Search | Genome Research

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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

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

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

Telomere-to-telomere assembly by preserving contained reads

Sudhanva Shyam Kamath
Mehak Bindra
Debnath Pal
Chirag Jain

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

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

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

Research

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

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

First Published October 15, 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

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

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

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

Genetics-driven risk predictions leveraging the Mendelian randomization framework

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

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

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

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

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

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

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

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

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

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

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

Research

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

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

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

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

Protein domain embeddings for fast and accurate similarity search

Iovino Benjamin Giovanni
Tang Haixu
Ye Yuzhen

First Published September 5, 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

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

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

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

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

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

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

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