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Method

Proxy panels enable privacy-aware outsourcing of genotype imputation

Degui Zhi
Xiaoqian Jiang
Arif Harmanci

First Published January 10, 2025

Method

Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes

Hongke Peng
Jafar S. Jabbari
Luyi Tian
Changqing Wang
Yupei You
Chong Chyn Chua Natasha S. Anstee Noorul Amin Andrew H. Wei Nadia M. Davidson
... [+5 authors] ...,
Andrew W. Roberts
David C.S. Huang
Matthew E. Ritchie
Rachel Thijssen

First Published January 10, 2025

Research

Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer

Liu Yang
Botelho João
Iranzo Jaime

First Published January 10, 2025

Research

Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths

Fangyuan Yang
Li-Jun Cao
Petr Nguyen
Zhong-Zheng Ma
Jin-Cui Chen
Wei Song
Shu-Jun Wei

First Published January 6, 2025

Research

Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency" > Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency

Benjamin Morledge-Hampton
Kathiresan Selvam
Manish Chauhan
Alan G. Goodman
John J. Wyrick

First Published January 6, 2025

Research

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Lewin Thomas D.
Liao Isabel Jiah-Yih
Chen Mu-En
Bishop John D.D.
Holland Peter W.H.
Luo Yi-Jyun

First Published January 6, 2025

Method

Identification of the shortest species-specific oligonucleotide sequences

Ioannis Mouratidis
Maxwell A. Konnaris
Nikol Chantzi
Candace S.Y. Chan
Michail Patsakis
Kimonas Provatas Austin Montgomery Fotis A. Baltoumas Congzhou M. Sha
... [+4 authors] ...,
Manvita Mareboina
Georgios A. Pavlopoulos
Dionysios V. Chartoumpekis
Ilias Georgakopoulos-Soares

First Published January 2, 2025

Method

Combining DNA and protein alignments to improve genome annotation with LiftOn

Kuan-Hao Chao
Jakob M. Heinz
Celine Hoh
Alan Mao
Alaina Shumate
Mihaela Pertea
Steven L. Salzberg

First Published December 27, 2024

Method

Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases

Ming Yan
Thea O. Andersen
Phillip B. Pope
Zhongtang Yu

First Published December 27, 2024

Reviewer Index

Reviewer Index, Volume 34, 2024

First Published December 23, 2024

Research

CRX retinopathy models" > Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models

Yiqiao Zheng
Gary D. Stormo
Shiming Chen

First Published December 23, 2024

Method

Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq

Alejandro Paniagua
Cristina Agustín-García
Francisco J. Pardo-Palacios
Thomas Brown
Maite De Maria
Nancy D. Denslow
Camila J. Mazzoni
Ana Conesa

First Published December 23, 2024

Method

KIT associated with depigmentation in white-headed cattle" > Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle

Sotiria Milia
Alexander S. Leonard
Xena Marie Mapel
Sandra Milena Bernal Ulloa
Cord Drögemüller
Hubert Pausch

First Published December 18, 2024

Method

Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet

Chuanyuan Wang
Zhi-Ping Liu

First Published December 18, 2024

Method

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq

Stephanie C. Bohaczuk
Zachary J. Amador
Chang Li
Benjamin J. Mallory
Elliott G. Swanson
Jane Ranchalis Mitchell R. Vollger Katherine M. Munson Tom Walsh
... [+4 authors] ...,
Morgan O. Hamm
Yizi Mao
Andre Lieber
Andrew B. Stergachis

First Published December 9, 2024

Method

MCHelper automatically curates transposable element libraries across eukaryotic species

Simon Orozco-Arias
Pío Sierra
Richard Durbin
Josefa González

First Published December 9, 2024

Research

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

Vanessa L. Porter
Michelle Ng
Kieran O'Neill
Signe MacLennan
Richard D. Corbett
Luka Culibrk Zeid Hamadeh Marissa Iden Rachel Schmidt Shirng-Wern Tsaih Carolyn Nakisige Martin Origa Jackson Orem Glenn Chang Jeremy Fan Ka Ming Nip Vahid Akbari Simon K. Chan James Hopkins Richard A. Moore Eric Chuah Karen L. Mungall Andrew J. Mungall
... [+18 authors] ...,
Inanc Birol
Steven J.M. Jones
Janet S. Rader
Marco A. Marra

First Published December 5, 2024

Resource

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

Chong Li
Marc Jan Bonder
Sabriya Syed
Matthew Jensen
Mark B. Gerstein
Michael C. Zody Mark J.P. Chaisson Michael E. Talkowski Tobias Marschall
... [+4 authors] ...,
Jan O. Korbel
Evan E. Eichler
Charles Lee
Xinghua Shi

First Published December 5, 2024

Research

Arabidopsis thaliana" > Characterization of DNA methylation reader proteins in Arabidopsis thaliana

Jonathan Cahn
James P.B. Lloyd
Ino D. Karemaker
Pascal W.T.C. Jansen
Jahnvi Pflueger
Owen Duncan Jakob Petereit
... [+2 authors] ...,
Ozren Bogdanovic
A. Harvey Millar
Michiel Vermeulen
Ryan Lister

