Volume 30, Issue 3 | March 2020

Review
- - Accurate and complete genomes from metagenomes
    Lin-Xing Chen
    Karthik Anantharaman
    Alon Shaiber
    A. Murat Eren
    Jillian F. Banfield
    First Published March 18, 2020
Research
- - Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
    Akihiro Fujimoto
    Masashi Fujita
    Takanori Hasegawa
    Jing Hao Wong
    Kazuhiro Maejima
    Aya Oku-Sasaki Kaoru Nakano Yuichi Shiraishi Satoru Miyano
    ...[+4 authors]...,
    Go Yamamoto
    Kiwamu Akagi
    Seiya Imoto
    Hidewaki Nakagawa
    First Published March 24, 2020
  - Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
    Swati Venkat
    Arwen A. Tisdale
    Johann R. Schwarz
    Abdulrahman A. Alahmari
    H. Carlo Maurer
    First Published February 6, 2020
  - Identification of FMR1-regulated molecular networks in human neurodevelopment
    Meng Li
    Junha Shin
    Ryan D. Risgaard
    Molly J. Parries
    Jianyi Wang
    Deborah Chasman
    ...[+1 authors]...,
    Shuang Liu
    Sushmita Roy
    Anita Bhattacharyya
    Xinyu Zhao
    First Published March 16, 2020
  - Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
    Yen-Ju Chen
    Chia-Ying Chen
    Te-Lun Mai
    Chih-Fan Chuang
    Yu-Chen Chen
    First Published March 3, 2020
  - Systems genetics of the Drosophila metabolome
    Shanshan Zhou
    Fabio Morgante
    Matthew S. Geisz
    Junwu Ma
    Robert R.H. Anholt
    First Published November 6, 2019
  - Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila
    Zhengyu Luo
    Tengfei Hu
    Hong Jiang
    Ruoyu Wang
    Qianlan Xu
    First Published March 12, 2020
Methods
- - Genomic loci susceptible to systematic sequencing bias in clinical whole genomes
    Timothy M. Freeman
    Dennis Wang
    Jason Harris
    John C. Ambrose
    Prabhu Arumugam
    Emma L. Baple Marta Bleda Freya Boardman-Pretty Jeanne M. Boissiere Christopher R. Boustred Mark J. Caulfield Georgia C. Chan Clare E.H. Craig Louise C. Daugherty Anna de Burca Andrew Devereau Greg Elgar Rebecca E. Foulger Tom Fowler Pedro Furió-Tarí Joanne M. Hackett Dina Halai Angela Hamblin Shirley Henderson James E. Holman Tim J.P. Hubbard Kristina Ibáñez Rob Jackson Louise J. Jones Dalia Kasperaviciute Melis Kayikci Lea Lahnstein Kay Lawson Sarah E.A. Leigh Ivonne U.S. Leong Javier F. Lopez Fiona Maleady-Crowe Joanne Mason Ellen M. McDonagh Loukas Moutsianas Michael Mueller Nirupa Murugaesu Anna C. Need Chris A. Odhams Christine Patch Daniel Perez-Gil Dimitris Polychronopoulos John Pullinger Tahrima Rahim Augusto Rendon Pablo Riesgo-Ferreiro Tim Rogers Mina Ryten Kevin Savage Kushmita Sawant Richard H. Scott Afshan Siddiq Alexander Sieghart Damian Smedley Katherine R. Smith Alona Sosinsky William Spooner Helen E. Stevens Alexander Stuckey Razvan Sultana Ellen R.A. Thomas Simon R. Thompson Carolyn Tregidgo Arianna Tucci Emma Walsh Sarah A. Watters Matthew J. Welland
    ...[+67 authors]...,
    Eleanor Williams
    Katarzyna Witkowska
    Suzanne M. Wood
    Magdalena Zarowiecki
    First Published March 10, 2020
  - Human auditory ossicles as an alternative optimal source of ancient DNA
    Kendra Sirak
    Daniel Fernandes
    Olivia Cheronet
    Eadaoin Harney
    Matthew Mah
    Swapan Mallick Nadin Rohland Nicole Adamski Nasreen Broomandkhoshbacht Kimberly Callan Francesca Candilio Ann Marie Lawson Kirsten Mandl Jonas Oppenheimer Kristin Stewardson Fatma Zalzala Alexandra Anders Juraj Bartík Alfredo Coppa Tumen Dashtseveg Sándor Évinger Zdeněk Farkaš Tamás Hajdu Jamsranjav Bayarsaikhan Lauren McIntyre Vyacheslav Moiseyev Mercedes Okumura Ildikó Pap Michael Pietrusewsky Pál Raczky Alena Šefčáková Andrei Soficaru Tamás Szeniczey Béla Miklós Szőke Dennis Van Gerven
    ...[+30 authors]...,
    Sergey Vasilyev
    Lynne Bell
    David Reich
    Ron Pinhasi
    First Published February 25, 2020
  - Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
    John Beaulaurier
    Elaine Luo
    John M. Eppley
    Paul Den Uyl
    Xiaoguang Dai
    Andrew Burger Daniel J. Turner
    ...[+2 authors]...,
    Matthew Pendelton
    Sissel Juul
    Eoghan Harrington
    Edward F. DeLong
    First Published February 19, 2020
  - Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals
    M. Jordan Rowley
    Axel Poulet
    Michael H. Nichols
    Brianna J. Bixler
    Adrian L. Sanborn
    Elizabeth A. Brouhard Karen Hermetz
    ...[+2 authors]...,
    Hannah Linsenbaum
    Gyorgyi Csankovszki
    Erez Lieberman Aiden
    Victor G. Corces
    First Published March 3, 2020
  - Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
    Yiming Kang
    Nikhil R. Patel
    Christian Shively
    Pamela Samantha Recio
    Xuhua Chen
    Bernd J. Wranik
    ...[+1 authors]...,
    Griffin Kim
    R. Scott McIsaac
    Robi Mitra
    Michael R. Brent
    First Published February 14, 2020
Resources
- - An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
    Guanjue Xiang
    Cheryl A. Keller
    Elisabeth Heuston
    Belinda M. Giardine
    Lin An
    Alexander Q. Wixom Amber Miller April Cockburn Michael E.G. Sauria Kathryn Weaver Jens Lichtenberg Berthold Göttgens Qunhua Li David Bodine Shaun Mahony James Taylor Gerd A. Blobel Mitchell J. Weiss Yong Cheng Feng Yue
    ...[+15 authors]...,
    Jim Hughes
    Douglas R. Higgs
    Yu Zhang
    Ross C. Hardison
    First Published March 4, 2020
  - Gene expression networks in the Drosophila Genetic Reference Panel
    Logan J. Everett
    Wen Huang
    Shanshan Zhou
    Mary Anna Carbone
    Richard F. Lyman
    Gunjan H. Arya Matthew S. Geisz Junwu Ma Fabio Morgante
    ...[+4 authors]...,
    Genevieve St. Armour
    Lavanya Turlapati
    Robert R.H. Anholt
    Trudy F.C. Mackay
    First Published March 6, 2020
  - Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants
    Alice Lunardon
    Nathan R. Johnson
    Emily Hagerott
    Tamia Phifer
    Seth Polydore
    First Published March 16, 2020
Corrigendum
- - Corrigendum: Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi
    Fantin Carpentier
    Ricardo C. Rodríguez de la Vega
    Sara Branco
    Alodie Snirc
    Marco A. Coelho
    First Published March 25, 2020

Table of Contents

Volume 30, Issue 3 | March 2020

Review

Accurate and complete genomes from metagenomes

Research

Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types

Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma

Identification of FMR1-regulated molecular networks in human neurodevelopment

Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism

Systems genetics of the Drosophila metabolome

Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila

Methods

Genomic loci susceptible to systematic sequencing bias in clinical whole genomes

Human auditory ossicles as an alternative optimal source of ancient DNA

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities

Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals

Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses

Resources

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

Gene expression networks in the Drosophila Genetic Reference Panel

Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants

Corrigendum

Corrigendum: Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi

Table of Contents

Volume 30, Issue 3 | March 2020

Share this issue

Review

Research

Methods

Resources

Corrigendum