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Research

Resf1 is required for proper placental development and configuration of trophoblast cell–specific heterochromatin" > Resf1 is required for proper placental development and configuration of trophoblast cell–specific heterochromatin

  • Kei Fukuda
  • Kimiko Inoue
  • Chikako Shimura
  • Moe Kitazawa
  • Michiko Hirose
  • Takashi Ishiuchi
  • Shogo Matoba
  • Atsuo Ogura
  • Yoichi Shinkai
  • First Published June 29, 2026
Method

A unified analysis of cell-type- and trajectory-associated pathways in single-cell data using Phoenix

  • Yudit Halperin
  • Daphna Nachmani
  • Michal Rabani
  • First Published June 29, 2026
Research

Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture

  • Kate Liddiard
  • Emmon Coral
  • Harsh Bhatt
  • Kez Cleal
  • Duncan M. Baird
  • First Published June 29, 2026
Method

Locations of consecutive G•C base pairs direct genomic nucleosome positioning

  • Hiroaki Kato
  • Tomohiro Fuse
  • Shoko Sato
  • Yohei Kurihara
  • Wataru Kagawa
  • Takeshi Urano
  • Yasuyuki Ohkawa
  • Hitoshi Kurumizaka
  • Mitsuhiro Shimizu
  • First Published June 25, 2026
Method

Spatially informed reference-free cell-type deconvolution for spatial transcriptomics with SpatialCD

  • Phuong Vo
  • Yuehua Cui
  • First Published June 22, 2026
Research

Spatially resolved profiling of steroid nuclear receptors reveals a role for the disordered N-terminal domains in genome targeting and AP-1 interaction

  • Inbal Zigdon
  • Achinoam Shoham
  • Vladimir Mindel
  • Wajd Manadre
  • David Jan
  • Beniamin Krupkin
  • Dekel Yahav Har-Shai
  • Yaron Antebi
  • Naama Barkai
  • First Published June 22, 2026
Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

  • Thomas R. Gingeras
  • First Published June 17, 2026
Method

Flexible and scalable inference of spatially varying correlation in spatial transcriptomics with spCorr

  • Chenxin Flora Jiang
  • Yuxin Yin
  • Paul Robson
  • Yuanhao James Li
  • Jingyi Jessica Li
  • Dongyuan Song
  • First Published June 17, 2026
Resource

Tracing genome size dynamics in sharks and rays with inclusive sequence analysis by the Squalomix Consortium

  • Shigehiro Kuraku
  • Yawako W. Kawaguchi
  • Taiki Niwa
  • Ryo Misawa
  • Yohey Ogawa
  • Mitsutaka Kadota Kazuhiro Saito Waichiro Godo Tatsuya Sakamoto
  • ... [+4 authors] ...,
  • Wataru Takagi
  • Sachiko Isobe
  • Kenta Shirasawa
  • Akane Kawaguchi
  • First Published June 16, 2026
Research

Covariation of genetic and epigenetic divergence in barn swallows

  • Sarah A. Mueller
  • Uthara Srinivasan
  • Zachary M. Laubach
  • Drew R. Schield
  • Jan A.C. von Rönn
  • Rebecca J. Safran
  • Jochen B.W. Wolf
  • First Published June 16, 2026
Method

MAPLE enables ultrasensitive detection of low-frequency cfDNA methylation haplotypes using short capture probes with cost-efficient performance

  • Nina G. Xie
  • Yangjunyi Li
  • Xiaowen He
  • Liyuan Zhao
  • Ying Mei
  • Jingjing Hou Xiaosheng He Shuang Guo Lingjian Yang Xiurui Zhu Congchong Wei Zhihui Xu Yalong Zhang
  • ... [+8 authors] ...,
  • Min Li
  • Yonghui Li
  • Xueguang Sun
  • Ping Lan
  • First Published June 16, 2026
Research

cis-regulatory elements on expression divergence in human segmental duplications" > Influence of cis-regulatory elements on expression divergence in human segmental duplications

  • Colin J. Shew
  • Gulhan Kaya
  • Sean P. McGinty
  • Megan Y. Dennis
  • First Published June 16, 2026
Research

Cyanophora paradoxa reveals unique repair signature" > Elevated DNA insertion rate in Cyanophora paradoxa reveals unique repair signature

  • Marc Krasovec
  • Anna Lipzen
  • Nigel Grimsley
  • Gilles Mirambeau
  • Kerrie Barry
  • Igor V. Grigoriev
  • Gwenael Piganeau
  • First Published June 12, 2026
Method

A comparison of ancient DNA yields across ossicles and the petrous bone reveals the best preservation in the stapes and incus