First Published December 4, 2024

Research

Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype" > Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype

Arne Sahm
Konstantin Riege
Marco Groth
Martin Bens
Johann Kraus
Martin Fischer Hans Kestler
... [+2 authors] ...,
Christoph Englert
Ralf Schaible
Matthias Platzer
Steve Hoffmann

First Published December 4, 2024

Method

Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts

Irmgard U. Haussmann
Thomas C. Dix
David W.J. McQuarrie
Veronica Dezi
Abdullah I. Hans
Roland Arnold
Matthias Soller

First Published December 3, 2024

Method

Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression

Howard J. Womersley
Daniel Muliaditan
Ramanuj DasGupta
Lih Feng Cheow

First Published December 2, 2024

Method

Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach

Fabien Wehbe
Levi Adams
Jordan Babadoudou
Samantha Yuen
Yoon-Seong Kim
Yoshiaki Tanaka

First Published December 2, 2024

Research

The rate and spectrum of new mutations in mice inferred by long-read sequencing

Eugenio López-Cortegano
Jobran Chebib
Anika Jonas
Anastasia Vock
Sven Künzel
Peter D. Keightley
Diethard Tautz

First Published December 2, 2024

Research

C. elegans" > A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans

Thiago L. Knittel
Brooke E. Montgomery
Alex J. Tate
Ennis W. Deihl
Anastasia S. Nawrocki
Frederic J. Hoerndli
Taiowa A. Montgomery

First Published December 2, 2024

Research

Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations

Yasine Malki
Guannan Kang
W.K. Jacky Lam
Qing Zhou
Suk Hang Cheng
Peter P.H. Cheung Jinyue Bai Ming Lok Chan Chui Ting Lee Wenlei Peng Yiqiong Zhang Wanxia Gai Winsome W.S. Wong Mary-Jane L. Ma Wenshuo Li Xinzhou Xu Zhuoran Gao Irene O.L. Tse Huimin Shang
... [+14 authors] ...,
L.Y. Lois Choy
Peiyong Jiang
K.C. Allen Chan
Y.M. Dennis Lo

First Published November 27, 2024

Research

Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging

Amy R. Vandiver
Allen Herbst
Paul Stothard
Jonathan Wanagat

First Published November 27, 2024

Method

A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples

Shuai Guo
Xiaoqian Liu
Xuesen Cheng
Yujie Jiang
Shuangxi Ji
Qingnan Liang Andrew Koval Yumei Li Leah A. Owen Ivana K. Kim Ana Aparicio Sanghoon Lee Anil K. Sood Scott Kopetz John Paul Shen
... [+10 authors] ...,
John N. Weinstein
Margaret M. DeAngelis
Rui Chen
Wenyi Wang

First Published November 25, 2024

Research

Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets

Matthew D. Pollard
Wynn K. Meyer
Emily E. Puckett

First Published November 22, 2024

Research

Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay

Bertille Montibus
James A. Cain
Rocio T. Martinez-Nunez
Rebecca J. Oakey

First Published November 22, 2024

Research

Bacteriovorax bacteria" > The chromatin landscape of the histone-possessing Bacteriovorax bacteria

Georgi K. Marinov
Benjamin Doughty
Anshul Kundaje
William J. Greenleaf

First Published November 21, 2024

Method

KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome

Samuel H. Kim
Georgi K. Marinov
William J. Greenleaf

First Published November 21, 2024

Review

Advancements in prospective single-cell lineage barcoding and their applications in research

Xiaoli Zhang
Yirui Huang
Yajing Yang
Qi-En Wang
Lang Li

First Published November 21, 2024

Editorial

Revolutionizing genomics and medicine—one long molecule at a time

Ana Conesa
Alexander Hoischen
Fritz J. Sedlazeck

First Published November 20, 2024

Review

Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics

Natan Belchikov
Justine Hsu
Xiang Jennie Li
Julien Jarroux
Wen Hu
Anoushka Joglekar
Hagen U. Tilgner

First Published November 20, 2024

Review

Leveraging the power of long reads for targeted sequencing

Shruti V. Iyer
Sara Goodwin
William Richard McCombie

First Published November 20, 2024

Perspective

Challenges in identifying mRNA transcript starts and ends from long-read sequencing data

Ezequiel Calvo-Roitberg
Rachel F. Daniels
Athma A. Pai

First Published November 20, 2024

Method

Modeling gene interactions in polygenic prediction via geometric deep learning

Han Li
Jianyang Zeng
Michael P. Snyder
Sai Zhang

First Published November 19, 2024

Resource

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Paige A. Byerly
Alina von Thaden
Evgeny Leushkin
Leon Hilgers
Shenglin Liu
Sven Winter Tilman Schell Charlotte Gerheim Alexander Ben Hamadou Carola Greve Christian Betz Hanno J. Bolz Sven Büchner Johannes Lang Holger Meinig Evax Marie Famira-Parcsetich Sarah P. Stubbe Alice Mouton Sandro Bertolino Goedele Verbeylen Thomas Briner Lídia Freixas
... [+17 authors] ...,
Lorenzo Vinciguerra
Sarah A. Mueller
Carsten Nowak
Michael Hiller

