Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus

Mammalian odorant receptors: functional evolution and variation

(2015) Yue Jiang et al.   CURRENT OPINION IN NEUROBIOLOGY

Potential Mechanisms for Cancer Resistance in Elephants and Comparative Cellular Response to DNA Damage in Humans

(2015) Lisa M. Abegglen et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic

(2015) Vincent J. Lynch et al.   Cell Reports

Insights into the Evolution of Longevity from the Bowhead Whale Genome

(2015) Michael Keane et al.   Cell Reports

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals

(2014) Yoshihito Niimura et al.   GENOME RESEARCH

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers

(2014) Hui Zhi et al.   NUCLEIC ACIDS RESEARCH

Low coverage sequencing of two Asian elephant (Elephas maximus) genomes

(2014) Akbar Dastjerdi et al.   GigaScience

Genome-wide signatures of convergent evolution in echolocating mammals

(2013) Joe Parker et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer

(2013) Zhou Du et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

Olfactory Receptor Multigene Family in Vertebrates: From the Viewpoint of Evolutionary Genomics

(2012) Yoshihito Niimura   CURRENT GENOMICS

The Chromosomes of Afrotheria and Their Bearing on Mammalian Genome Evolution

(2012) M. Svartman et al.   CYTOGENETIC AND GENOME RESEARCH

Elephant Transcriptome Provides Insights into the Evolution of Eutherian Placentation

(2012) Zhuo-Cheng Hou et al.   Genome Biology and Evolution

A Comparison of Social Organization in Asian Elephants and African Savannah Elephants

(2012) Shermin de Silva et al.   INTERNATIONAL JOURNAL OF PRIMATOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant

(2012) Reeta Sharma et al.   PLoS One

A Central Role for Long Non-Coding RNA in Cancer

(2012) Sheetal A. Mitra et al.   Frontiers in Genetics

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

The functional role of long non-coding RNA in human carcinomas

(2011) Ewan A Gibb et al.   Molecular Cancer

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Insightful Problem Solving in an Asian Elephant

(2011) Preston Foerder et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Diverse factors are involved in maintaining X chromosome inactivation

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Degeneration of Olfactory Receptor Gene Repertories in Primates: No Direct Link to Full Trichromatic Vision

(2010) A. Matsui et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants

(2010) Nadin Rohland et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ecological adaptation determines functional mammalian olfactory subgenomes

(2009) S. Hayden et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Vocalizations of wild Asian elephants (Elephas maximus): Structural classification and social context

(2009) Smita Nair et al.   JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Dental eruption in afrotherian mammals

(2008) Robert J Asher et al.   BMC BIOLOGY

Elephant cognition

(2008) Lucy A. Bates et al.   CURRENT BIOLOGY

Afrotherian mammals: a review of current data

(2008) Rodolphe Tabuce et al.   MAMMALIA

Comparative genomics and the study of evolution by natural selection

(2008) HANS ELLEGREN   MOLECULAR ECOLOGY

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants

(2008) T.N.C Vidya et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology