Volume 19, issue 1, December 2018
229 articles in this issue
-
-
Bottlenecks for genome-edited crops on the road from lab to farm
Authors
- Armin Scheben
- David Edwards
- Content type: Opinion
- Open Access
- Published: 26 October 2018
- Article: 178
This is part of 1 collection: -
CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Authors (first, second and last of 5)
- Ferhat Alkan
- Anne Wenzel
- Jan Gorodkin
- Content type: Research
- Open Access
- Published: 26 October 2018
- Article: 177
This is part of 1 collection: -
Alternative polyadenylation factors link cell cycle to migration
Authors (first, second and last of 12)
- Mithun Mitra
- Elizabeth L Johnson
- Hilary A Coller
- Content type: Research
- Open Access
- Published: 25 October 2018
- Article: 176
This is part of 1 collection: -
Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
Authors (first, second and last of 10)
- Hua Ying
- Ira Cooke
- David J. Miller
- Content type: Research
- Open Access
- Published: 02 November 2018
- Article: 175
This is part of 1 collection: -
Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors
Authors (first, second and last of 4)
- Xiaoyan Ma
- Daphne Ezer
- Tim J. Stevens
- Content type: Research
- Open Access
- Published: 25 October 2018
- Article: 174
-
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants
Authors (first, second and last of 6)
- Corneliu A. Bodea
- Adele A. Mitchell
- Shamil R. Sunyaev
- Content type: Software
- Open Access
- Published: 25 October 2018
- Article: 173
-
Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data
Authors
- Basel Abu-Jamous
- Steven Kelly
- Content type: Software
- Open Access
- Published: 25 October 2018
- Article: 172
-
Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
Authors (first, second and last of 11)
- Rebecca E O’Connor
- Marta Farré
- Darren K Griffin
- Content type: Research
- Open Access
- Published: 24 October 2018
- Article: 171
This is part of 1 collection: -
Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing
Authors (first, second and last of 15)
- Tao Guo
- Yi-Li Feng
- An-Yong Xie
- Content type: Research
- Open Access
- Published: 19 October 2018
- Article: 170
This is part of 1 collection: -
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Authors (first, second and last of 10)
- Vivien A. C. Schoonenberg
- Mitchel A. Cole
- Daniel E. Bauer
- Content type: Method
- Open Access
- Published: 19 October 2018
- Article: 169
This is part of 1 collection: -
Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial
Authors (first, second and last of 17)
- Emma E. Davenport
- Tiffany Amariuta
- Soumya Raychaudhuri
- Content type: Research
- Open Access
- Published: 19 October 2018
- Article: 168
-
SeqOthello: querying RNA-seq experiments at scale
Authors (first, second and last of 8)
- Ye Yu
- Jinpeng Liu
- Jinze Liu
- Content type: Method
- Open Access
- Published: 19 October 2018
- Article: 167
-
Chromosome evolution at the origin of the ancestral vertebrate genome
Authors (first, second and last of 5)
- Christine Sacerdot
- Alexandra Louis
- Hugues Roest Crollius
- Content type: Research
- Open Access
- Published: 17 October 2018
- Article: 166
This is part of 1 collection: -
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Authors (first, second and last of 4)
- Daniel J. Nasko
- Sergey Koren
- Todd J. Treangen
- Content type: Open Letter
- Open Access
- Published: 30 October 2018
- Article: 165
-
CRISPR-induced exon skipping is dependent on premature termination codon mutations
Authors (first, second and last of 8)
- Tingting Sui
- Yuning Song
- Zhanjun Li
- Content type: Short report
- Open Access
- Published: 17 October 2018
- Article: 164
-
Holo-Seq: single-cell sequencing of holo-transcriptome
Authors (first, second and last of 10)
- Zhengyun Xiao
- Guo Cheng
- Junling Jia
- Content type: Method
- Open Access
- Published: 17 October 2018
- Article: 163
-
A comparative study of endoderm differentiation in humans and chimpanzees
Authors (first, second and last of 8)
- Lauren E. Blake
- Samantha M. Thomas
- Bryan J. Pavlovic
- Content type: Research
- Open Access
- Published: 15 October 2018
- Article: 162
This is part of 1 collection: -
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
Authors (first, second and last of 4)
- Bogdan Budnik
- Ezra Levy
- Nikolai Slavov
- Content type: Method
- Open Access
- Published: 22 October 2018
- Article: 161
-
CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops
Authors (first, second and last of 6)
- Yu Guo
- Andrew A. Perez
- Peggy J. Farnham
- Content type: Research
- Open Access
- Published: 08 October 2018
- Article: 160
This is part of 1 collection: -
CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens
Authors (first, second and last of 6)
- Timothy P. Daley
- Zhixiang Lin
- Lei S. Qi
- Content type: Method
- Open Access
- Published: 08 October 2018
- Article: 159
-
PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
Authors (first, second and last of 14)
- Sungsik Kim
- Amos Chungwon Lee
- Sunghoon Kwon
- Content type: Method
- Open Access
- Published: 08 October 2018
- Article: 158
-
Modularity of genes involved in local adaptation to climate despite physical linkage
Authors (first, second and last of 5)
- Katie E Lotterhos
- Sam Yeaman
- Kathryn A Hodgins
- Content type: Research
- Open Access
- Published: 05 October 2018
- Article: 157
This is part of 1 collection: -
Evolutionary and developmental dynamics of sex-biased gene expression in common frogs with proto-Y chromosomes
Authors (first, second and last of 5)
- Wen-Juan Ma
- Paris Veltsos
- Nicolas Perrin
- Content type: Research
- Open Access
- Published: 05 October 2018
- Article: 156
This is part of 1 collection: -
Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes
Authors (first, second and last of 5)
- Joana Damas
- Jaebum Kim
- Denis M Larkin
- Content type: Research
- Open Access
- Published: 05 October 2018
- Article: 155
This is part of 1 collection: -
A novel long noncoding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1
Authors (first, second and last of 10)
- Erbao Zhang
- Xuezhi He
- Wei De
- Content type: Research
- Open Access
- Published: 04 October 2018
- Article: 154
-
SKESA: strategic k-mer extension for scrupulous assemblies
Authors
- Alexandre Souvorov
- Richa Agarwala
- David J. Lipman
- Content type: Software
- Open Access
- Published: 04 October 2018
- Article: 153
-
Predicting microRNA targeting efficacy in Drosophila
Authors (first, second and last of 5)
- Vikram Agarwal
- Alexander O. Subtelny
- David P. Bartel
- Content type: Research
- Open Access
- Published: 04 October 2018
- Article: 152
-
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
Authors (first, second and last of 13)
- Yanli Wang
- Fan Song
- Feng Yue
- Content type: Method
- Open Access
- Published: 04 October 2018
- Article: 151
-
A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains
Authors (first, second and last of 15)
- Abdulrahman Salhab
- Karl Nordström
- Jörn Walter
- Content type: Research
- Open Access
- Published: 28 September 2018
- Article: 150
-
Manipulating plant RNA-silencing pathways to improve the gene editing efficiency of CRISPR/Cas9 systems
Authors (first, second and last of 6)
- Yanfei Mao
- Xiaoxuan Yang
- Jian-Kang Zhu
- Content type: Research
- Open Access
- Published: 28 September 2018
- Article: 149
-
Ankyrin domain encoding genes from an ancient horizontal transfer are functionally integrated into Nasonia developmental gene regulatory networks
Authors
- Daniel Pers
- Jeremy A. Lynch
- Content type: Research
- Open Access
- Published: 28 September 2018
- Article: 148
This is part of 1 collection: -
The advantage of parallel selection of domestication genes to accelerate crop improvement
Authors
- Martha Rendón-Anaya
- Alfredo Herrera-Estrella
- Content type: Research Highlight
- Open Access
- Published: 28 September 2018
- Article: 147
-
Insights from the 2018 Biology of Genomes meeting
Authors
- Ninad Oak
- Sharon E. Plon
- Content type: Meeting report
- Open Access
- Published: 28 September 2018
- Article: 146
-
ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
Authors (first, second and last of 4)
- Champak R. Beeravolu
- Michael J. Hickerson
- Konrad Lohse
- Content type: Method
- Open Access
- Published: 25 September 2018
- Article: 145
This is part of 1 collection: -
Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence
Authors (first, second and last of 7)
- Yue Lu
- Qiutao Xu
- Dao-Xiu Zhou
- Content type: Research
- Open Access
- Published: 25 September 2018
- Article: 144
-
The continuously evolving CRISPR barcoding toolbox
Authors
- Thomas Gaj
- Pablo Perez-Pinera
- Content type: Research Highlight
- Open Access
- Published: 25 September 2018
- Article: 143
This is part of 1 collection: -
Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis
Authors (first, second and last of 19)
- Siyuan Ma
- Shuji Ogino
- Levi Waldron
- Content type: Research
- Open Access
- Published: 25 September 2018
- Article: 142
-
BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference
Authors (first, second and last of 8)
- Elior Rahmani
- Regev Schweiger
- Eran Halperin
- Content type: Method
- Open Access
- Published: 21 September 2018
- Article: 141
-
Genomic approaches for studying crop evolution
Authors
- Mona Schreiber
- Nils Stein
- Martin Mascher
- Content type: Review
- Open Access
- Published: 21 September 2018
- Article: 140
This is part of 1 collection: -
Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations
Authors (first, second and last of 36)
- Kristiina Tambets
- Bayazit Yunusbayev
- Mait Metspalu
- Content type: Research
- Open Access
- Published: 21 September 2018
- Article: 139
This is part of 1 collection: -
Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation
Authors (first, second and last of 5)
- Alexis Vandenbon
- Yutaro Kumagai
- Kenta Nakai
- Content type: Research
- Open Access
- Published: 19 September 2018
- Article: 138
-
All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo
Authors (first, second and last of 6)
- Raed Ibraheim
- Chun-Qing Song
- Erik J. Sontheimer
- Content type: Research
- Open Access
- Published: 19 September 2018
- Article: 137
This is part of 1 collection: -
Epigenetic prediction of complex traits and death
Authors (first, second and last of 21)
- Daniel L. McCartney
- Robert F. Hillary
- Riccardo E. Marioni
- Content type: Research
- Open Access
- Published: 27 September 2018
- Article: 136
-
Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture
Authors
- Xavier Grau-Bové
- Iñaki Ruiz-Trillo
- Manuel Irimia
- Content type: Research
- Open Access
- Published: 17 September 2018
- Article: 135
This is part of 1 collection: -
Diverse model systems reveal common principles of meiosis
Authors
- Weronika E. Borek
- Adele L. Marston
- Content type: Meeting report
- Open Access
- Published: 14 September 2018
- Article: 134
This is part of 1 collection: -
Alternative splicing links histone modifications to stem cell fate decision
Authors (first, second and last of 5)
- Yungang Xu
- Weiling Zhao
- Xiaobo Zhou
- Content type: Research
- Open Access
- Published: 14 September 2018
- Article: 133
-
Reduced intrinsic DNA curvature leads to increased mutation rate
Authors (first, second and last of 7)
- Chaorui Duan
- Qing Huan
- Wenfeng Qian
- Content type: Research
- Open Access
- Published: 14 September 2018
- Article: 132
-
Conservation of biodiversity in the genomics era
Authors
- Megan A. Supple
- Beth Shapiro
- Content type: Review
- Open Access
- Published: 11 September 2018
- Article: 131
This is part of 1 collection: -
Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity
Authors (first, second and last of 9)
- Paul Geeleher
- Aritro Nath
- R. Stephanie Huang
- Content type: Method
- Open Access
- Published: 11 September 2018
- Article: 130