List of works - Joshua D Welch

A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration

scientific article published on 16 January 2020

A multimodal cell census and atlas of the mammalian primary motor cortex

scientific article

A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs.

scientific article

A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues

scientific article

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

Construction of Genomic Regulatory Encyclopedias: Strategies and Case Studies

Deep sequencing shows multiple oligouridylations are required for 3' to 5' degradation of histone mRNAs on polyribosomes

scientific article

EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates

scientific article published on 26 May 2015

Jointly defining cell types from multiple single-cell datasets using LIGER

scientific article published on 12 October 2020

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

scientific article

MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networks

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

scientific article

PyLiger: scalable single-cell multi-omic data integration in Python

scientific article published in 2022

Robust detection of alternative splicing in a population of single cells

scientific article published on 5 January 2016

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

scientific article

Selective single cell isolation for genomics using microraft arrays

scientific article published on 16 August 2016

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

scientific article published on 06 June 2019

Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming

scientific article published on 20 June 2019

Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte.

scientific article published on 25 October 2017

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

scientific article

TUT7 catalyzes the uridylation of the 3' end for rapid degradation of histone mRNA.

scientific article published on 8 September 2016

The word landscape of the non-coding segments of the Arabidopsis thaliana genome

scientific article

UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization

scientific article published in 2022

Word-based characterization of promoters involved in human DNA repair pathways

scientific article

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

scientific article

List of works by Joshua D Welch

A Wnt-mediated transformation of the bone marrow stromal cell identity orchestrates skeletal regeneration

A multimodal cell census and atlas of the mammalian primary motor cortex

A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs.

A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Construction of Genomic Regulatory Encyclopedias: Strategies and Case Studies

Deep sequencing shows multiple oligouridylations are required for 3' to 5' degradation of histone mRNAs on polyribosomes

EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates

Jointly defining cell types from multiple single-cell datasets using LIGER

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networks

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

PyLiger: scalable single-cell multi-omic data integration in Python

Robust detection of alternative splicing in a population of single cells

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Selective single cell isolation for genomics using microraft arrays

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming

Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte.

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

TUT7 catalyzes the uridylation of the 3' end for rapid degradation of histone mRNA.

The word landscape of the non-coding segments of the Arabidopsis thaliana genome

UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization

Word-based characterization of promoters involved in human DNA repair pathways

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures