相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。The Genomic Challenge to Adaptationism
Sahotra Sarkar
BRITISH JOURNAL FOR THE PHILOSOPHY OF SCIENCE (2015)
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
Xiu Cheng Quek et al.
NUCLEIC ACIDS RESEARCH (2015)
Conceptual and Empirical Challenges of Ascribing Functions to Transposable Elements
Tyler A. Elliott et al.
AMERICAN NATURALIST (2014)
The Noncoding RNA Revolution-Trashing Old Rules to Forge New Ones
Thomas R. Cech et al.
CELL (2014)
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
Ariel A. Bazzini et al.
EMBO JOURNAL (2014)
Distinguishing between Function and Effect in Genome Biology
W. Ford Doolittle et al.
GENOME BIOLOGY AND EVOLUTION (2014)
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
Iakes Ezkurdia et al.
HUMAN MOLECULAR GENETICS (2014)
An atlas of active enhancers across human cell types and tissues
Robin Andersson et al.
NATURE (2014)
Alternative splicing at GYNNGY 5′ splice sites: more noise, less regulation
Meng Wang et al.
NUCLEIC ACIDS RESEARCH (2014)
Human coding RNA editing is generally nonadaptive
Guixia Xu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
The new frontier of genome engineering with CRISPR-Cas9
Jennifer A. Doudna et al.
SCIENCE (2014)
RNA and dynamic nuclear organization
John Rinn et al.
SCIENCE (2014)
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
Aurelie Kapusta et al.
TRENDS IN GENETICS (2014)
Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes
Nicholas T. Ingolia et al.
CELL REPORTS (2014)
lncRNA and gene looping What's the connection?
Youtaro Shibayama et al.
TRANSCRIPTION-AUSTIN (2014)
Expanded identification and characterization of mammalian circular RNAs
Junjie U. Guo et al.
GENOME BIOLOGY (2014)
Can ENCODE tell us how much junk DNA we carry in our genome?
Deng-Ke Niu et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2013)
Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases
Ping Wu et al.
BRAIN RESEARCH BULLETIN (2013)
lincRNAs: Genomics, Evolution, and Mechanisms
Igor Ulitsky et al.
CELL (2013)
Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins
Mitchell Guttman et al.
CELL (2013)
The ENCODE project: Missteps overshadowing a success
Sean R. Eddy
CURRENT BIOLOGY (2013)
On the Immortality of Television Sets: Function in the Human Genome According to the Evolution-Free Gospel of ENCODE
Dan Graur et al.
GENOME BIOLOGY AND EVOLUTION (2013)
Widespread and extensive lengthening of 3′ UTRs in the mammalian brain
Pedro Miura et al.
GENOME RESEARCH (2013)
Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
Flavio S. J. de Souza et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
Fan Lai et al.
NATURE (2013)
Circular RNAs are a large class of animal RNAs with regulatory potency
Sebastian Memczak et al.
NATURE (2013)
LNCipedia: a database for annotated human lncRNA transcript sequences and structures
Pieter-Jan Volders et al.
NUCLEIC ACIDS RESEARCH (2013)
Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
Michael A. White et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Is junk DNA bunk? A critique of ENCODE
W. Ford Doolittle
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Circular RNAs are abundant, conserved, and associated with ALU repeats
William R. Jeck et al.
RNA (2013)
A Circuitous Route to Noncoding RNA
Jeremy E. Wilusz et al.
SCIENCE (2013)
Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames
Emile G. Magny et al.
SCIENCE (2013)
The Vast, Conserved Mammalian lincRNome
David Managadze et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression
Mathilde Paris et al.
PLOS GENETICS (2013)
Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs
Matthew J. Hangauer et al.
PLOS GENETICS (2013)
ALREX-elements and introns: two identity elements that promote mRNA nuclear export
Alexander F. Palazzo et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2013)
Trafficking of mRNAs containing ALREX-promoting elements through nuclear speckles
Abdalla Akef et al.
NUCLEUS (2013)
Nuclear export as a key arbiter of mRNA identity in eukaryotes
Alexander F. Palazzo et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2012)
The C-value paradox, junk DNA and ENCODE
Sean R. Eddy
CURRENT BIOLOGY (2012)
Why Transcription Factor Binding Sites Are Ten Nucleotides Long
Alexander J. Stewart et al.
GENETICS (2012)
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs
Hagen Tilgner et al.
GENOME RESEARCH (2012)
Long noncoding RNAs are rarely translated in two human cell lines
Balazs Banfai et al.
GENOME RESEARCH (2012)
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
Thomas Derrien et al.
GENOME RESEARCH (2012)
HP1Swi6 Mediates the Recognition and Destruction of Heterochromatic RNA Transcripts
Claudia Keller et al.
MOLECULAR CELL (2012)
FORUM: Genomics ENCODE explained
Joseph R. Ecker
NATURE (2012)
Landscape of transcription in human cells
Sarah Djebali et al.
NATURE (2012)
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
Colin R. Lickwar et al.
NATURE (2012)
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
NATURE (2012)
Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules
Yang Wang et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)
Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types
Julia Salzman et al.
PLOS ONE (2012)
Gene Loops Enhance Transcriptional Directionality
Sue Mei Tan-Wong et al.
SCIENCE (2012)
GENOMICS ENCODE Project Writes Eulogy For Junk DNA
Elizabeth Pennisi
SCIENCE (2012)
Nascent-Seq reveals novel features of mouse circadian transcriptional regulation
Jerome S. Menet et al.
ELIFE (2012)
Pervasive transcription - Lessons from yeast
Mathieu Tisseur et al.
BIOCHIMIE (2011)
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
Nicholas T. Ingolia et al.
CELL (2011)
Animal Transcription Networks as Highly Connected, Quantitative Continua
Mark D. Biggin
DEVELOPMENTAL CELL (2011)
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
Moran N. Cabili et al.
GENES & DEVELOPMENT (2011)
Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs
David Managadze et al.
GENOME BIOLOGY AND EVOLUTION (2011)
Molecular Mechanisms of Long Noncoding RNAs
Kevin C. Wang et al.
MOLECULAR CELL (2011)
U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation
Daisuke Kaida et al.
NATURE (2010)
Digital Genome-Wide ncRNA Expression, Including SnoRNAs, across 11 Human Tissues Using PolyA-Neutral Amplification
John C. Castle et al.
PLOS ONE (2010)
Genome-wide computational identification and manual annotation of human long noncoding RNA genes
Hui Jia et al.
RNA (2010)
A global view of genomic information - moving beyond the gene and the master regulator
John S. Mattick et al.
TRENDS IN GENETICS (2010)
Most Dark Matter'' Transcripts Are Associated With Known Genes
Harm van Bakel et al.
PLOS BIOLOGY (2010)
Evolution and Functions of Long Noncoding RNAs
Chris P. Ponting et al.
CELL (2009)
Focus on the centre: the role of chromatin on the regulation of centromere identity and function
Monica Torras-Llort et al.
EMBO JOURNAL (2009)
Long noncoding RNAs: functional surprises from the RNA world
Jeremy E. Wilusz et al.
GENES & DEVELOPMENT (2009)
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Mitchell Guttman et al.
NATURE (2009)
Bidirectional promoters generate pervasive transcription in yeast
Zhenyu Xu et al.
NATURE (2009)
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
Helen Neil et al.
NATURE (2009)
Small RNAs in transcriptional gene silencing and genome defence
Danesh Moazed
NATURE (2009)
Effective population size and patterns of molecular evolution and variation
Brian Charlesworth
NATURE REVIEWS GENETICS (2009)
The Peculiarities of Large Intron Splicing in Animals
Samuel Shepard et al.
PLOS ONE (2009)
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
Ahmad M. Khalil et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Absolute quantification of microRNAs by using a universal reference
Ute Bissels et al.
RNA (2009)
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Daniel Ramskold et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Evidence against the energetic cost hypothesis for the short introns in highly expressed genes
Yi-Fei Huang et al.
BMC EVOLUTIONARY BIOLOGY (2008)
A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts
Laura Milligan et al.
MOLECULAR AND CELLULAR BIOLOGY (2008)
Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin
Lidia Vasilieva et al.
MOLECULAR CELL (2008)
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi et al.
NATURE METHODS (2008)
RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters
Pascal Preker et al.
SCIENCE (2008)
Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome
Vanessa Cheung et al.
PLOS BIOLOGY (2008)
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
Xiao-Yong Li et al.
PLOS BIOLOGY (2008)
Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome
Julia A. Chekanova et al.
CELL (2007)
The signal sequence coding region promotes nuclear export of mRNA
Alexander F. Palazzo et al.
PLOS BIOLOGY (2007)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Ewan Birney et al.
NATURE (2007)
Association of protein biogenesis factors at the yeast ribosomal tunnel exit is affected by the translational status and nascent polypeptide sequence
Uta Raue et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2007)
Transcriptional noise and the fidelity of initiation by RNA polymerase II
Kevin Struhl
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2007)
Transcription termination and nuclear degradation of cryptic unstable transcripts: A role for the Nrd1-Nab3 pathway in genome surveillance
Marilyne Thiebaut et al.
MOLECULAR CELL (2006)
Genome-wide analysis of mammalian promoter architecture and evolution
Piero Carninci et al.
NATURE GENETICS (2006)
Introns and the origin of nucleus-cytosol compartmentalization
W Martin et al.
NATURE (2006)
Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae
CA Davis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
The transcriptional landscape of the mammalian genome
P Carninci et al.
SCIENCE (2005)
Cryptic Pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase
F Wyers et al.
CELL (2005)
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray
MG Carter et al.
GENOME BIOLOGY (2005)
Nonsense-mediated mRNA decay: terminating erroneous gene expression
KE Baker et al.
CURRENT OPINION IN CELL BIOLOGY (2004)
Physical stability of proteins in aqueous solution: Mechanism and driving forces in nonnative protein aggregation
EY Chi et al.
PHARMACEUTICAL RESEARCH (2003)
Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells
SH Lu et al.
RNA (2003)
Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases
BJ Blencowe
TRENDS IN BIOCHEMICAL SCIENCES (2000)