Volume 20, issue 1, December 2019
299 articles in this issue
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Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles
Authors (first, second and last of 13)
- Mathieu Seppey
- Panagiotis Ioannidis
- Nadir Alvarez
- Content type: Research
- Open Access
- Published: 17 May 2019
- Article: 98
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Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight
Authors (first, second and last of 20)
- Mark T. W. Ebbert
- Tanner D. Jensen
- John D. Fryer
- Content type: Research
- Open Access
- Published: 20 May 2019
- Article: 97
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Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches
Authors (first, second and last of 10)
- Gabriele Andrea Lugli
- Christian Milani
- Marco Ventura
- Content type: Short Report
- Open Access
- Published: 16 May 2019
- Article: 96
This is part of 1 collection: -
Comments on the model parameters in “SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models”
Authors (first, second and last of 5)
- Hamim Zafar
- Anthony Tzen
- Luay Nakhleh
- Content type: Correspondence
- Open Access
- Published: 16 May 2019
- Article: 95
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Addressing confounding artifacts in reconstruction of gene co-expression networks
Authors (first, second and last of 6)
- Princy Parsana
- Claire Ruberman
- Jeffrey T. Leek
- Content type: Short Report
- Open Access
- Published: 16 May 2019
- Article: 94
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At the forefront of the sequencing revolution—notes from the RNGS19 conference
Authors
- Sander Wuyts
- Nicola Segata
- Content type: Meeting Report
- Open Access
- Published: 30 May 2019
- Article: 93
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Next-generation genome annotation: we still struggle to get it right
Authors
- Steven L. Salzberg
- Content type: Editorial
- Open Access
- Published: 16 May 2019
- Article: 92
This is part of 1 collection: -
VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer
Authors (first, second and last of 7)
- Andrew N. Holding
- Federico M. Giorgi
- Florian Markowetz
- Content type: Research
- Open Access
- Published: 13 May 2019
- Article: 91
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CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
Authors (first, second and last of 7)
- Chuner Guo
- Wenjun Kong
- Samantha A. Morris
- Content type: Method
- Open Access
- Published: 09 May 2019
- Article: 90
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Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
Authors (first, second and last of 33)
- Warren A. Cheung
- Xiaojian Shao
- Elin Grundberg
- Content type: Correction
- Open Access
- Published: 07 May 2019
- Article: 89
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SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data
Authors (first, second and last of 4)
- Tao Peng
- Qin Zhu
- Kai Tan
- Content type: Method
- Open Access
- Published: 06 May 2019
- Article: 88
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Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery
Authors (first, second and last of 8)
- Bo Hu
- Nan Wang
- Chang Liu
- Content type: Research
- Open Access
- Published: 30 April 2019
- Article: 87
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The tech for the next decade: promises and challenges in genome biology
Authors
- Iman Hajirasouliha
- Hagen U. Tilgner
- Content type: Meeting Report
- Open Access
- Published: 30 April 2019
- Article: 86
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Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification
Authors (first, second and last of 11)
- Daryl M. Gohl
- Alessandro Magli
- Kenneth B. Beckman
- Content type: Method
- Open Access
- Published: 29 April 2019
- Article: 85
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Translation of the circular RNA circβ-catenin promotes liver cancer cell growth through activation of the Wnt pathway
Authors (first, second and last of 11)
- Wei-Cheng Liang
- Cheuk-Wa Wong
- Jin-Fang Zhang
- Content type: Research
- Open Access
- Published: 26 April 2019
- Article: 84
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CRISPR enables directed evolution in plants
Authors
- Yingxiao Zhang
- Yiping Qi
- Content type: Research Highlight
- Open Access
- Published: 30 April 2019
- Article: 83
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African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations
Authors (first, second and last of 17)
- Shaohua Fan
- Derek E. Kelly
- Sarah A. Tishkoff
- Content type: Research
- Open Access
- Published: 26 April 2019
- Article: 82
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TransLiG: a de novo transcriptome assembler that uses line graph iteration
Authors (first, second and last of 4)
- Juntao Liu
- Ting Yu
- Guojun Li
- Content type: Method
- Open Access
- Published: 23 April 2019
- Article: 81
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Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses
Authors (first, second and last of 7)
- Devang Mehta
- Alessandra Stürchler
- Hervé Vanderschuren
- Content type: Research
- Open Access
- Published: 25 April 2019
- Article: 80
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Whole genomes and transcriptomes reveal adaptation and domestication of pistachio
Authors (first, second and last of 17)
- Lin Zeng
- Xiao-Long Tu
- Dong-Dong Wu
- Content type: Research
- Open Access
- Published: 18 April 2019
- Article: 79
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Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data
Authors
- Simon P. Sadedin
- Alicia Oshlack
- Content type: Software
- Open Access
- Published: 18 April 2019
- Article: 78
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Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations
Authors (first, second and last of 12)
- Belen Lorente-Galdos
- Oscar Lao
- David Comas
- Content type: Research
- Open Access
- Published: 26 April 2019
- Article: 77
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Machine learning and complex biological data
Authors
- Chunming Xu
- Scott A. Jackson
- Content type: Editorial
- Open Access
- Published: 16 April 2019
- Article: 76
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DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis
Authors (first, second and last of 4)
- Bin Xiong
- Yiben Yang
- Ji-Ping Wang
- Content type: Method
- Open Access
- Published: 16 April 2019
- Article: 75
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Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean
Authors (first, second and last of 7)
- Jinyu Wang
- Xianran Li
- Jianming Yu
- Content type: Research
- Open Access
- Published: 25 April 2019
- Article: 74
This is part of 1 collection: -
CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors
Authors (first, second and last of 7)
- Haroon Butt
- Ayman Eid
- Magdy M. Mahfouz
- Content type: Method
- Open Access
- Published: 30 April 2019
- Article: 73
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Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
Authors (first, second and last of 20)
- Alexa B. R. McIntyre
- Rachid Ounit
- Christopher E. Mason
- Content type: Correction
- Open Access
- Published: 05 April 2019
- Article: 72
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BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing
Authors (first, second and last of 8)
- Daniel Alpern
- Vincent Gardeux
- Bart Deplancke
- Content type: Method
- Open Access
- Published: 19 April 2019
- Article: 71
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Comparative analysis of sequencing technologies for single-cell transcriptomics
Authors (first, second and last of 15)
- Kedar Nath Natarajan
- Zhichao Miao
- Sarah A. Teichmann
- Content type: Short Report
- Open Access
- Published: 09 April 2019
- Article: 70
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Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency
Authors (first, second and last of 11)
- Laura-Jayne Gardiner
- Luzie U. Wingen
- Anthony Hall
- Content type: Research
- Open Access
- Published: 15 April 2019
- Article: 69
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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Authors (first, second and last of 13)
- Joanna Hård
- Ezeddin Al Hakim
- Jonas Frisén
- Content type: Software
- Open Access
- Published: 01 April 2019
- Article: 68
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Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list
Authors (first, second and last of 4)
- Paul F. Harrison
- Andrew D. Pattison
- Traude H. Beilharz
- Content type: Method
- Open Access
- Published: 28 March 2019
- Article: 67
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All models are wrong, but some organoids may be useful
Authors
- Benjamin E. Mead
- Jeffrey M. Karp
- Content type: Editorial
- Open Access
- Published: 27 March 2019
- Article: 66
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Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
Authors (first, second and last of 5)
- Avi Srivastava
- Laraib Malik
- Rob Patro
- Content type: Method
- Open Access
- Published: 27 March 2019
- Article: 65
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Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome
Authors (first, second and last of 83)
- Kristen A. Panfilio
- Iris M. Vargas Jentzsch
- Stephen Richards
- Content type: Research
- Open Access
- Published: 02 April 2019
- Article: 64
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EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Authors (first, second and last of 7)
- Aaron T. L. Lun
- Samantha Riesenfeld
- John C. Marioni
- Content type: Method
- Open Access
- Published: 22 March 2019
- Article: 63
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Interactive roles of chromatin regulation and circadian clock function in plants
Authors
- Z. Jeffrey Chen
- Paloma Mas
- Content type: Review
- Open Access
- Published: 22 March 2019
- Article: 62
This is part of 1 collection: -
Melissa: Bayesian clustering and imputation of single-cell methylomes
Authors
- Chantriolnt-Andreas Kapourani
- Guido Sanguinetti
- Content type: Method
- Open Access
- Published: 21 March 2019
- Article: 61
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TAD fusion score: discovery and ranking the contribution of deletions to genome structure
Authors
- Linh Huynh
- Fereydoun Hormozdiari
- Content type: Method
- Open Access
- Published: 21 March 2019
- Article: 60
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PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Authors (first, second and last of 9)
- F. Alexander Wolf
- Fiona K. Hamey
- Fabian J. Theis
- Content type: Method
- Open Access
- Published: 19 March 2019
- Article: 59
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Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads
Authors (first, second and last of 10)
- Satomi Mitsuhashi
- Martin C. Frith
- Naomichi Matsumoto
- Content type: Method
- Open Access
- Published: 19 March 2019
- Article: 58
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Measuring the reproducibility and quality of Hi-C data
Authors (first, second and last of 19)
- Galip Gürkan Yardımcı
- Hakan Ozadam
- William S. Noble
- Content type: Research
- Open Access
- Published: 19 March 2019
- Article: 57
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Exploring human host–microbiome interactions in health and disease—how to not get lost in translation
Authors
- Sarah Lebeer
- Irina Spacova
- Content type: Meeting Report
- Open Access
- Published: 15 March 2019
- Article: 56
This is part of 1 collection: -
RnBeads 2.0: comprehensive analysis of DNA methylation data
Authors (first, second and last of 7)
- Fabian Müller
- Michael Scherer
- Christoph Bock
- Content type: Software
- Open Access
- Published: 14 March 2019
- Article: 55
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clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
Authors (first, second and last of 17)
- Kieran R. Campbell
- Adi Steif
- Sohrab P. Shah
- Content type: Method
- Open Access
- Published: 12 March 2019
- Article: 54
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Correction to: DNA copy number evolution in Drosophila cell lines
Authors (first, second and last of 20)
- Hangnoh Lee
- C. Joel McManus
- David MacAlpine
- Content type: Correction
- Open Access
- Published: 11 March 2019
- Article: 53
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I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms
Authors (first, second and last of 8)
- Kin Yau Wong
- Cheng Fan
- Charles M. Perou
- Content type: Method
- Open Access
- Published: 07 March 2019
- Article: 52
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Assessing taxonomic metagenome profilers with OPAL
Authors (first, second and last of 6)
- Fernando Meyer
- Andreas Bremges
- David Koslicki
- Content type: Software
- Open Access
- Published: 04 March 2019
- Article: 51
This is part of 1 collection: -
Analysis of error profiles in deep next-generation sequencing data
Authors (first, second and last of 19)
- Xiaotu Ma
- Ying Shao
- Jinghui Zhang
- Content type: Research
- Open Access
- Published: 14 March 2019
- Article: 50