Comparative transcriptomics in human and mouse

Lineage-specific genomics: Frequent birth and death in the human genome

(2016) Robert S. Young   BIOESSAYS

Toward more predictive genetic mouse models of Alzheimer's disease

(2016) Kristen D. Onos et al.   BRAIN RESEARCH BULLETIN

Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification

(2016) Ferdinand von Meyenn et al.   DEVELOPMENTAL CELL

Using the mouse to model human disease: increasing validity and reproducibility

(2016) Monica J. Justice et al.   Disease Models & Mechanisms

Defining the consequences of genetic variation on a proteome-wide scale

(2016) Joel M. Chick et al.   NATURE

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

A developmental coordinate of pluripotency among mice, monkeys and humans

(2016) Tomonori Nakamura et al.   NATURE

Down syndrome and the complexity of genome dosage imbalance

(2016) Stylianos E. Antonarakis   NATURE REVIEWS GENETICS

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

ncRNA orthologies in the vertebrate lineage

(2016) Miguel Pignatelli et al.   Database-The Journal of Biological Databases and Curation

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

(2015) Olgert Denas et al.   BMC GENOMICS

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Animal models of Duchenne muscular dystrophy: from basic mechanisms to gene therapy

(2015) J. W. McGreevy et al.   Disease Models & Mechanisms

Single‐cell transcriptomes reveal characteristic features of human pancreatic islet cell types

(2015) Jin Li et al.   EMBO REPORTS

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

High-Resolution Gene Expression Profiling Using RNA Sequencing in Patients With Inflammatory Bowel Disease and in Mouse Models of Colitis

(2015) Kristine Holgersen et al.   Journal of Crohns & Colitis

Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages

(2015) Alasdair W. Jubb et al.   JOURNAL OF IMMUNOLOGY

Collaborative Cross and Diversity Outbred data resources in the Mouse Phenome Database

(2015) Molly A. Bogue et al.   MAMMALIAN GENOME

Creating reference gene annotation for the mouse C57BL6/J genome assembly

(2015) Jonathan M. Mudge et al.   MAMMALIAN GENOME

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

(2015) Hagen Tilgner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Mouse genome database 2016

(2015) Carol J. Bult et al.   NUCLEIC ACIDS RESEARCH

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

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

(2015) et al.   SCIENCE

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

(2015) Dmitri D. Pervouchine et al.   Nature Communications

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

BLT humanized mice as a small animal model of HIV infection

(2015) Marshall E Karpel et al.   Current Opinion in Virology

Evidence for a common evolutionary rate in metazoan transcriptional networks

(2015) Anne-Ruxandra Carvunis et al.   eLife

RNA-seq: impact of RNA degradation on transcript quantification

(2014) Irene Gallego Romero et al.   BMC BIOLOGY

Comparative studies of gene regulatory mechanisms

(2014) Athma A Pai et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A Mouse Geneticist's Practical Guide to CRISPR Applications

(2014) P. Singh et al.   GENETICS

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

(2014) S. Washietl et al.   GENOME RESEARCH

Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains

(2014) Sara Mostafavi et al.   JOURNAL OF IMMUNOLOGY

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

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

(2014) Barbara Treutlein et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Clinical development success rates for investigational drugs

(2014) Michael Hay et al.   NATURE BIOTECHNOLOGY

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Mouse Tumor Biology (MTB): a database of mouse models for human cancer

(2014) Carol J. Bult et al.   NUCLEIC ACIDS RESEARCH

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Genomic responses in mouse models greatly mimic human inflammatory diseases

(2014) Keizo Takao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional divergence and conservation of human and mouse erythropoiesis

(2014) N. Pishesha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of the transcriptional landscapes between human and mouse tissues

(2014) Shin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic responses to inflammation in mouse models mimic humans: We concur, apples to oranges comparisons won’t do

(2014) Tal Shay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mice are not men

(2014) H. Shaw Warren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Animal models of neurodegenerative diseases

(2014) Fabiola Mara Ribeiro et al.   REVISTA BRASILEIRA DE PSIQUIATRIA

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

(2014) Benoit Ballester et al.   eLife

Molecular functions of small regulatory noncoding RNA

(2013) Yong Huang et al.   BIOCHEMISTRY-MOSCOW

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

(2013) Young-suk Lee et al.   BIOINFORMATICS

An expression atlas of human primary cells: inference of gene function from coexpression networks

(2013) Neil A Mabbott et al.   BMC GENOMICS

Long non-coding RNAs: A new frontier in the study of human diseases

(2013) Xuefei Shi et al.   CANCER LETTERS

Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation

(2013) Olga A. Vakhrusheva et al.   Genome Biology and Evolution

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

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

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

The mouse as a model organism in aging research: Usefulness, pitfalls and possibilities

(2012) Valerie Vanhooren et al.   AGEING RESEARCH REVIEWS

Birth and expression evolution of mammalian microRNA genes

(2012) J. Meunier et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Human Tumor Xenografts: The Good, the Bad, and the Ugly

(2012) Richard A Morgan   MOLECULAR THERAPY

ENCODE: The human encyclopaedia

(2012) Brendan Maher   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs

(2012) Julien Roux et al.   NUCLEIC ACIDS RESEARCH

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

(2012) K. Schroder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

MicroRNAs in Common Human Diseases

(2012) Yu Li et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Saitohin, which is nested within the tau gene, interacts with tau and Abl and its human-specific allele influences Abl phosphorylation

(2011) Yan Wang et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Europe to map the human epigenome

(2011) Alison Abbott   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes

(2011) Claudia Kutter et al.   NATURE GENETICS

Subspecific origin and haplotype diversity in the laboratory mouse

(2011) Hyuna Yang et al.   NATURE GENETICS

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

Large scale comparison of global gene expression patterns in human and mouse

(2011) Xiangqun Zheng-Bradley et al.   GENOME BIOLOGY

Assessment of orthologous splicing isoforms in human and mouse orthologous genes

(2010) Federico Zambelli et al.   BMC GENOMICS

Assessment of Feeding Behavior in Laboratory Mice

(2010) Kate L.J. Ellacott et al.   Cell Metabolism

Functional clustering and lineage markers: Insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations

(2010) David A. Hume et al.   GENOMICS

Analysis of microRNA knockouts in mice

(2010) C. Y. Park et al.   HUMAN MOLECULAR GENETICS

Animal model for study of human hepatitis viruses

(2010) Kazuaki Chayama et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Constraints and plasticity in genome and molecular-phenome evolution

(2010) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

Behavioural phenotyping assays for mouse models of autism

(2010) Jill L. Silverman et al.   NATURE REVIEWS NEUROSCIENCE

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

Of mice and men: comparative proteomics of bronchoalveolar fluid

(2009) S. A. Gharib et al.   EUROPEAN RESPIRATORY JOURNAL

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

Evolution of the Vertebrate Gene Regulatory Network Controlled by the Transcriptional Repressor REST

(2009) R. Johnson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

Contemporary approaches for modifying the mouse genome

(2008) David J. Adams et al.   PHYSIOLOGICAL GENOMICS