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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

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

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

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

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

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

Editorial

Revolutionizing genomics and medicine—one long molecule at a time

Ana Conesa
Alexander Hoischen
Fritz J. Sedlazeck

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

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

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

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

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

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

Geometric deep learning framework for de novo genome assembly

Lovro Vrček
Xavier Bresson
Thomas Laurent
Martin Schmitz
Kenji Kawaguchi
Mile Šikić

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

Mini-Review

The chromatin tapestry as a framework for neurodevelopment

Ben Nolan
Timothy E. Reznicek
Christopher T. Cummings
M. Jordan Rowley

First Published October 29, 2024

Method

An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing

Kathleen Zeglinski
Christian Montellese
Matthew E. Ritchie
Monther Alhamdoosh
Cédric Vonarburg
Rory Bowden
... [+1 authors] ...,
Monika Jordi
Quentin Gouil
Florian Aeschimann
Arthur Hsu

First Published October 28, 2024

Research

Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques

Nanine de Groot
Marit van der Wiel
Ngoc Giang Le
Natasja G. de Groot
Jesse Bruijnesteijn
Ronald E. Bontrop

First Published October 23, 2024

Resource

Generation and analysis of a mouse multitissue genome annotation atlas

Matthew Adams
Christopher Vollmers

First Published October 23, 2024

Method

Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors

Mara Lohde
Gabriel E. Wagner
Johanna Dabernig-Heinz
Adrian Viehweger
Sascha D. Braun
Stefan Monecke Celia Diezel Claudia Stein
... [+3 authors] ...,
Mike Marquet
Ralf Ehricht
Mathias W. Pletz
Christian Brandt

First Published October 23, 2024

Research

Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events" > Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events

Marin Volarić
Evelin Despot-Slade
Damira Veseljak
Brankica Mravinac
Nevenka Meštrović

First Published October 22, 2024

Research

Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres" > Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres

Ursula Oggenfuss
Robert T. Todd
Natthapon Soisangwan
Bailey Kemp
Alison Guyer
Annette Beach
Anna Selmecki

First Published October 22, 2024

Resource

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

Michelle Kudron
Louis Gevirtzman
Alec Victorsen
Bridget C. Lear
Jiahao Gao
Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
... [+16 authors] ...,
LaDeana Hillier
Susan E. Celniker
Valerie Reinke
Robert H. Waterston

First Published October 22, 2024

Method

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR

Artem Mikelov
George Nefediev
Alexander Tashkeev
Oscar L. Rodriguez
Diego Aguilar Ortmans
Valeriia Skatova Mark Izraelson Alexey N. Davydov Stanislav Poslavsky Souad Rahmouni
... [+5 authors] ...,
Corey T. Watson
Dmitriy Chudakov
Scott D. Boyd
Dmitry Bolotin

First Published October 21, 2024

Research

Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development

Song Zhang
Chao Wang
Shenghua Qin
Choulin Chen
Yongzhou Bao
Yuanyuan Zhang Lingna Xu Qingyou Liu
... [+3 authors] ...,
Yunxiang Zhao
Kui Li
Zhonglin Tang
Yuwen Liu

First Published October 21, 2024

Method

Inferring ancestry with the hierarchical soft clustering approach tangleGen

Klara Elisabeth Burger
Solveig Klepper
Ulrike von Luxburg
Franz Baumdicker

First Published October 21, 2024

Research

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer

Yueqiang Song
Fuyuan Li
Shangzi Wang
Yuntong Wang
Cong Lai
Lian Chen Ning Jiang
... [+2 authors] ...,
Jin Li
Xingdong Chen
Swneke D. Bailey
Xiaoyang Zhang

First Published October 18, 2024

Resource

Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level

Wankun Deng
Citu Citu
Andi Liu
Zhongming Zhao

First Published October 18, 2024

Research

De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes

Basanta Bista
Laura González-Rodelas
Lucía Álvarez-González
Zhi-qiang Wu
Eugenia E. Montiel
Ling Sze Lee Daleen B. Badenhorst Srihari Radhakrishnan Robert Literman Beatriz Navarro-Dominguez John B. Iverson
... [+6 authors] ...,
Simon Orozco-Arias
Josefa González
Aurora Ruiz-Herrera
Nicole Valenzuela

First Published October 16, 2024

Method

Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data

Alicia Petrany
Ruoyu Chen
Shaoqiang Zhang
Yong Chen

First Published October 15, 2024

Research

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Luis E. Valentin-Alvarado
Ling-Dong Shi
Kathryn E. Appler
Alexander Crits-Christoph
Valerie De Anda
Benjamin A. Adler Michael L. Cui Lynn Ly Pedro Leão Richard J. Roberts
... [+5 authors] ...,
Rohan Sachdeva
Brett J. Baker
David F. Savage
Jillian F. Banfield

First Published October 15, 2024

Research

Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries

Shaoqiang Hu
Xiangguo Zeng
Yuguo Liu
Yongping Li
Minghao Qu
Wen-Biao Jiao
Yongchao Han
Chunying Kang

First Published October 15, 2024

Resource

PWAS Hub for exploring gene-based associations of common complex diseases

Guy Kelman
Roei Zucker
Nadav Brandes
Michal Linial

First Published October 15, 2024

Method

k-mer analysis" > Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis

Romain Derelle
Johanna von Wachsmann
Tommi Mäklin
Joel Hellewell
Timothy Russell
Ajit Lalvani
... [+1 authors] ...,
Leonid Chindelevitch
Nicholas J. Croucher
Simon R. Harris
John A. Lees

First Published October 15, 2024

Method

Telomere-to-telomere assembly by preserving contained reads

Sudhanva Shyam Kamath
Mehak Bindra
Debnath Pal
Chirag Jain

First Published October 15, 2024

Method

otter" > Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter

Niccoló Tesi
Alex Salazar
Yaran Zhang
Sven van der Lee
Marc Hulsman
Lydian Knoop Sanduni Wijesekera Jana Krizova Anne-Fleur Schneider Maartje Pennings
... [+5 authors] ...,
Kristel Sleegers
Erik-Jan Kamsteeg
Marcel Reinders
Henne Holstege

First Published October 15, 2024

Method

Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework

Haotian Teng
Marcus Stoiber
Ziv Bar-Joseph
Carl Kingsford

First Published October 15, 2024

Editorial

Innovations in computational biology: RECOMB 2024 Special Issue

Jian Ma
Bonnie Berger

First Published October 11, 2024

Research

bla_KPC" > Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla_KPC

Angela Gomez-Simmonds
Medini K. Annavajhala
Dwayne Seeram
Todd W. Hokunson
Heekuk Park
Anne-Catrin Uhlemann

First Published October 4, 2024

Resource

High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation

Jonas A. Gustafson
Sophia B. Gibson
Nikhita Damaraju
Miranda P.G. Zalusky
Kendra Hoekzema
David Twesigomwe Lei Yang Anthony A. Snead Phillip A. Richmond Wouter De Coster Nathan D. Olson Andrea Guarracino Qiuhui Li Angela L. Miller Joy Goffena Zachary B. Anderson Sophie H.R. Storz Sydney A. Ward Maisha Sinha Claudia Gonzaga-Jauregui Wayne E. Clarke Anna O. Basile André Corvelo Catherine Reeves Adrienne Helland Rajeeva Lochan Musunuri Mahler Revsine Karynne E. Patterson Cate R. Paschal Christina Zakarian Sara Goodwin Tanner D. Jensen Esther Robb William Richard McCombie Fritz J. Sedlazeck Justin M. Zook Stephen B. Montgomery Erik Garrison Mikhail Kolmogorov Michael C. Schatz Richard N. McLaughlin Harriet Dashnow Michael C. Zody
... [+38 authors] ...,
Matt Loose
Miten Jain
Evan E. Eichler
Danny E. Miller

First Published October 2, 2024

Method

Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications

Xudong Liu
Ying Ni
Lianwei Ye
Zhihao Guo
Lu Tan
Jun Li
Mengsu Yang
Sheng Chen
Runsheng Li

First Published October 2, 2024

Method

Genetics-driven risk predictions leveraging the Mendelian randomization framework

Daniel Sens
Liubov Shilova
Ludwig Gräf
Maria Grebenshchikova
Bjoern M. Eskofier
Francesco Paolo Casale

First Published September 27, 2024

Research

Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples

Taishan Hu
Timothy L. Mosbruger
Nikolaos G. Tairis
Amalia Dinou
Pushkala Jayaraman
Mahdi Sarmady Kingham Brewster
... [+2 authors] ...,
Yang Li
Tristan J. Hayeck
Jamie L. Duke
Dimitri S. Monos

First Published September 26, 2024

Research

Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists

Marcin P. Sajek
Danielle Y. Bilodeau
Michael A. Beer
Emma Horton
Yukiko Miyamoto
Katrina B. Velle
... [+1 authors] ...,
Lars Eckmann
Lillian Fritz-Laylin
Olivia S. Rissland
Neelanjan Mukherjee

First Published September 26, 2024

Method

Designing realistic regulatory DNA with autoregressive language models

Avantika Lal
David Garfield
Tommaso Biancalani
Gokcen Eraslan

First Published September 25, 2024

Research

CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain" > Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

James L. Shepherdson
David M. Granas
Jie Li
Zara Shariff
Stephen P. Plassmeyer
Alex S. Holehouse
Michael A. White
Barak A. Cohen

First Published September 25, 2024

Method

Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads

Seong Woo Han
San Jewell
Andrei Thomas-Tikhonenko
Yoseph Barash

First Published September 25, 2024

Method

Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories

Borislav Hrisimirov Hristov
William Stafford Noble
Alessandro Bertero

First Published September 25, 2024

Method

Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change

Apurva Narechania
Dean Bobo
Kevin Deitz
Rob DeSalle
Paul J. Planet
Barun Mathema

First Published September 25, 2024

Research

AGAP duplicons associate with structural diversity at Chromosome 10q11.22" > AGAP duplicons associate with structural diversity at Chromosome 10q11.22

Stefania Fornezza
Vincenza Simona Delvecchio
William T. Harvey
Philip C. Dishuck
Evan E. Eichler
Giuliana Giannuzzi

First Published September 25, 2024

Research

Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders

Susan M. Hiatt
James M.J. Lawlor
Lori H. Handley
Donald R. Latner
Zachary T. Bonnstetter
Candice R. Finnila Michelle L. Thompson Lori Beth Boston Melissa Williams Ivan Rodriguez Nunez Jerry Jenkins Whitley V. Kelley E. Martina Bebin Michael A. Lopez Anna C.E. Hurst
... [+10 authors] ...,
Bruce R. Korf
Jeremy Schmutz
Jane Grimwood
Gregory M. Cooper

First Published September 19, 2024

Resource

Saccharomyces bayanus genome divergence after hybridization" > Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization

Cory Gardner
Junhao Chen
Christina Hadfield
Zhaolian Lu
David Debruin
Yu Zhan
Maureen J. Donlin
Tae-Hyuk Ahn
Zhenguo Lin

First Published September 17, 2024

Resource

Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations

Wenyu Zhang
Anja Guenther
Yuanxiao Gao
Kristian Ullrich
Bruno Huettel
Aftab Ahmad
Lei Duan
Kaizong Wei
Diethard Tautz

First Published September 17, 2024

Research

Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion

Joshua Lee
Elizabeth A. Snell
Joanne Brown
Charlotte E. Booth
Rosamonde E. Banks
Daniel J. Turner
Naveen S. Vasudev
Dimitris Lagos

First Published September 16, 2024

Method

Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing

Sena A. Gocuk
James Lancaster
Shian Su
Jasleen K. Jolly
Thomas L. Edwards
Doron G. Hickey
... [+1 authors] ...,
Matthew E. Ritchie
Marnie E. Blewitt
Lauren N. Ayton
Quentin Gouil

First Published September 16, 2024

Research

SF3B1 mutations" > Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations

Alicja Pacholewska
Matthias Lienhard
Mirko Brüggemann
Heike Hänel
Lorina Bilalli
Anja Königs Felix Heß Kerstin Becker Karl Köhrer Jesko Kaiser Holger Gohlke Norbert Gattermann Michael Hallek Carmen D. Herling Julian König
... [+10 authors] ...,
Christina Grimm
Ralf Herwig
Kathi Zarnack
Michal R. Schweiger

First Published September 13, 2024

Research

Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models

Gregor Diensthuber
Leszek P. Pryszcz
Laia Llovera
Morghan C. Lucas
Anna Delgado-Tejedor
Sonia Cruciani
Jean-Yves Roignant
Oguzhan Begik
Eva Maria Novoa

First Published September 13, 2024

Research

Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes

Suleyman Gulsuner
Amal AbuRayyan
Jessica B. Mandell
Ming K. Lee
Greta V. Bernier
Barbara M. Norquist
Sarah B. Pierce
Mary-Claire King
Tom Walsh

