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Resource

MPRAbase a Massively Parallel Reporter Assay database

Jingjing Zhao
Fotis A Baltoumas
Maxwell A Konnaris
Ioannis Mouratidis
Zhe Liu
Jasmine Sims
... [+1 authors] ...,
Vikram Agarwal
Georgios A Pavlopoulos
Ilias Georgakopoulos-Soares
Nadav Ahituv

First Published April 22, 2025

Method

Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data

Lulu Yan
Jinyu Cheng
Qing Nie
Xiaoqiang Sun

First Published April 22, 2025

Research

Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology" > Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology

Abigail L. Lind
Nathan A. McDonald
Elias R. Gerrick
Ami S. Bhatt
Katherine S. Pollard

First Published April 22, 2025

Research

Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis

Olga M. Sigalova
Mattia Forneris
Frosina Stojanovska
Bingqing Zhao
Rebecca R. Viales
Adam Rabinowitz
... [+1 authors] ...,
Fayrouz Hammal
Benoît Ballester
Judith B. Zaugg
Eileen E.M. Furlong

First Published April 15, 2025

Research

cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia" > Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia

Hao Zhu
Jiao Zhang
Soumya Rao
Matthew D. Durbin
Ying Li
Ruirui Lang Jiqiang Liu Baichuan Xiao Hailin Shan Ziqiu Meng Jinmo Wang Xiaokai Tang Zhenni Shi Liza L. Cox Shouqin Zhao Stephanie M. Ware Tiong Y. Tan Michelle de Silva Lyndon Gallacher Ting Liu Jie Mi Changqing Zeng Hou-Feng Zheng
... [+18 authors] ...,
Qingguo Zhang
Stylianos E. Antonarakis
Timothy C. Cox
Yong-Biao Zhang

First Published April 15, 2025

Resource

Building better genome annotations across the tree of life

Adam H. Freedman
Timothy B. Sackton

First Published April 15, 2025

Mini-Review

Evolution of genome-wide methylation profiling technologies

Carolina Montano
Winston Timp

First Published April 14, 2025

Perspective

The impact of long-read sequencing on human population-scale genomics

Tobias Rausch
Tobias Marschall
Jan O. Korbel

First Published April 14, 2025

Mini-Review

A Hitchhiker's Guide to long-read genomic analysis

Medhat Mahmoud
Daniel P. Agustinho
Fritz J. Sedlazeck

First Published April 14, 2025

Editorial

Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases

Ana Conesa
Alexander Hoischen
Fritz J. Sedlazeck

First Published April 14, 2025

Research

Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus

Rita Tam
Mareike Möller
Runpeng Luo
Zhenyan Luo
Ashley Jones
Sambasivam Periyannan
John P. Rathjen
Benjamin Schwessinger

First Published April 11, 2025

Method

Analytical validation of germline small variant detection using long-read HiFi genome sequencing

Nathan Hammond
Linda Liao
Pun Wai Tong
Zena Ng
Thuy-Mi P. Nguyen
Chandler Ho
Yao Yang
Stuart A. Scott

First Published April 11, 2025

Method

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

Byron J. Smith
Chunyu Zhao
Veronika Dubinkina
Xiaofan Jin
Liron Zahavi
Saar Shoer
Jacqueline Moltzau-Anderson
Eran Segal
Katherine S. Pollard

First Published April 10, 2025

Research

C. elegans" > Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans

Jun Kim
Haoyu Wang
Sevinç Ercan

First Published April 10, 2025

Research

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

Fu Xiang Quah
Miguel Vasconcelos Almeida
Moritz Blumer
Chengwei Ulrika Yuan
Bettina Fischer
Kirsten See Ben Jackson Richard Zatha Bosco Rusuwa George F. Turner M. Emília Santos
... [+6 authors] ...,
Hannes Svardal
Martin Hemberg
Richard Durbin
Eric Miska

First Published April 10, 2025

Method

k-mer manifold approximation and projection for visualizing DNA sequences" > k-mer manifold approximation and projection for visualizing DNA sequences

Chengbo Fu
Einari A. Niskanen
Gong-Hong Wei
Zhirong Yang
Marta Sanvicente-García
Marc Güell
Lu Cheng

