Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

The contribution of cell cycle to heterogeneity in single-cell RNA-seq data

(2016) Andrew McDavid et al.   NATURE BIOTECHNOLOGY

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Modeling ALS with motor neurons derived from human induced pluripotent stem cells

(2016) Samuel Sances et al.   NATURE NEUROSCIENCE

Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex

(2016) L. Telley et al.   SCIENCE

Inference of Ancestral Recombination Graphs through Topological Data Analysis

(2016) Pablo G. Cámara et al.   PLoS Computational Biology

Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination

(2016) Pablo G. Camara et al.   Cell Systems

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development

(2015) Mathieu Quesnel-Vallières et al.   GENES & DEVELOPMENT

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

Identification of type 2 diabetes subgroups through topological analysis of patient similarity

(2015) Li Li et al.   Science Translational Medicine

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long intergenic non-coding RNA HOTAIRM1 regulates cell cycle progression during myeloid maturation in NB4 human promyelocytic leukemia cells

(2014) Xueqing Zhang et al.   RNA Biology

RNA Protein Interaction in Neurons

(2013) Robert B. Darnell   Annual Review of Neuroscience

The regulation of Hox gene expression during animal development

(2013) Moisés Mallo et al.   DEVELOPMENT

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

Intricate interplay between astrocytes and motor neurons in ALS

(2013) H. P. Phatnani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topology of viral evolution

(2013) J. M. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retinoic acid signalling during development

(2012) M. Rhinn et al.   DEVELOPMENT

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

(2011) Mingyan Lin et al.   PLoS One

Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival

(2011) M. Nicolau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

Engineering the embryoid body microenvironment to direct embryonic stem cell differentiation

(2009) Andrés M. Bratt-Leal et al.   BIOTECHNOLOGY PROGRESS

Regulation of Vertebrate Nervous System Alternative Splicing and Development by an SR-Related Protein

(2009) John A. Calarco et al.   CELL

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH