Volume 33, Issue 4 | April 2023

Perspective
- - Challenges and considerations for reproducibility of STARR-seq assays
    Maitreya Das
    Ayaan Hossain
    Deepro Banerjee
    Craig Alan Praul
    Santhosh Girirajan
    First Published May 2, 2023
Research
- - Gaps and complex structurally variant loci in phased genome assemblies
    David Porubsky
    Mitchell R. Vollger
    William T. Harvey
    Allison N. Rozanski
    Peter Ebert
    Glenn Hickey Patrick Hasenfeld Ashley D. Sanders Catherine Stober Jan O. Korbel Benedict Paten Tobias Marschall Evan E. Eichler Haley J. Abel Lucinda L. Antonacci-Fulton Mobin Asri Gunjan Baid Carl A. Baker Anastasiya Belyaeva Konstantinos Billis Guillaume Bourque Silvia Buonaiuto Andrew Carroll Mark J.P. Chaisson Pi-Chuan Chang Xian H. Chang Haoyu Cheng Justin Chu Sarah Cody Vincenza Colonna Daniel E. Cook Robert M. Cook-Deegan Omar E. Cornejo Mark Diekhans Daniel Doerr Peter Ebert Jana Ebler Evan E. Eichler Jordan M. Eizenga Susan Fairley Olivier Fedrigo Adam L. Felsenfeld Xiaowen Feng Christian Fischer Paul Flicek Giulio Formenti Adam Frankish Robert S. Fulton Yan Gao Shilpa Garg Erik Garrison Nanibaa’ A. Garrison Carlos Garcia Giron Richard E. Green Cristian Groza Andrea Guarracino Leanne Haggerty Ira M. Hall William T. Harvey Marina Haukness David Haussler Simon Heumos Glenn Hickey Kendra Hoekzema Thibaut Hourlier Kerstin Howe Miten Jain Erich D. Jarvis Hanlee P. Ji Eimear E. Kenny Barbara A. Koenig Alexey Kolesnikov Jan O. Korbel Jennifer Kordosky Sergey Koren HoJoon Lee Alexandra P. Lewis Heng Li Wen-Wei Liao Shuangjia Lu Tsung-Yu Lu Julian K. Lucas Hugo Magalhães Santiago Marco-Sola Pierre Marijon Charles Markello Tobias Marschall Fergal J. Martin Ann McCartney Jennifer McDaniel Karen H. Miga Matthew W. Mitchell Jean Monlong Jacquelyn Mountcastle Katherine M. Munson Moses Njagi Mwaniki Maria Nattestad Adam M. Novak Sergey Nurk Hugh E. Olsen Nathan D. Olson Benedict Paten Trevor Pesout Adam M. Phillippy Alice B. Popejoy David Porubsky Pjotr Prins Daniela Puiu Mikko Rautiainen Allison A. Regier Arang Rhie Samuel Sacco Ashley D. Sanders Valerie A. Schneider Baergen I. Schultz Kishwar Shafin Jonas A. Sibbesen Jouni Sirén Michael W. Smith Heidi J. Sofia Ahmad N. Abou Tayoun Françoise Thibaud-Nissen Chad Tomlinson Francesca Floriana Tricomi Flavia Villani Mitchell R. Vollger Justin Wagner Brian Walenz
    ...[+123 authors]...,
    Ting Wang
    Jonathan M.D. Wood
    Aleksey V. Zimin
    Justin M. Zook
    First Published May 10, 2023
  - The motif composition of variable number tandem repeats impacts gene expression
    Tsung-Yu Lu
    Paulina N. Smaruj
    Geoffrey Fudenberg
    Nicholas Mancuso
    Mark J.P. Chaisson
    First Published April 10, 2023
  - Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
    Étienne Fafard-Couture
    Pierre-Étienne Jacques
    Michelle S. Scott
    First Published April 18, 2023
  - MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain
    Jiayang Chen
    Nicole A. Fuhler
    Kevin K. Noguchi
    Joseph D. Dougherty
    First Published April 26, 2023
  - High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
    Yuan Lu
    Edward Rice
    Kang Du
    Susanne Kneitz
    Magali Naville
    Corentin Dechaud Jean-Nicolas Volff Mikki Boswell William Boswell LaDeana Hillier Chad Tomlinson
    ...[+6 authors]...,
    Kremitzki Milin
    Ronald B. Walter
    Manfred Schartl
    Wesley C. Warren
    First Published May 5, 2023
  - Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
    Hiroto S. Fukushima
    Hiroyuki Takeda
    Ryohei Nakamura
    First Published April 28, 2023
  - Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
    Yiguan Wang
    Paul McNeil
    Rashidatu Abdulazeez
    Marta Pascual
    Susan E. Johnston
    First Published April 10, 2023
  - Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa
    Mariana Villalba de la Peña
    Pauliina A.M. Summanen
    Martta Liukkonen
    Ilkka Kronholm
    First Published March 15, 2023
Methods
- - Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
    Yuhong Sun
    Zhanwen Cheng
    Xiang Li
    Qing Yang
    Bixi Zhao
    First Published April 11, 2023
  - Density separation of petrous bone powders for optimized ancient DNA yields
    Daniel M. Fernandes
    Kendra A. Sirak
    Olivia Cheronet
    Mario Novak
    Florian Brück
    Evelyn Zelger Alejandro Llanos-Lizcano Anna Wagner Anna Zettl Kirsten Mandl Kellie Sara Duffet Carlson Victoria Oberreiter Kadir T. Özdoğan Susanna Sawyer Francesco La Pastina Emanuela Borgia Alfredo Coppa Miroslav Dobeš
    ...[+13 authors]...,
    Petr Velemínský
    David Reich
    Lynne S. Bell
    Ron Pinhasi
    First Published April 18, 2023
  - Inferring the mode and strength of ongoing selection
    Gustavo V. Barroso
    Kirk E. Lohmueller
    First Published April 13, 2023
  - Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
    Yongkang Long
    Bin Zhang
    Shuye Tian
    Jia Jia Chan
    Juexiao Zhou
    Zhongxiao Li Yisheng Li Zheng An Xingyu Liao Yu Wang Shiwei Sun
    ...[+6 authors]...,
    Ying Xu
    Yvonne Tay
    Wei Chen
    Xin Gao
    First Published April 28, 2023
Resource
- - A single-cell transcriptome atlas of the maturing zebrafish telencephalon
    Shristi Pandey
    Anna J. Moyer
    Summer B. Thyme
    First Published April 18, 2023

Table of Contents

Volume 33, Issue 4 | April 2023

Perspective

Challenges and considerations for reproducibility of STARR-seq assays

Research

Gaps and complex structurally variant loci in phased genome assemblies

The motif composition of variable number tandem repeats impacts gene expression

Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates

MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain

High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis

Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development

Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans

Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa

Methods

Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing

Density separation of petrous bone powders for optimized ancient DNA yields

Inferring the mode and strength of ongoing selection

Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ

Resource

A single-cell transcriptome atlas of the maturing zebrafish telencephalon

Table of Contents

Volume 33, Issue 4 | April 2023

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Perspective

Research

Methods

Resource