First Published April 10, 2025

Method

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data

Chen Li
Sijie Chen
Yixin Chen
Haiyang Bian
Minsheng Hao
Lei Wei
Xuegong Zhang

First Published April 10, 2025

Research

Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes

Yu-Chi Chen
David L.J. Vendrami
Maximilian L. Huber
Luisa E.Y. Handel
Christopher R. Cooney
Joseph I. Hoffman
Toni I. Gossmann

First Published March 31, 2025

Research

Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing

Wouter Steyaert
Lydia Sagath
German Demidov
Vicente A. Yépez
Anna Esteve-Codina
Julien Gagneur Kornelia Ellwanger Ronny Derks Marjan Weiss Amber den Ouden Simone van den Heuvel Hilde Swinkels Nick Zomer Marloes Steehouwer Luke O'Gorman Galuh Astuti Kornelia Neveling Rebecca Schüle Jishu Xu Matthis Synofzik Danique Beijer Holger Hengel Ludger Schöls Kristl G. Claeys Jonathan Baets Liedewei Van de Vondel Alessandra Ferlini Rita Selvatici Heba Morsy Marwa Saeed Abd Elmaksoud Volker Straub Juliane Müller Veronica Pini Luke Perry Anna Sarkozy Irina Zaharieva Francesco Muntoni Enrico Bugiardini Kiran Polavarapu Rita Horvath Evan Reid Hanns Lochmüller Marco Spinazzi Marco Savarese Leslie Matalonga Steven Laurie Han G. Brunner Holm Graessner Sergi Beltran
... [+44 authors] ...,
Stephan Ossowski
Lisenka E.L.M. Vissers
Christian Gilissen
Alexander Hoischen

First Published March 26, 2025

Method

An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride

Inswasti Cahyani
John Tyson
Nadine Holmes
Josh Quick
Chris Moore
Nick Loman
Matthew Loose

First Published March 24, 2025

Research

Analysis of canine gene constraint identifies new variants for orofacial clefts and stature

Reuben M. Buckley
Nüket Bilgen
Alexander C. Harris
Peter Savolainen
Cafer Tepeli
Metin Erdoğan Aitor Serres Armero Dayna L. Dreger Frank G. van Steenbeek Marjo K. Hytönen Heidi G. Parker Jessica Hale
... [+7 authors] ...,
Hannes Lohi
Bengi Çınar Kul
Adam R. Boyko
Elaine A. Ostrander

First Published March 24, 2025

Method

De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies

John Beaulaurier
Lynn Ly
J. Andrew Duty
Carly Tyer
Christian Stevens
Chuan-Tien Hung Akash Sookdeo Alex W. Drong Shreyas Kowdle Axel Guzman-Solis Domenico Tortorella
... [+6 authors] ...,
Daniel J. Turner
Sissel Juul
Scott Hickey
Benhur Lee

First Published March 21, 2025

Research

Optical genome mapping enables accurate testing of large repeat expansions

Bart van der Sanden
Kornelia Neveling
Syukri Shukor
Michael D. Gallagher
Joyce Lee
Stephanie L. Burke Maartje Pennings Ronald van Beek Michiel Oorsprong Ellen Kater-Baats Eveline Kamping Alide A. Tieleman Nicol C. Voermans Ingrid E. Scheffer Jozef Gecz Mark A. Corbett Lisenka E.L.M. Vissers
... [+12 authors] ...,
Andy Wing Chun Pang
Alex Hastie
Erik-Jan Kamsteeg
Alexander Hoischen

First Published March 20, 2025

Research

Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA

Cristian Groza
Bing Ge
Warren A. Cheung
Tomi Pastinen
Guillaume Bourque

First Published March 20, 2025

Method

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

Tanner D. Jensen
Bohan Ni
Chloe M. Reuter
John E. Gorzynski
Sarah Fazal
Devon Bonner Rachel A. Ungar Pagé C. Goddard Archana Raja Euan A. Ashley Jonathan A. Bernstein Stephan Zuchner Michael D. Greicius
... [+8 authors] ...,
Stephen B. Montgomery
Michael C. Schatz
Matthew T. Wheeler
Alexis Battle

First Published March 20, 2025

Research

Unexpectedly low recombination rates and presence of hotspots in termite genomes

Turid Everitt
Tilman Rönneburg
Daniel Elsner
Anna Olsson
Yuanzhen Liu
Tuuli Larva
Judith Korb
Matthew T. Webster

