(2018) Danilo Bzdok et al.   NATURE METHODS

Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis

(2018) Fumitaka Mizoguchi et al.   Nature Communications

Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases

(2018) Michelle M. Clark et al.   npj Genomic Medicine

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data

(2018) Felix Brechtmann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Landscape of X chromosome inactivation across human tissues

(2017) Taru Tukiainen et al.   NATURE

The impact of rare variation on gene expression across tissues

(2017) Xin Li et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Alternative splicing as a regulator of development and tissue identity

(2017) Francisco E. Baralle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

(2017) Beryl B. Cummings et al.   Science Translational Medicine

Concise Review: Induced Pluripotent Stem Cell Research in the Era of Precision Medicine

(2017) Takashi Hamazaki et al.   STEM CELLS

Genetic diagnosis of Mendelian disorders via RNA sequencing

(2017) Laura S. Kremer et al.   Nature Communications

A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood

(2016) Jing Zhao et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

(2016) Lawrence H. Uricchio et al.   GENOME RESEARCH

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care

(2015) S.L. Sawyer et al.   CLINICAL GENETICS

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Effect of predicted protein-truncating genetic variants on the human transcriptome

(2015) M. A. Rivas et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Aberrant Gene Expression in Humans

(2015) Yong Zeng et al.   PLoS Genetics

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

Transcriptome Sequencing of a Large Human Family Identifies the Impact of Rare Noncoding Variants

(2014) Xin Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression

(2014) Iwona Pawlikowska et al.   BIOINFORMATICS

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Investigating human disease using stem cell models

(2014) Jared L. Sterneckert et al.   NATURE REVIEWS GENETICS

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Protein post-translational modifications and regulation of pluripotency in human stem cells

(2013) Yu-Chieh Wang et al.   CELL RESEARCH

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing

(2013) Hagen Tilgner et al.   G3-Genes Genomes Genetics

Intron-centric estimation of alternative splicing from RNA-seq data

(2012) D. D. Pervouchine et al.   BIOINFORMATICS

Genetic Variants Contribute to Gene Expression Variability in Humans

(2012) A. M. Hulse et al.   GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Pre-mRNA splicing in disease and therapeutics

(2012) Ravi K. Singh et al.   TRENDS IN MOLECULAR MEDICINE

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

Principal component analysis based methods in bioinformatics studies

(2011) S. Ma et al.   BRIEFINGS IN BIOINFORMATICS

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Alternative splicing and disease

(2008) Jamal Tazi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS