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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

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

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

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

Haplotype-aware sequence alignment to pangenome graphs

Ghanshyam Chandra
Daniel Gibney
Chirag Jain

First Published July 16, 2024

Method

High-fidelity, large-scale targeted profiling of microsatellites

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

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

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

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 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

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

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

Mini-Review

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

Buckley Reuben M.
Ostrander Elaine A.

First Published July 2, 2024

Research

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

Wang Xuejing
Heckel Gerald

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

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

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

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

Size-based expectation maximization for characterizing nucleosome positions and subtypes

Jianyu Yang
Kuangyu Yen
Shaun Mahony

First Published June 17, 2024

Method

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

Ulrich Jens-Uwe
Renard Bernhard Y.

First Published June 17, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

First Published April 17, 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

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

Research

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

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

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

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

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

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

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

Selvaraju Divya
Wierzbicki Filip
Kofler Robert

First Published March 15, 2024

Review

The structure, function, and evolution of plant centromeres

Matthew Naish
Ian R. Henderson

First Published March 14, 2024

Research

cis-regulatory codes in eukaryotes" > Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes

Ting-Ying Wu
Ya-Ru Li
Kai-Jyun Chang
Jhen-Cheng Fang
Daisuke Urano
Ming-Jung Liu

First Published March 13, 2024

Research

Major impacts of widespread structural variation on sorghum

Zhihai Zhang
Joao Paulo Gomes Viana
Bosen Zhang
Kimberly K.O. Walden
Hans Müller Paul
Stephen P. Moose Geoffrey P. Morris
... [+2 authors] ...,
Chris Daum
Kerrie W. Barry
Nadia Shakoor
Matthew E. Hudson

First Published March 13, 2024

Resource

Haplotype-resolved 3D chromatin architecture of the hybrid pig

Yu Lin
Jing Li
Yiren Gu
Long Jin
Jingyi Bai
Jiaman Zhang Yujie Wang Pengliang Liu Keren Long Mengnan He Diyan Li Can Liu Ziyin Han Yu Zhang Xiaokai Li Bo Zeng Lu Lu Fanli Kong Ying Sun Yongliang Fan Xun Wang Tao Wang An'an Jiang Jideng Ma Linyuan Shen Li Zhu Yanzhi Jiang Guoqing Tang Xiaolan Fan Qingyou Liu Hua Li Jinyong Wang Li Chen
... [+28 authors] ...,
Liangpeng Ge
Xuewei Li
Qianzi Tang
Mingzhou Li

First Published March 13, 2024

Research

RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels

Brigitta Szabo
Therese C. Mandl
Bernhard Woldrich
Gregor Diensthuber
David Martin
Michael F. Jantsch
Konstantin Licht

First Published March 12, 2024

Research

N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus" > Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus

Yongqiang Liu
Junhua Niu
Fei Ye
Therese Solberg
Borong Lu
Chundi Wang
Mariusz Nowacki
Shan Gao

First Published March 12, 2024

Research

Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage

Kamal Ajit
Adele Alagia
Kaspar Burger
Monika Gullerova

First Published March 11, 2024

Resource

Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes

Wenjuan Yu
Haohui Luo
Jinbao Yang
Shengchen Zhang
Heling Jiang
Xianjia Zhao Xingqi Hui Da Sun
... [+3 authors] ...,
Liang Li
Xiu-qing Wei
Stefano Lonardi
Weihua Pan

First Published March 1, 2024

Research

Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma

Huiwen Che
Peiyong Jiang
L.Y. Lois Choy
Suk Hang Cheng
Wenlei Peng
Rebecca W.Y. Chan Jing Liu Qing Zhou W.K. Jacky Lam Stephanie C.Y. Yu So Ling Lau Tak Y. Leung John Wong Vincent Wai-Sun Wong
... [+9 authors] ...,
Grace L.H. Wong
Stephen L. Chan
K.C. Allen Chan
Y.M. Dennis Lo

First Published February 26, 2024

Research

Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments

John T. Chamberlin
Younghee Lee
Gabor T. Marth
Aaron R. Quinlan

First Published February 14, 2024

Research

Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA

Uditi Bhatt
Anne Cucchiarini
Yu Luo
Cameron W. Evans
Jean-Louis Mergny
K. Swaminathan Iyer
Nicole M. Smith

First Published February 14, 2024

Research

CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors" > Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors

James L. Shepherdson
Ryan Z. Friedman
Yiqiao Zheng
Chi Sun
Inez Y. Oh
David M. Granas
Barak A. Cohen
Shiming Chen
Michael A. White