First Published March 20, 2025

Method

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

Da-Inn Lee
Sushmita Roy

First Published March 20, 2025

Perspective

Unraveling the hidden complexity of cancer through long-read sequencing

Qiuhui Li
Ayse G. Keskus
Justin Wagner
Michal B. Izydorczyk
Winston Timp
Fritz J. Sedlazeck
... [+1 authors] ...,
Alison P. Klein
Justin M. Zook
Mikhail Kolmogorov
Michael C. Schatz

First Published March 20, 2025

Research

Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids

Tülay Karakulak
Natalia Zajac
Hella Anna Bolck
Anna Bratus-Neuenschwander
Qin Zhang
Weihong Qi Debleena Basu Tamara Carrasco Oltra
... [+3 authors] ...,
Hubert Rehrauer
Christian von Mering
Holger Moch
Abdullah Kahraman

First Published March 19, 2025

Research

Optical genome mapping identifies rare structural variants in neural tube defects

Nikhil S. Sahajpal
Jane Dean
Benjamin Hilton
Timothy Fee
Cindy Skinner
Alex Hastie
... [+1 authors] ...,
Barbara R. DuPont
Alka Chaubey
Michael J. Friez
Roger E. Stevenson

First Published March 19, 2025

Method

De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data

Arthur Dondi
Nico Borgsmüller
Pedro F. Ferreira
Brian J. Haas
Francis Jacob
Viola Heinzelmann-Schwarz
Niko Beerenwinkel

First Published March 19, 2025

Research

Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T

Luis F. Paulin
Jeremy Fan
Kieran O'Neill
Erin Pleasance
Vanessa L. Porter
Steven J.M. Jones
Fritz J. Sedlazeck

First Published March 17, 2025

Method

BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries

Yangyang Liu
Bingqiang Liu
Juntao Liu

First Published March 17, 2025

Method

Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution

Qian Qin
Victoria Popic
Kirsty Wienand
Houlin Yu
Emily White
Akanksha Khorgade Asa Shin Christophe Georgescu Catarina D. Campbell Arthur Dondi
... [+5 authors] ...,
Niko Beerenwinkel
Francisca Vazquez
Aziz M. Al'Khafaji
Brian J. Haas

First Published March 14, 2025

Method

Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity

Mayank Murali
Jamie Saquing
Senbao Lu
Ziyang Gao
Emily F. Watts
Ben Jordan Zachary Peters Wakefield Ana Fiszbein
... [+3 authors] ...,
David R. Cooper
Peter J. Castaldi
Dmitry Korkin
Gloria M. Sheynkman

First Published March 14, 2025

Research

KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution

Kai Otsuka
Akihiko Sakashita
So Maezawa
Richard M. Schultz
Satoshi H. Namekawa

First Published March 12, 2025

Research

Assessing DNA methylation detection for primary human tissue using Nanopore sequencing

Rylee Genner
Stuart Akeson
Melissa Meredith
Pilar Alvarez Jerez
Laksh Malik
Breeana Baker Abigail Miano-Burkhardt
... [+2 authors] ...,
Benedict Paten
Kimberley J. Billingsley
Cornelis Blauwendraat
Miten Jain

First Published March 7, 2025

Research

Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina

Meng Wang
Yumei Li
Jun Wang
Soo Hwan Oh
Yexuan Cao
Rui Chen

First Published March 6, 2025

Method

Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs

Xiaoyue Duan
Chaolei Chen
Chang Du
Liang Guo
Jun Liu
Naipeng Hou Pan Li Xiaolan Qi
... [+3 authors] ...,
Fei Gao
Xuguang Du
Jiangping Song
Sen Wu

First Published March 5, 2025

Research

Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly

Kang Du
Oliver Deusch
Ilja Bezrukov
Christa Lanz
Yann Guiguen
Margarete Hoffmann
... [+1 authors] ...,
Anette Habring
Detlef Weigel
Manfred Schartl
Christine Dreyer

