Role of non-coding sequence variants in cancer

E Khurana, Y Fu, D Chakravarty, F Demichelis… - Nature Reviews …, 2016 - nature.com
Patients with cancer carry somatic sequence variants in their tumour in addition to the
germline variants in their inherited genome. Although variants in protein-coding regions …

Overcoming challenges and dogmas to understand the functions of pseudogenes

SW Cheetham, GJ Faulkner, ME Dinger - Nature Reviews Genetics, 2020 - nature.com
Pseudogenes are defined as regions of the genome that contain defective copies of genes.
They exist across almost all forms of life, and in mammalian genomes are annotated in …

GENCODE reference annotation for the human and mouse genomes

A Frankish, M Diekhans, AM Ferreira… - Nucleic acids …, 2019 - academic.oup.com
The accurate identification and description of the genes in the human and mouse genomes
is a fundamental requirement for high quality analysis of data informing both genome …

GENCODE: the reference human genome annotation for The ENCODE Project

J Harrow, A Frankish, JM Gonzalez, E Tapanari… - Genome …, 2012 - genome.cshlp.org
The GENCODE Consortium aims to identify all gene features in the human genome using a
combination of computational analysis, manual annotation, and experimental validation …

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

MN Cabili, C Trapnell, L Goff, M Koziol… - Genes & …, 2011 - genesdev.cshlp.org
Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse
cellular processes. Determining the function of individual lincRNAs remains a challenge …

A super pan-genomic landscape of rice

L Shang, X Li, H He, Q Yuan, Y Song, Z Wei, H Lin… - Cell Research, 2022 - nature.com
Pan-genomes from large natural populations can capture genetic diversity and reveal
genomic complexity. Using de novo long-read assembly, we generated a graph-based …

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

P Lamesch, TZ Berardini, D Li, D Swarbreck… - Nucleic acids …, 2012 - academic.oup.com
Abstract The Arabidopsis Information Resource (TAIR, http://arabidopsis. org) is a genome
database for Arabidopsis thaliana, an important reference organism for many fundamental …

ENCODE data in the UCSC Genome Browser: year 5 update

KR Rosenbloom, CA Sloan, VS Malladi… - Nucleic acids …, 2012 - academic.oup.com
Abstract The Encyclopedia of DNA Elements (ENCODE), http://encodeproject. org, has
completed its fifth year of scientific collaboration to create a comprehensive catalog of …

A user's guide to the encyclopedia of DNA elements (ENCODE)

ENCODE Project Consortium - PLoS biology, 2011 - journals.plos.org
The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the
scientific and medical communities to interpret the human genome sequence and apply it to …

Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum

Q Gao, K **, SH Ying, Y Zhang, G **ao, Y Shang… - PLoS …, 2011 - journals.plos.org
Metarhizium spp. are being used as environmentally friendly alternatives to chemical
insecticides, as model systems for studying insect-fungus interactions, and as a resource of …