Volume 21, issue 1, December 2020
306 articles in this issue
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Author Correction: Stairway Plot 2: demographic history inference with folded SNP frequency spectra
Authors
- Xiaoming Liu
- Yun-Xin Fu
- Content type: Author Correction
- Open Access
- Published: 27 December 2020
- Article: 305
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Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models
Authors (first, second and last of 15)
- Michael R. Garvin
- Erica T. Prates
- Daniel Jacobson
- Content type: Research
- Open Access
- Published: 23 December 2020
- Article: 304
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FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
Authors
- Kai Kruse
- Clemens B. Hug
- Juan M. Vaquerizas
- Content type: Software
- Open Access
- Published: 17 December 2020
- Article: 303
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Convergent network effects along the axis of gene expression during prostate cancer progression
Authors (first, second and last of 30)
- Konstantina Charmpi
- Tiannan Guo
- Andreas Beyer
- Content type: Research
- Open Access
- Published: 14 December 2020
- Article: 302
This is part of 1 collection: -
Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome
Authors (first, second and last of 12)
- Emma K. Accorsi
- Eric A. Franzosa
- Curtis Huttenhower
- Content type: Research
- Open Access
- Published: 11 December 2020
- Article: 301
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GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data
Authors
- Ye Yuan
- Ziv Bar-Joseph
- Content type: Method
- Open Access
- Published: 10 December 2020
- Article: 300
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Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing
Authors (first, second and last of 15)
- Simon M. Hoser
- Anne Hoffmann
- Alexander Huettenhofer
- Content type: Research
- Open Access
- Published: 08 December 2020
- Article: 299
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STARRPeaker: uniform processing and accurate identification of STARR-seq active regions
Authors (first, second and last of 11)
- Donghoon Lee
- Manman Shi
- Mark Gerstein
- Content type: Method
- Open Access
- Published: 08 December 2020
- Article: 298
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Response to “A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication”
Authors
- Gökçe Aköz
- Magnus Nordborg
- Content type: Correspondence
- Open Access
- Published: 08 December 2020
- Article: 297
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Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Authors (first, second and last of 12)
- Ying Feng
- Yao Wang
- Hanhui Ma
- Content type: Research
- Open Access
- Published: 08 December 2020
- Article: 296
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A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication
Authors
- Tao Shi
- Jinming Chen
- Content type: Correspondence
- Open Access
- Published: 08 December 2020
- Article: 295
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Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
Authors (first, second and last of 15)
- Shuai He
- Lin-He Wang
- Zhiyong Guo
- Content type: Research
- Open Access
- Published: 07 December 2020
- Article: 294
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Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Authors (first, second and last of 5)
- Daniel R. Utter
- Gary G. Borisy
- Jessica L. Mark Welch
- Content type: Research
- Open Access
- Published: 16 December 2020
- Article: 293
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Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Authors (first, second and last of 16)
- Alon Shaiber
- Amy D. Willis
- A. Murat Eren
- Content type: Research
- Open Access
- Published: 16 December 2020
- Article: 292
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The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
Authors (first, second and last of 36)
- Ping-Li Liu
- Xi Zhang
- Jinxing Lin
- Content type: Research
- Open Access
- Published: 02 December 2020
- Article: 291
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Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
Authors (first, second and last of 13)
- Ida Höijer
- Josefin Johansson
- Adam Ameur
- Content type: Research
- Open Access
- Published: 01 December 2020
- Article: 290
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Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants
Authors (first, second and last of 4)
- Syed Shan-e-Ali Zaidi
- Ahmed Mahas
- Magdy M. Mahfouz
- Content type: Review
- Open Access
- Published: 30 November 2020
- Article: 289
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Human A-to-I RNA editing SNP loci are enriched in GWAS signals for autoimmune diseases and under balancing selection
Authors (first, second and last of 9)
- Hui Zhang
- Qiang Fu
- Rui Zhang
- Content type: Research
- Open Access
- Published: 30 November 2020
- Article: 288
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Response to Brinkmann et al. “Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States”
Authors
- Ana T. Duggan
- Edward C. Holmes
- Hendrik N. Poinar
- Content type: Correspondence
- Open Access
- Published: 04 December 2020
- Article: 287
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Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the USA
Authors (first, second and last of 5)
- Annika Brinkmann
- Aline R. V. Souza
- Clarissa R. Damaso
- Content type: Correspondence
- Open Access
- Published: 04 December 2020
- Article: 286
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From FAANG to fork: application of highly annotated genomes to improve farmed animal production
Authors (first, second and last of 14)
- Emily L. Clark
- Alan L. Archibald
- Elisabetta Giuffra
- Content type: Review
- Open Access
- Published: 24 November 2020
- Article: 285
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The evolution of relapse of adult T cell acute lymphoblastic leukemia
Authors (first, second and last of 16)
- Inés Sentís
- Santiago Gonzalez
- Nuria Lopez-Bigas
- Content type: Research
- Open Access
- Published: 23 November 2020
- Article: 284
This is part of 1 collection: -
DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis
Authors (first, second and last of 14)
- Pierre Bourguet
- Leticia López-González
- Olivier Mathieu
- Content type: Research
- Open Access
- Published: 25 November 2020
- Article: 283
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A pitfall for machine learning methods aiming to predict across cell types
Authors (first, second and last of 4)
- Jacob Schreiber
- Ritambhara Singh
- William Stafford Noble
- Content type: Short Report
- Open Access
- Published: 19 November 2020
- Article: 282
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Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus
Authors (first, second and last of 28)
- Prithvi Raj
- Ran Song
- Edward K. Wakeland
- Content type: Research
- Open Access
- Published: 19 November 2020
- Article: 281
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Stairway Plot 2: demographic history inference with folded SNP frequency spectra
Authors
- Xiaoming Liu
- Yun-Xin Fu
- Content type: Method
- Open Access
- Published: 17 November 2020
- Article: 280
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A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila
Authors (first, second and last of 4)
- Nhan Huynh
- Noah Depner
- Kirst King-Jones
- Content type: Method
- Open Access
- Published: 17 November 2020
- Article: 279
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Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription
Authors
- Haitham A. Shaban
- Roman Barth
- Kerstin Bystricky
- Content type: Review
- Open Access
- Published: 17 November 2020
- Article: 278
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A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos
Authors (first, second and last of 7)
- Chengchen Zhao
- Naiqian Zhang
- Yong Zhang
- Content type: Research
- Open Access
- Published: 16 November 2020
- Article: 277
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Do malignant cells sleep at night?
Authors (first, second and last of 7)
- Luis Enrique Cortés-Hernández
- Zahra Eslami-S
- Catherine Alix-Panabières
- Content type: Review
- Open Access
- Published: 12 November 2020
- Article: 276
This is part of 1 collection: -
Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
Authors (first, second and last of 21)
- Marco Gerdol
- Rebeca Moreira
- Antonio Figueras
- Content type: Research
- Open Access
- Published: 10 November 2020
- Article: 275
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SVFX: a machine learning framework to quantify the pathogenicity of structural variants
Authors (first, second and last of 4)
- Sushant Kumar
- Arif Harmanci
- Mark B. Gerstein
- Content type: Method
- Open Access
- Published: 09 November 2020
- Article: 274
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Pathway information extracted from 25 years of pathway figures
Authors (first, second and last of 4)
- Kristina Hanspers
- Anders Riutta
- Alexander R. Pico
- Content type: Database
- Open Access
- Published: 09 November 2020
- Article: 273
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Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage
Authors (first, second and last of 8)
- Yasutaka Kakui
- Christopher Barrington
- Frank Uhlmann
- Content type: Research
- Open Access
- Published: 05 November 2020
- Article: 272
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Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity
Authors (first, second and last of 46)
- Won-Chul Lee
- Alexandre Reuben
- Jianjun Zhang
- Content type: Research
- Open Access
- Published: 04 November 2020
- Article: 271
This is part of 1 collection: -
Publisher Correction: Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics
Authors (first, second and last of 4)
- Kwangbom Choi
- Yang Chen
- Gary A. Churchill
- Content type: Publisher Correction
- Open Access
- Published: 03 November 2020
- Article: 270
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Cis-acting lnc-eRNA SEELA directly binds histone H4 to promote histone recognition and leukemia progression
Authors (first, second and last of 12)
- Ke Fang
- Wei Huang
- Yue-Qin Chen
- Content type: Research
- Open Access
- Published: 03 November 2020
- Article: 269
This is part of 1 collection: -
RNA editing in cancer impacts mRNA abundance in immune response pathways
Authors (first, second and last of 8)
- Tracey W. Chan
- Ting Fu
- Xinshu Xiao
- Content type: Research
- Open Access
- Published: 26 October 2020
- Article: 268
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Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions
Authors (first, second and last of 22)
- Enrique Navas-Pérez
- Cristina Vicente-García
- Jordi Garcia-Fernàndez
- Content type: Research
- Open Access
- Published: 26 October 2020
- Article: 267
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High throughput single-cell detection of multiplex CRISPR-edited gene modifications
Authors (first, second and last of 16)
- Elisa ten Hacken
- Kendell Clement
- Catherine J. Wu
- Content type: Short Report
- Open Access
- Published: 20 October 2020
- Article: 266
This is part of 1 collection: -
The design and construction of reference pangenome graphs with minigraph
Authors
- Heng Li
- Xiaowen Feng
- Chong Chu
- Content type: Method
- Open Access
- Published: 16 October 2020
- Article: 265
This is part of 1 collection: -
Multiomics kaleidoscope to visualize cancer hallmarks
Authors
- Shengtao Zhou
- Content type: Editorial
- Open Access
- Published: 15 October 2020
- Article: 264
This is part of 1 collection: -
Clonal tracing reveals diverse patterns of response to immune checkpoint blockade
Authors (first, second and last of 26)
- Shengqing Stan Gu
- Xiaoqing Wang
- X. Shirley Liu
- Content type: Research
- Open Access
- Published: 15 October 2020
- Article: 263
This is part of 1 collection: -
Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screens
Authors (first, second and last of 4)
- Merve Dede
- Megan McLaughlin
- Traver Hart
- Content type: Research
- Open Access
- Published: 15 October 2020
- Article: 262
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iMOKA: k-mer based software to analyze large collections of sequencing data
Authors (first, second and last of 6)
- Claudio Lorenzi
- Sylvain Barriere
- William Ritchie
- Content type: Method
- Open Access
- Published: 13 October 2020
- Article: 261
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AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
Authors (first, second and last of 12)
- Yadollah Shahryary
- Aikaterini Symeonidi
- Frank Johannes
- Content type: Software
- Open Access
- Published: 06 October 2020
- Article: 260
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A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa
Authors (first, second and last of 25)
- Brigitte T. Hofmeister
- Johanna Denkena
- Robert J. Schmitz
- Content type: Research
- Open Access
- Published: 06 October 2020
- Article: 259
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An integrated peach genome structural variation map uncovers genes associated with fruit traits
Authors (first, second and last of 15)
- Jian Guo
- Ke Cao
- Lirong Wang
- Content type: Research
- Open Access
- Published: 06 October 2020
- Article: 258
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Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize
Authors (first, second and last of 11)
- Yuan-Yuan Jiang
- Yi-Ping Chai
- Qi-Jun Chen
- Content type: Short Report
- Open Access
- Published: 06 October 2020
- Article: 257