First Published February 14, 2024

Resource

Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle

Alexander S. Leonard
Xena M. Mapel
Hubert Pausch

First Published February 14, 2024

Corrigendum

Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons

Qicheng Ma
Satyam P. Srivastav
Stephanie Gamez
Gargi Dayama
Fabiana Feitosa-Suntheimer
Edward I. Patterson Rebecca M. Johnson Erik M. Matson Alexander S. Gold Douglas E. Brackney John H. Connor Tonya M. Colpitts Grant L. Hughes
... [+8 authors] ...,
Jason L. Rasgon
Tony Nolan
Omar S. Akbari
Nelson C. Lau

First Published February 7, 2024

Perspective

Why community consultation matters in genomic research benefit-sharing models

Sarah LeBaron von Baeyer
Rebecca Crocker
Rindra Rakotoarivony
Jean Freddy Ranaivoarisoa
Germain Jules Spiral
Stephane Castel Andrew Farnum
... [+2 authors] ...,
Holly Vance
Noah Collins
Keolu Fox
Kaja Wasik

First Published January 31, 2024

Research

Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci

Richard D.W. Kelly
Kristy R. Stengel
Aditya Chandru
Lyndsey C. Johnson
Scott W. Hiebert
Shaun M. Cowley

First Published January 30, 2024

Research

Oxidative stress accelerates intestinal tumorigenesis by enhancing 8-oxoguanine-mediated mutagenesis in MUTYH-deficient mice

Mizuki Ohno
Noriko Takano
Kyoko Hidaka
Fumiko Sasaki
Kazumi Yamauchi
Yasunobu Aoki
... [+1 authors] ...,
Takehiko Nohmi
Yusaku Nakabeppu
Yoshimichi Nakatsu
Teruhisa Tsuzuki

First Published January 30, 2024

Method

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 January 30, 2024

Resource

GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis

Robyn L. Ball
Molly A. Bogue
Hongping Liang
Anuj Srivastava
David G. Ashbrook
Anna Lamoureux Matthew W. Gerring Alexander S. Hatoum Matthew J. Kim Hao He Jake Emerson Alexander K. Berger David O. Walton Keith Sheppard Baha El Kassaby Francisco Castellanos Govindarajan Kunde-Ramamoorthy Lu Lu John Bluis Sejal Desai Beth A. Sundberg Gary Peltz Zhuoqing Fang Gary A. Churchill Robert W. Williams
... [+20 authors] ...,
Arpana Agrawal
Carol J. Bult
Vivek M. Philip
Elissa J. Chesler

First Published January 30, 2024

Method

A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data

Yi Qiao
Xiaomeng Huang
Philip J. Moos
Jonathan M. Ahmann
Anthony D. Pomicter
Michael W. Deininger
... [+1 authors] ...,
John C. Byrd
Jennifer A. Woyach
Deborah M. Stephens
Gabor T. Marth

First Published January 9, 2024

Method

Bombyx mori" > High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori

Sanyuan Ma
Tong Zhang
Ruolin Wang
Pan Wang
Yue Liu
Jiasong Chang Aoming Wang Xinhui Lan Le Sun Hao Sun Run Shi Wei Lu Dan Liu Na Zhang Wenbo Hu
... [+10 authors] ...,
Xiaogang Wang
Weiqing Xing
Ling Jia
Qingyou Xia

First Published January 8, 2024

Research

Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement

Audano Peter A.
Beck Christine R.

First Published January 4, 2024

Method

Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication

Zihao Wang
Zhenquan Zhang
Songhao Luo
Tianshou Zhou
Jiajun Zhang

First Published January 3, 2024

Reviewer Index

Reviewer Index, Volume 33, 2023

First Published December 27, 2023

Research

C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis" > Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis

Mariateresa Mazzetto
Lauren E. Gonzalez
Nancy Sanchez
Valerie Reinke

First Published December 26, 2023

Research

Xenopus sperm and male pronuclei" > Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei

Gregor Jessberger
Csilla Várnai
Roman R. Stocsits
Wen Tang
Georg Stary
Jan-Michael Peters

First Published December 21, 2023

Research

De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression

Mark E. Gill
Alexia Rohmer
Serap Erkek-Ozhan
Ching-Yeu Liang
Sunwoo Chun
Evgeniy A. Ozonov
Antoine H.F.M. Peters

First Published December 21, 2023

Research

Revisiting chromatin packaging in mouse sperm

Qiangzong Yin
Chih-Hsiang Yang
Olga S. Strelkova
Jingyi Wu
Yu Sun
Sneha Gopalan Liyan Yang Job Dekker
... [+3 authors] ...,
Thomas G. Fazzio
Xin Zhiguo Li
Johan Gibcus
Oliver J. Rando

First Published December 21, 2023

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