First Published November 14, 2024

Resource

High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration

Zihe Li
Ziyu Xu
Lei Zhu
Tao Qin
Jinrui Ma
Zhanying Feng Huishan Yue Qing Guan Botong Zhou Ge Han Guokun Zhang Chunyi Li Shuaijun Jia
... [+8 authors] ...,
Qiang Qiu
Dingjun Hao
Yong Wang
Wen Wang

First Published November 14, 2024

Research

Paramecium" > ISWI1 complex proteins facilitate developmental genome editing in Paramecium

Aditi Singh
Lilia Häußermann
Christiane Emmerich
Emily Nischwitz
Brandon K.B. Seah
Falk Butter
Mariusz Nowacki
Estienne C. Swart

First Published November 14, 2024

Method

Multisample motif discovery and visualization for tandem repeats

Yaran Zhang
Marc Hulsman
Alex Salazar
Niccolò Tesi
Lydian Knoop
Sven van der Lee
... [+1 authors] ...,
Sanduni Wijesekera
Jana Krizova
Erik-Jan Kamsteeg
Henne Holstege

First Published November 13, 2024

Research

Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome

Lisanne Vervoort
Nicolas Dierckxsens
Marta Sousa Santos
Senne Meynants
Erika Souche
Ruben Cools Tracy Heung Koen Devriendt Hilde Peeters Donna M. McDonald-McGinn Ann Swillen Jeroen Breckpot
... [+7 authors] ...,
Beverly S. Emanuel
Hilde Van Esch
Anne S. Bassett
Joris R. Vermeesch

First Published November 13, 2024

Resource

Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding

Kai Li
Melissa L. Smith
J. Chris Blazier
Kelli J. Kochan
Jonathan M.D. Wood
Kerstin Howe Anne E. Kwitek Melinda R. Dwinell Hao Chen Julia L. Ciosek
... [+5 authors] ...,
Patrick Masterson
Terence D. Murphy
Theodore S. Kalbfleisch
Peter A. Doris

First Published November 8, 2024

Method

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

Sergey Koren
Zhigui Bao
Andrea Guarracino
Shujun Ou
Sara Goodwin
Katharine M. Jenike Julian Lucas Brandy McNulty Jimin Park Mikko Rautiainen Arang Rhie Dick Roelofs Harrie Schneiders Ilse Vrijenhoek Koen Nijbroek Olle Nordesjo Sergey Nurk Mike Vella Katherine R. Lawrence Doreen Ware Michael C. Schatz Erik Garrison Sanwen Huang
... [+18 authors] ...,
William Richard McCombie
Karen H. Miga
Alexander H.J. Wittenberg
Adam M. Phillippy

First Published November 6, 2024

Method

Factors impacting target-enriched long-read sequencing of resistomes and mobilomes

Ilya B. Slizovskiy
Nathalie Bonin
Jonathan E. Bravo
Peter M. Ferm
Jacob Singer
Christina Boucher
Noelle R. Noyes

First Published November 5, 2024

Research

Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps

Kristine Bilgrav Saether
Jesper Eisfeldt
Jesse D. Bengtsson
Ming Yin Lun
Christopher M. Grochowski
Medhat Mahmoud Hsiao-Tuan Chao Jill A. Rosenfeld Pengfei Liu Marlene Ek Jakob Schuy Adam Ameur Hongzheng Dai James Paul Hwang Fritz J. Sedlazeck Weimin Bi Ronit Marom
... [+12 authors] ...,
Josephine Wincent
Ann Nordgren
Claudia M.B. Carvalho
Anna Lindstrand

First Published November 1, 2024

Research

Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing

Jesper Eisfeldt
Edward J. Higginbotham
Felix Lenner
Jennifer Howe
Bridget A. Fernandez
Anna Lindstrand
Stephen W. Scherer
Lars Feuk

First Published October 29, 2024

Research

A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities

Jesper Eisfeldt
Adam Ameur
Felix Lenner
Esmee Ten Berk de Boer
Marlene Ek
Josephine Wincent Raquel Vaz Jesper Ottosson Tord Jonson Sofie Ivarsson Sofia Thunström Alexandra Topa Simon Stenberg Anna Rohlin Anna Sandestig Margareta Nordling Pia Palmebäck Magnus Burstedt Frida Nordin Eva-Lena Stattin Maria Sobol Panagiotis Baliakas Marie-Louise Bondeson Ida Höijer Kristine Bilgrav Saether Lovisa Lovmar
... [+21 authors] ...,
Hans Ehrencrona
Malin Melin
Lars Feuk
Anna Lindstrand

First Published October 29, 2024

Method

N⁶-methyladenosine modifications" > Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications

Dayea Park
Can Cenik

First Published October 29, 2024

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