First Published September 13, 2024

Resource

Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize

Laura E. Tibbs-Cortes
Tingting Guo
Carson M. Andorf
Xianran Li
Jianming Yu

First Published September 13, 2024

Method

A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma

Jan Müller
Christina Hartwig
Mirko Sonntag
Lisa Bitzer
Christopher Adelmann
Yevhen Vainshtein Karolina Glanz Sebastian O. Decker
... [+3 authors] ...,
Thorsten Brenner
Georg F. Weber
Arndt von Haeseler
Kai Sohn

First Published September 13, 2024

Research

Evidence for compensatory evolution within pleiotropic regulatory elements

Zane Kliesmete
Peter Orchard
Victor Yan Kin Lee
Johanna Geuder
Simon M. Krauß
Mari Ohnuki
... [+1 authors] ...,
Jessica Jocher
Beate Vieth
Wolfgang Enard
Ines Hellmann

First Published September 10, 2024

Method

Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies

Tsung-Kai Hung
Wan-Chi Liu
Sheng-Kai Lai
Hui-Wen Chuang
Yi-Che Lee
Hong-Ye Lin Chia-Lang Hsu
... [+2 authors] ...,
Chien-Yu Chen
Ya-Chien Yang
Jacob Shujui Hsu
Pei-Lung Chen

First Published September 9, 2024

Research

Differences in activity and stability drive transposable element variation in tropical and temperate maize

Shujun Ou
Armin Scheben
Tyler Collins
Yinjie Qiu
Arun S. Seetharam
Claire C. Menard Nancy Manchanda Jonathan I. Gent
... [+3 authors] ...,
Michael C. Schatz
Sarah N. Anderson
Matthew B. Hufford
Candice N. Hirsch

First Published September 9, 2024

Method

Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption

Meir Goldenberg
Loay Mualem
Amit Shahar
Sagi Snir
Adi Akavia

First Published September 5, 2024

Method

Protein domain embeddings for fast and accurate similarity search

Benjamin Giovanni Iovino
Haixu Tang
Yuzhen Ye

First Published September 5, 2024

Method

A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data

Cameron Park
Shouvik Mani
Nicolas Beltran-Velez
Katie Maurer
Teddy Huang
Shuqiang Li Satyen Gohil
... [+2 authors] ...,
Kenneth J. Livak
David A. Knowles
Catherine J. Wu
Elham Azizi

First Published September 5, 2024

Method

A best-match approach for gene set analyses in embedding spaces

Lechuan Li
Ruth Dannenfelser
Charlie Cruz
Vicky Yao

First Published September 4, 2024

Method

Spatial Cellular Networks from omics data with SpaCeNet

Stefan Schrod
Niklas Lück
Robert Lohmayer
Stefan Solbrig
Dennis Völkl
Tina Wipfler Katherine H. Shutta Marouen Ben Guebila Andreas Schäfer Tim Beißbarth
... [+5 authors] ...,
Helena U. Zacharias
Peter J. Oefner
John Quackenbush
Michael Altenbuchinger

First Published September 4, 2024

Method

Matrix sketching framework for linear mixed models in association studies

Myson Burch
Aritra Bose
Gregory Dexter
Laxmi Parida
Petros Drineas

First Published September 4, 2024

Method

k-mer selection for large and evolutionarily diverse reference libraries" > Memory-bound k-mer selection for large and evolutionarily diverse reference libraries

Ali Osman Berk Şapcı
Siavash Mirarab

First Published August 29, 2024

Research

Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage

Kavitha Uthanumallian
Andrea Del Cortona
Susana M. Coelho
Olivier De Clerck
Sebastian Duchene
Heroen Verbruggen

First Published August 29, 2024

Method

A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits

Boyang Fu
Prateek Anand
Aakarsh Anand
Joel Mefford
Sriram Sankararaman

First Published August 29, 2024

Resource

Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs

Ashlyn G. Anderson
Belle A. Moyers
Jacob M. Loupe
Ivan Rodriguez-Nunez
Stephanie A. Felker
James M.J. Lawlor William E. Bunney Blynn G. Bunney Preston M. Cartagena Adolfo Sequeira Stanley J. Watson
... [+6 authors] ...,
Huda Akil
Eric M. Mendenhall
Gregory M. Cooper
Richard M. Myers