First Published March 5, 2025

Research

Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches

Merel Stemerdink
Tabea Riepe
Nick Zomer
Renee Salz
Michael Kwint
Jaap Oostrik Raoul Timmermans Barbara Ferrari Stefano Ferrari Alfredo Dueñas Rey Emma Delanote Suzanne E. de Bruijn Hannie Kremer Susanne Roosing Frauke Coppieters Alexander Hoischen
... [+11 authors] ...,
Frans P.M. Cremers
Peter A.C. ‘t Hoen
Erwin van Wijk
Erik de Vrieze

First Published March 4, 2025

Method

RAmbler resolves complex repeats in human Chromosomes 8, 19, and X

Sakshar Chakravarty
Glennis Logsdon
Stefano Lonardi

First Published March 4, 2025

Research

Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth

Hadar Medini
Dan Mishmar

First Published March 4, 2025

Method

Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm

Samuel T. Horsfield
Basil C.T. Fok
Yuhan Fu
Paul Turner
John A. Lees
Nicholas J. Croucher

First Published March 4, 2025

Research

Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis

Tianfu Zeng
Haotian Liao
Lin Xia
Siyao You
Yanqun Huang
Jiaxun Zhang
Yahui Liu
Xuyan Liu
Dan Xie

First Published March 4, 2025

Research

Spirodela polyrhiza" > Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza

Rodolphe Dombey
Daniel Buendía-Ávila
Verónica Barragán-Borrero
Laura Diezma-Navas
Arturo Ponce-Mañe
José Mario Vargas-Guerrero
Rana Elias
Arturo Marí-Ordóñez

First Published March 4, 2025

Research

Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements

Hosiana Abewe
Alexandra Richey
Jeffery M. Vahrenkamp
Matthew Ginley-Hidinger
Craig M. Rush
Noel Kitchen
Xiaoyang Zhang
Jason Gertz

First Published March 3, 2025

Perspective

Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation

Carolina Monzó
Adam Frankish
Ana Conesa

First Published March 3, 2025

Method

Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads

Netanya Keil
Carolina Monzó
Lauren McIntyre
Ana Conesa

First Published March 3, 2025

Research

A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia

Haloom Rafehi
Liam G. Fearnley
Justin Read
Penny Snell
Kayli C. Davies
Liam Scott Greta Gillies Genevieve C. Thompson Tess A. Field Aleena Eldo Simon Bodek Ernest Butler Luke Chen John Drago Himanshu Goel Anna Hackett G. Michael Halmagyi Andrew Hannaford Katya Kotschet Kishore R. Kumar Smitha Kumble Matthew Lee-Archer Abhishek Malhotra Mark Paine Michael Poon Kate Pope Katrina Reardon Steven Ring Anne Ronan Matthew Silsby Renee Smyth Chloe Stutterd Mathew Wallis John Waterston Thomas Wellings Kirsty West Christine Wools Kathy H.C. Wu
... [+33 authors] ...,
David J. Szmulewicz
Martin B. Delatycki
Melanie Bahlo
Paul J. Lockhart

First Published February 27, 2025

Resource

Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

Jiawei Shen
Siyuan Cheng
Deepak Purushotham
Xiaoyu Zhuo
Alan Y Du
Wenjin Zhang
Daofeng Li
Ting Wang

First Published February 21, 2025

Research

The genomic consequences and persistence of sociality in spiders

Jilong Ma
Jesper Bechsgaard
Anne Aagaard
Palle Villesen
Trine Bilde
Mikkel Heide Schierup

First Published February 20, 2025

Research

Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia

Gage S. Black
Xiaomeng Huang
Yi Qiao
Philip Moos
Deepa Sampath
Deborah M. Stephens
Jennifer A. Woyach
Gabor T. Marth

First Published February 18, 2025

Research

Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved

Yang Li
Jianzhi Zhang

First Published February 18, 2025

Method

A unified analysis of atlas single-cell data

Hao Chen
Nam D. Nguyen
Matthew Ruffalo
Ziv Bar-Joseph

First Published February 18, 2025

Research

Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes

Diana Lobo
Hernán E. Morales
Cock Van Oosterhout
José Vicente López-Bao
Pedro Silva
Luis Llaneza Carolina Pacheco Diana Castro Germán Hernández-Alonso George Pacheco
... [+5 authors] ...,
John Archer
M. Thomas P. Gilbert
Nuno Ferrand
Raquel Godinho

