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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

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

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

Benjamin Giovanni Iovino
Haixu Tang
Yuzhen Ye

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

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

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

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

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

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

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

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

Accurate assembly of circular RNAs with TERRACE

Tasfia Zahin
Qian Shi
Xiaofei Carl Zang
Mingfu Shao

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

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

Corrigendum

Corrigendum: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere

Lee H. Wong
Kate H. Brettingham-Moore
Lyn Chan
Julie M. Quach
Melissa A. Anderson
Emma L. Northrop Ross Hannan
... [+2 authors] ...,
Richard Saffery
Margaret L. Shaw
Evan Williams
K.H. Andy Choo

First Published July 23, 2024

Resource

Global compositional and functional states of the human gut microbiome in health and disease

Sunjae Lee
Theo Portlock
Emmanuelle Le Chatelier
Fernando Garcia-Guevara
Frederick Clasen
Florian Plaza Oñate Nicolas Pons Neelu Begum Azadeh Harzandi Ceri Proffitt Dorines Rosario Stefania Vaga Junseok Park Kalle von Feilitzen Fredric Johansson Cheng Zhang Lindsey A. Edwards Vincent Lombard Franck Gauthier Claire J. Steves David Gomez-Cabrero Bernard Henrissat Doheon Lee Lars Engstrand Debbie L. Shawcross Gordon Proctor Mathieu Almeida Jens Nielsen Adil Mardinoglu
... [+24 authors] ...,
David L. Moyes
Stanislav Dusko Ehrlich
Mathias Uhlen
Saeed Shoaie

First Published July 22, 2024

Method

Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy

Moonseong Jeong
Ali Pazokitoroudi
Zhengtong Liu
Sriram Sankararaman

First Published July 22, 2024

Method

Graph-based self-supervised learning for repeat detection in metagenomic assembly

Ali Azizpour
Advait Balaji
Todd J. Treangen
Santiago Segarra

First Published July 19, 2024

Method

High-fidelity, large-scale targeted profiling of microsatellites

Caitlin A. Loh
Danielle A. Shields
Adam Schwing
Gilad D. Evrony

First Published July 16, 2024

Method

Haplotype-aware sequence alignment to pangenome graphs

Ghanshyam Chandra
Daniel Gibney
Chirag Jain

First Published July 16, 2024

Research

6A RNA modifications in the hippocampus" > Single-cell discovery of m⁶A RNA modifications in the hippocampus

Shuangshuang Feng
Maitena Tellaetxe-Abete
Yujie Zhang
Yan Peng
Han Zhou
Mingjie Dong
... [+1 authors] ...,
Erika Larrea
Liang Xue
Li Zhang
Magdalena J. Koziol

First Published July 15, 2024

Resource

DEAD box RNA helicases are pervasive protein kinase interactors and activators

Alexander Hirth
Edoardo Fatti
Eugen Netz
Sergio P. Acebron
Dimitris Papageorgiou
Andrea Švorinić Cristina-Maria Cruciat Emil Karaulanov Alexandr Gopanenko Tianheng Zhu
... [+5 authors] ...,
Irmgard Sinning
Jeroen Krijgsveld
Oliver Kohlbacher
Christof Niehrs

First Published July 10, 2024

Method

Accurate allocation of multimapped reads enables regulatory element analysis at repeats

Alexis Morrissey
Jeffrey Shi
Daniela Q. James
Shaun Mahony

First Published July 10, 2024

Method

Accurate estimation of pathway activity in single cells for clustering and differential analysis

Daniel Davis
Avishai Wizel
Yotam Drier

First Published July 9, 2024

Method

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing

Kaiyuan Zhu
Matthew G. Jones
Jens Luebeck
Xinxin Bu
Hyerim Yi
King L. Hung Ivy Tsz-Lo Wong
... [+2 authors] ...,
Shu Zhang
Paul S. Mischel
Howard Y. Chang
Vineet Bafna

First Published July 9, 2024

Research

Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins

Nikolaos Vakirlis
Anne Kupczok

First Published July 8, 2024

Research

Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue

Aarthi Venkat
Maximillian J. Carlino
Betty R. Lawton
Manju L. Prasad
Matthew Amodio
Courtney E. Gibson
... [+1 authors] ...,
Caroline J. Zeiss
Scott E. Youlten
Smita Krishnaswamy
Diane S. Krause

First Published July 8, 2024

Research

Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States" > Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States

Greta Bellinzona
Tiago Nardi
Michele Castelli
Gherard Batisti Biffignandi
Karim Adjou
Martha Betson Yannick Blanchard Ioana Bujila Rachel Chalmers Rebecca Davidson Nicoletta D'Avino Tuulia Enbom Jacinto Gomes Gregory Karadjian Christian Klotz Emma Östlund Judith Plutzer Ruska Rimhanen-Finne Guy Robinson Anna Rosa Sannella Jacek Sroka Christen Rune Stensvold Karin Troell Paolo Vatta
... [+19 authors] ...,
Barbora Zalewska
Claudio Bandi
Davide Sassera
Simone M. Cacciò

First Published July 8, 2024

Mini-Review

Large-scale genomic analysis of the domestic dog informs biological discovery

Reuben M. Buckley
Elaine A. Ostrander

First Published July 2, 2024

Research

Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles

Xuejing Wang
Gerald Heckel

First Published July 2, 2024

Resource

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Guanjue Xiang
Xi He
Belinda M. Giardine
Kathryn J. Isaac
Dylan J. Taylor
Rajiv C. McCoy Camden Jansen Cheryl A. Keller Alexander Q. Wixom April Cockburn Amber Miller Qian Qi Yanghua He Yichao Li Jens Lichtenberg Elisabeth F. Heuston Stacie M. Anderson Jing Luan Marit W. Vermunt Feng Yue Michael E.G. Sauria Michael C. Schatz James Taylor Berthold Göttgens Jim R. Hughes Douglas R. Higgs Mitchell J. Weiss Yong Cheng Gerd A. Blobel David M. Bodine
... [+25 authors] ...,
Yu Zhang
Qunhua Li
Shaun Mahony
Ross C. Hardison

First Published July 1, 2024

Method

CodonBERT large language model for mRNA vaccines

Sizhen Li
Saeed Moayedpour
Ruijiang Li
Michael Bailey
Saleh Riahi
Lorenzo Kogler-Anele Milad Miladi Jacob Miner Fabien Pertuy Dinghai Zheng Jun Wang Akshay Balsubramani Khang Tran Minnie Zacharia Monica Wu Xiaobo Gu Ryan Clinton Carla Asquith Joseph Skaleski Lianne Boeglin Sudha Chivukula Anusha Dias Tod Strugnell
... [+18 authors] ...,
Fernando Ulloa Montoya
Vikram Agarwal
Ziv Bar-Joseph
Sven Jager

First Published July 1, 2024

Resource

Wolffia australiana" > Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana

Tom Denyer
Pin-Jou Wu
Kelly Colt
Bradley W. Abramson
Zhili Pang
Pavel Solansky Allen Mamerto Tatsuya Nobori
... [+3 authors] ...,
Joseph R. Ecker
Eric Lam
Todd P. Michael
Marja C.P. Timmermans

First Published July 1, 2024

Erratum

O(m log n) time through an average-case analysis of the seed-chain-extend heuristic" > Erratum: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

Jim Shaw
Yun William Yu

First Published June 25, 2024

Method

Delineating yeast cleavage and polyadenylation signals using deep learning

Emily Kunce Stroup
Zhe Ji

First Published June 24, 2024

Method

Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution

Pratibha Jagannatha
Alexandra T. Tankka
Daniel A. Lorenz
Tao Yu
Brian A. Yee
Kristopher W. Brannan
Cathy J. Zhou
Jason G. Underwood
Gene W. Yeo

First Published June 21, 2024

Method

Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters

Jens-Uwe Ulrich
Bernhard Y. Renard

First Published June 17, 2024

Method

Size-based expectation maximization for characterizing nucleosome positions and subtypes

Jianyu Yang
Kuangyu Yen
Shaun Mahony

First Published June 17, 2024

Method

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Lars Gabriel
Tomáš Brůna
Katharina J. Hoff
Matthis Ebel
Alexandre Lomsadze
Mark Borodovsky
Mario Stanke

First Published June 12, 2024

Method

GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes

Tomáš Brůna
Alexandre Lomsadze
Mark Borodovsky

First Published June 12, 2024

Research

Ostrinia furnacalis)" > Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)

Pengfei Lv
Xingzhuo Yang
Xianguo Zhao
Zhangwu Zhao
Juan Du

First Published June 12, 2024

Method

Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine

Bo Yan
Duan Wang
Laurence Ettwiller

First Published June 10, 2024

Method

Identifying genes within pathways in unannotated genomes with PaGeSearch

Sohyoung Won
Jaewoong Yu
Heebal Kim

First Published June 10, 2024

Method

fibertools" > DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools

Anupama Jha
Stephanie C. Bohaczuk
Yizi Mao
Jane Ranchalis
Benjamin J. Mallory
Alan T. Min Morgan O. Hamm Elliott Swanson Danilo Dubocanin Connor Finkbeiner Tony Li
... [+6 authors] ...,
Dale Whittington
William Stafford Noble
Andrew B. Stergachis
Mitchell R. Vollger

First Published June 7, 2024

Mini-Review

Toward telomere-to-telomere cat genomes for precision medicine and conservation biology

William J. Murphy
Andrew J. Harris

First Published June 7, 2024

$Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation$

Method

Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation

Alexander J. Ritter
Jolene M. Draper
Christopher Vollmers
Jeremy R. Sanford

First Published June 5, 2024

Research

Cardiocondyla obscurior" > Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior

Mohammed Errbii
Jürgen Gadau
Kerstin Becker
Lukas Schrader
Jan Oettler

First Published June 5, 2024

Method

Full-resolution HLA and KIR gene annotations for human genome assemblies

Ying Zhou
Li Song
Heng Li

First Published June 5, 2024

Research

Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy

Lujia Chen
Xiangduo Kong
Kevin G. Johnston
Ali Mortazavi
Todd C. Holmes
Zhiqun Tan
Kyoko Yokomori
Xiangmin Xu

First Published May 22, 2024

Research

Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

Milad Razavi-Mohseni
Weitai Huang
Yu A. Guo
Dustin Shigaki
Shamaine Wei Ting Ho
Patrick Tan
Anders J. Skanderup
Michael A. Beer

First Published May 22, 2024

Research

Drosophila melanogaster ovary" > Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

Satyam P. Srivastav
Cédric Feschotte
Andrew G. Clark

First Published May 15, 2024

Resource

A harmonized public resource of deeply sequenced diverse human genomes

Zan Koenig
Mary T. Yohannes
Lethukuthula L. Nkambule
Xuefang Zhao
Julia K. Goodrich
Heesu Ally Kim Michael W. Wilson Grace Tiao Stephanie P. Hao Nareh Sahakian Katherine R. Chao Mark A. Walker Yunfei Lyu Heidi L. Rehm Benjamin M. Neale Michael E. Talkowski Mark J. Daly
... [+12 authors] ...,
Harrison Brand
Konrad J. Karczewski
Elizabeth G. Atkinson
Alicia R. Martin

First Published May 15, 2024

Research

N⁶-adenine methylation in a unicellular eukaryote" > Semiconservative transmission of DNA N⁶-adenine methylation in a unicellular eukaryote

Yalan Sheng
Yuanyuan Wang
Wentao Yang
Xue Qing Wang
Jiuwei Lu
Bo Pan Bei Nan Yongqiang Liu Fei Ye Chun Li
... [+5 authors] ...,
Jikui Song
Yali Dou
Shan Gao
Yifan Liu

First Published May 14, 2024

Perspective

Ribosome decision graphs for the representation of eukaryotic RNA translation complexity

Jack A.S. Tierney
Michał Świrski
Håkon Tjeldnes
Jonathan M. Mudge
Joanna Kufel
Nicola Whiffin
Eivind Valen
Pavel V. Baranov

First Published May 7, 2024

Method

A new framework for exploratory network mediator analysis in omics data

Qingpo Cai
Yinghao Fu
Cheng Lyu
Zihe Wang
Shun Rao
Jessica A. Alvarez
Yun Bai
Jian Kang
Tianwei Yu

First Published May 7, 2024

Research

Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions

Stacey E.P. Joosten
Sebastian Gregoricchio
Suzan Stelloo
Elif Yapıcı
Chia-Chi Flora Huang
Kerim Yavuz Maria Donaldson Collier Tunç Morova Umut Berkay Altintaş Yongsoo Kim Sander Canisius Cathy B. Moelans Paul J. van Diest Gozde Korkmaz
... [+9 authors] ...,
Nathan A. Lack
Michiel Vermeulen
Sabine C. Linn
Wilbert Zwart

First Published May 6, 2024

Research

Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy

Dhanur P. Iyer
Lambert Moyon
Lars Wittler
Chieh-Yu Cheng
Francisca R. Ringeling
Stefan Canzar
Annalisa Marsico
Aydan Bulut-Karslioğlu

First Published May 6, 2024

Research

Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription

Christine R. Keenan
Hannah D. Coughlan
Nadia Iannarella
Andres Tapia del Fierro
Andrew Keniry
Timothy M. Johanson Wing Fuk Chan Alexandra L. Garnham
... [+3 authors] ...,
Lachlan W. Whitehead
Marnie E. Blewitt
Gordon K. Smyth
Rhys S. Allan

First Published May 6, 2024

Review

Navigating the landscape of epitranscriptomics and host immunity

Elaine Huang
Clara Frydman
Xinshu Xiao

First Published May 3, 2024

Research

Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice

Leandros Boukas
Teresa Romeo Luperchio
Afrooz Razi
Kasper D. Hansen
Hans T. Bjornsson

First Published May 3, 2024

Method

Simulation of nanopore sequencing signal data with tunable parameters

Hasindu Gamaarachchi
James M. Ferguson
Hiruna Samarakoon
Kisaru Liyanage
Ira W. Deveson

First Published May 1, 2024

Corrigendum

Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data

Fei Qin
Guoshuai Cai
Christopher I. Amos
Feifei Xiao

First Published April 25, 2024

Method

cis-regulatory elements" > Probabilistic association of differentially expressed genes with cis-regulatory elements

Brian S. Roberts
Ashlyn G. Anderson
E. Christopher Partridge
Gregory M. Cooper
Richard M. Myers

First Published April 17, 2024

Method

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Ryan Lorig-Roach
Melissa Meredith
Jean Monlong
Miten Jain
Hugh E. Olsen
Brandy McNulty David Porubsky Tessa G. Montague Julian K. Lucas Chris Condon Jordan M. Eizenga Sissel Juul Sean K. McKenzie Sara E. Simmonds Jimin Park Mobin Asri Sergey Koren Evan E. Eichler Richard Axel
... [+14 authors] ...,
Bruce Martin
Paolo Carnevali
Karen H. Miga
Benedict Paten

First Published April 16, 2024

Review

A systematic review on the biochemical threshold of mitochondrial genetic variants

Karan K. Smith
Jesse D. Moreira
Callum R. Wilson
June O. Padera
Ashlee N. Lamason
Liying Xue
Deepa M. Gopal
David B. Flynn
Jessica L. Fetterman

First Published April 16, 2024

Research

Oikopleura dioica cryptic species" > Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species

Charles Plessy
Michael J. Mansfield
Aleksandra Bliznina
Aki Masunaga
Charlotte West
Yongkai Tan Andrew W. Liu Jan Grašič María Sara del Río Pisula Gaspar Sánchez-Serna Marc Fabrega-Torrus Alfonso Ferrández-Roldán Vittoria Roncalli Pavla Navratilova Eric M. Thompson
... [+10 authors] ...,
Takeshi Onuma
Hiroki Nishida
Cristian Cañestro
Nicholas M. Luscombe

First Published April 15, 2024

Research

Systematic identification and characterization of exon–intron circRNAs

Yinchun Zhong
Yan Yang
Xiaolin Wang
Bingbing Ren
Xueren Wang
Ge Shan
Liang Chen

First Published April 12, 2024

Research

Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites

João L. Reis-Cunha
Samuel A. Pimenta-Carvalho
Laila V. Almeida
Anderson Coqueiro-dos-Santos
Catarina A. Marques
Jennifer A. Black
... [+1 authors] ...,
Jeziel Damasceno
Richard McCulloch
Daniella C. Bartholomeu
Daniel C. Jeffares

First Published April 11, 2024

Research

Drosophila knock-in tauopathy model" > Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model

Hassan Bukhari
Vanitha Nithianandam
Rachel A. Battaglia
Anthony Cicalo
Souvarish Sarkar
Aram Comjean
... [+1 authors] ...,
Yanhui Hu
Matthew J. Leventhal
Xianjun Dong
Mel B. Feany

First Published April 10, 2024

Research

Eucalyptus is driven by structural rearrangements that promote sequence divergence" > Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence

Scott Ferguson
Ashley Jones
Kevin Murray
Rose Andrew
Benjamin Schwessinger
Justin Borevitz

First Published April 8, 2024

Method

Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples

Shuangxi Ji
Tong Zhu
Ankit Sethia
Wenyi Wang

First Published April 8, 2024

Method

Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches

Muyoung Lee
Qingqing Guo
Mijeong Kim
Joonhyuk Choi
Alia Segura
Alper Genceroglu Lucy LeBlanc Nereida Ramirez Yu Jin Jang
... [+4 authors] ...,
Yeejin Jang
Bum-Kyu Lee
Edward M. Marcotte
Jonghwan Kim

First Published April 5, 2024

Method

Robust chromatin state annotation

Mehdi Foroozandeh Shahraki
Marjan Farahbod
Maxwell W. Libbrecht

First Published March 21, 2024

Resource

Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals" > The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

Christine E. Schnitzler
E. Sally Chang
Justin Waletich
Gonzalo Quiroga-Artigas
Wai Yee Wong
Anh-Dao Nguyen Sofia N. Barreira Liam B. Doonan Paul Gonzalez Sergey Koren James M. Gahan Steven M. Sanders Brian Bradshaw Timothy Q. DuBuc Febrimarsa Danielle de Jong Eric P. Nawrocki Alexandra Larson Samantha Klasfeld Sebastian G. Gornik R. Travis Moreland Tyra G. Wolfsberg Adam M. Phillippy James C. Mullikin Oleg Simakov
... [+20 authors] ...,
Paulyn Cartwright
Matthew Nicotra
Uri Frank
Andreas D. Baxevanis

First Published March 20, 2024

Research

Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation

Blandine C. Mercier
Emmanuel Labaronne
David Cluet
Laura Guiguettaz
Nicolas Fontrodona
Alicia Bicknell Antoine Corbin Mélanie Wencker Fabien Aube Laurent Modolo
... [+5 authors] ...,
Karina Jouravleva
Didier Auboeuf
Melissa J. Moore
Emiliano P. Ricci

First Published March 20, 2024

Research

Inference of selective forces on house mouse genomes during secondary contact in East Asia

Kazumichi Fujiwara
Shunpei Kubo
Toshinori Endo
Toyoyuki Takada
Toshihiko Shiroishi
Hitoshi Suzuki
Naoki Osada

First Published March 20, 2024

Research

Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements" > Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements

Divya Selvaraju
Filip Wierzbicki
Robert Kofler

First Published March 15, 2024

Review

The structure, function, and evolution of plant centromeres

Matthew Naish
Ian R. Henderson

First Published March 14, 2024

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