First Published August 16, 2024

Research

Widespread natural selection on metabolite levels in humans

Yanina Timasheva
Kaido Lepik
Orsolya Liska
Balázs Papp
Zoltán Kutalik

First Published August 16, 2024

Research

Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage

Emily Lowry
Yiqing Wang
Tal Dagan
Amir Mitchell

First Published August 16, 2024

Method

A simple method for finding related sequences by adding probabilities of alternative alignments

Martin C. Frith

First Published August 16, 2024

Method

Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries

Matthew Wiens
Hossein Farahani
R. Wilder Scott
T. Michael Underhill
Ali Bashashati

First Published August 15, 2024

Resource

Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR

Wouter De Coster
Ida Höijer
Inge Bruggeman
Svenn D'Hert
Malin Melin
Adam Ameur
Rosa Rademakers

First Published August 15, 2024

Resource

C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types" > A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types

Felicia Peng
C. Erik Nordgren
John Isaac Murray

First Published August 14, 2024

Method

A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data

Siyuan Chen
Jiuming Wang
Inkyung Jung
Zhaowen Qiu
Xin Gao
Yu Li

First Published August 13, 2024

Method

A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data

Mengyuan Zhao
Jiawei Li
Xiaoyi Liu
Ke Ma
Jijun Tang
Fei Guo

First Published August 12, 2024

Method

Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs

Juri Kuronen
Samuel T. Horsfield
Anna K. Pöntinen
Sudaraka Mallawaarachchi
Sergio Arredondo-Alonso
Harry Thorpe Rebecca A. Gladstone Rob J.L. Willems Stephen D. Bentley Nicholas J. Croucher
... [+5 authors] ...,
Johan Pensar
John A. Lees
Gerry Tonkin-Hill
Jukka Corander

First Published August 12, 2024

Method

Bayesian inference of sample-specific coexpression networks

Enakshi Saha
Viola Fanfani
Panagiotis Mandros
Marouen Ben Guebila
Jonas Fischer
Katherine H. Shutta
Dawn L. DeMeo
Camila M. Lopes-Ramos
John Quackenbush

First Published August 12, 2024

Research

The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores

Yulong Liu
Gang Zhai
Jingzhi Su
Yulong Gong
Bingyuan Yang
Qisheng Lu Longwei Xi Yutong Zheng Jingyue Cao Haokun Liu Junyan Jin Zhimin Zhang Yunxia Yang Xiaoming Zhu Zhongwei Wang Gaorui Gong Jie Mei
... [+12 authors] ...,
Zhan Yin
Rodolphe E. Gozlan
Shouqi Xie
Dong Han

First Published August 9, 2024

Method

Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil

Mădălina Giurgiu
Nadine Wittstruck
Elias Rodriguez-Fos
Rocío Chamorro González
Lotte Brückner
Annabell Krienelke-Szymansky Konstantin Helmsauer Anne Hartebrodt Philipp Euskirchen
... [+4 authors] ...,
Richard P. Koche
Kerstin Haase
Knut Reinert
Anton G. Henssen

First Published August 7, 2024

Method

Secure discovery of genetic relatives across large-scale and distributed genomic data sets

Matthew M. Hong
David Froelicher
Ricky Magner
Victoria Popic
Bonnie Berger
Hyunghoon Cho

First Published August 7, 2024

Research

TBC1D3 gene family in humans" > Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans

Xavi Guitart
David Porubsky
DongAhn Yoo
Max L. Dougherty
Philip C. Dishuck
Katherine M. Munson Alexandra P. Lewis Kendra Hoekzema
... [+3 authors] ...,
Jordan Knuth
Stephen Chang
Tomi Pastinen
Evan E. Eichler

First Published August 6, 2024

Research

The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution

Xinghua Li
Judith E. Mank
Liping Ban

First Published August 5, 2024

Method

Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences

Chencheng Xu
Suying Bao
Ye Wang
Wenxing Li
Hao Chen
Yufeng Shen
Tao Jiang
Chaolin Zhang

First Published July 26, 2024

Method

Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction

Shuai Zeng
Duolin Wang
Lei Jiang
Dong Xu

First Published July 26, 2024

Method

Accurate assembly of circular RNAs with TERRACE

Tasfia Zahin
Qian Shi
Xiaofei Carl Zang
Mingfu Shao

First Published July 26, 2024

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