First Published February 14, 2025

Research

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection

Jian-Hai Chen
Patrick Landback
Deanna Arsala
Alexander Guzzetta
Shengqian Xia
Jared Atlas Dylan Sosa
... [+2 authors] ...,
Yong E. Zhang
Jingqiu Cheng
Bairong Shen
Manyuan Long

First Published February 14, 2025

Research

Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing

Karine Choquet
Louis-Philippe Chaumont
Simon Bache
Autum R. Baxter-Koenigs
L. Stirling Churchman

First Published February 14, 2025

Research

cis-regulatory element evolution after whole-genome duplication" > The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication

Øystein Monsen
Lars Grønvold
Alex Datsomor
Thomas Harvey
James Kijas
Alexander Suh
Torgeir R. Hvidsten
Simen Rød Sandve

First Published February 12, 2025

Method

Fast sequence alignment for centromeres with RaMA

Pinglu Zhang
Yanming Wei
Qinzhong Tian
Quan Zou
Yansu Wang

First Published February 12, 2025

Research

Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites

Patrick D. Wilson
Xinyang Yu
Christopher R. Handelmann
Michael J. Buck

First Published February 10, 2025

Research

Variation in the fitness impact of translationally optimal codons among animals

Florian Bénitière
Tristan Lefébure
Laurent Duret

First Published February 10, 2025

Method

Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains

Hang Zhang
Yi Zhang
Kai Ming Ting
Jie Zhang
Qiuran Zhao

First Published February 5, 2025

Mini-Review

The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases

Giulia F. Del Gobbo
Kym M. Boycott

First Published February 3, 2025

Review

k-mer approaches for biodiversity genomics" > k-mer approaches for biodiversity genomics

Katharine M. Jenike
Lucía Campos-Domínguez
Marilou Boddé
José Cerca
Christina N. Hodson
Michael C. Schatz
Kamil S. Jaron

First Published January 31, 2025

Method

Enhancing nanopore adaptive sampling for PromethION using readfish at scale

Rory Munro
Alexander Payne
Nadine Holmes
Chris Moore
Inswasti Cahyani
Matthew Loose

First Published January 30, 2025

Method

Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger

Leszek P. Pryszcz
Gregor Diensthuber
Laia Llovera
Rebeca Medina
Anna Delgado-Tejedor
Luca Cozzuto
Julia Ponomarenko
Eva Maria Novoa

First Published January 29, 2025

Review

Artificial intelligence and machine learning in cell-free-DNA-based diagnostics

W.H. Adrian Tsui
Spencer C. Ding
Peiyong Jiang
Y.M. Dennis Lo

First Published January 22, 2025

Resource

Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution

Yujie Chen
Yiran Hou
Qinglin Zeng
Irene Wang
Meiru Shang
Kwangdeok Shin Christopher Hemauer
... [+2 authors] ...,
Xiaoyun Xing
Junsu Kang
Guoyan Zhao
Ting Wang

First Published January 14, 2025

Research

Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations

Mikkel Dahl-Jessen
Thorkild Terkelsen
Rasmus O. Bak
Uffe Birk Jensen

First Published January 13, 2025

Method

Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration

Zepu Miao
Jia-Xing Yue

First Published January 13, 2025

Method

Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling

Li-Ting Chen
Myrthe Jager
Dàmi Rebergen
Geertruid J. Brink
Tom van den Ende
Willem Vanderlinden Pauline Kolbeck Marc Pagès-Gallego Ymke van der Pol Nicolle Besselink Norbert Moldovan Nizar Hami Wigard P. Kloosterman Hanneke van Laarhoven Florent Mouliere Ronald Zweemer
... [+11 authors] ...,
Jan Lipfert
Sarah Derks
Alessio Marcozzi
Jeroen de Ridder

First Published January 13, 2025

Method

Proxy panels enable privacy-aware outsourcing of genotype imputation

Degui Zhi
Xiaoqian Jiang
Arif Harmanci

First Published January 10, 2025

Research

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

Yang Liu
João Botelho
Jaime Iranzo

First Published January 10, 2025

Research

DDX3X and DDX3Y" > Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y

Shruthi Rengarajan
Jason Derks
Daniel W. Bellott
Nikolai Slavov
David C. Page

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

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

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

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

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