  • Ekin Sağlıcan
  • Arda Sevkar
  • Duygu Deniz Kazancı
  • Gonzalo Oteo-García
  • Sevgi Yorulmaz
  • Kıvılcım Başak Vural Gökhan Çakan Gökçen Adiloğlu Duru Buldak Güneş Duru Aliye Öztan Brenna Hassett Nurcan Kayacan Aslı Erim Özdoğan Anders Götherström
  • ... [+10 authors] ...,
  • Füsun Özer
  • Ömür Dilek Erdal
  • Yılmaz Selim Erdal
  • Mehmet Somel
  • First Published June 11, 2026
Research

Evolution of an adaptive, inducible defensive trait in a model crustacean

  • Zhixiong Deng
  • Sen Xu
  • Dengqing Li
  • Guo Yu
  • Swatantra Neupane
  • Li Wang
  • ... [+1 authors] ...,
  • David Blair
  • Wei Hu
  • Adam Petrusek
  • Mingbo Yin
  • First Published June 5, 2026
Method

Reference-informed spatial domain detection using weak supervision for spatial transcriptomics

  • Xin Ma
  • Weijia Jin
  • Qing Lu
  • Ramon C. Sun
  • Li Chen
  • First Published June 3, 2026
Method

Transfer learning enhances clinical utility of polygenic scores with small, phenotypically refined cohorts

  • YuChung Lin
  • Christoph Patrick Beier
  • Zuzana Sobiskova
  • Khalid Hamandi
  • Tommy Stödberg
  • Ching Ching Ng Danielle M. Andrade Marte Roa Syvertsen Elena Gardella Alessandro Orsini Choong Yi Fong Jana Zarubova Michaela Kajsová Kheng Seang Lim Kaja Kristine Selmer Emanuele Cerulli Irelli
  • ... [+11 authors] ...,
  • Guido Rubboli
  • Pasquale Striano
  • Deb K. Pal
  • Lisa J. Strug
  • First Published June 2, 2026
Method

Augmenting transcriptome annotations through the lens of splicing evolution

  • Xiaofei Carl Zang
  • Ke Chen
  • Irtesam Mahmud Khan
  • Mingfu Shao
  • First Published May 29, 2026
Research

Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and introgression

  • George Chung
  • Lewis Stevens
  • Xiaoguang Dai
  • Scott Hickey
  • Karin Kiontke
  • Priyesh Rughani Manuela R. Kieninger Joanna C. Collins Sissel Juul
  • ... [+4 authors] ...,
  • Fabio Piano
  • David H.A. Fitch
  • Mark Blaxter
  • Kristin C. Gunsalus
  • First Published May 29, 2026
Research

Transposable element small RNAs and large RNAs in aging brains and implications in Huntington's and Parkinson's disease

  • Gargi Dayama
  • Jou-Hsuan Roxie Lee
  • Shruti Gupta
  • Christian Brion
  • Brianne K. Connizzo
  • Adam T. Labadorf
  • Richard H. Myers
  • Nelson C. Lau
  • First Published May 28, 2026
Resource

A comprehensive single-cell atlas of monoallelic expression across various tissues in zebrafish

  • Hui Zeng
  • Zhan Liu
  • Huimin Xiang
  • Boliang Liu
  • Di Zhang
  • Xionglei He
  • Shanjun Deng
  • Li Liu
  • First Published May 28, 2026
Research

Whole-genome variant detection in long-read sequencing data from ultralow input patient samples

  • Katherine Wang
  • Cera J. Aex
  • Hayan Lee
  • Lucas Finot
  • Kevin Zhu
  • Julianna R. Chang Aaron M. Horning William J. Rowell
  • ... [+3 authors] ...,
  • Philip Li
  • Sarah B. Kingan
  • Michael P. Snyder
  • Graham S. Erwin
  • First Published May 28, 2026
Method

RECOMBINE identifies recurrent composite markers of cell types and states

  • Xubin Li
  • Justin Nguyen
  • Anil Korkut
  • First Published May 20, 2026
Research

Interplay between purging and admixture shapes genetic load in an invasive guppy population

  • Katarzyna Burda
  • Mary J. Janecka
  • Ryan S. Mohammed
  • David R. Clark
  • Rachael Kramp
  • Jessica F. Stephenson
  • Jacek Radwan
  • Mateusz Konczal
  • First Published May 20, 2026
Research

Herbaria provide a valuable resource for obtaining informative mRNA

  • Alexa S. Tyszka
  • Khong-Sam Chia
  • Eric C. Bretz
  • Linda Mansour
  • Drew A. Larson
  • Nathanael Walker-Hale
  • Philip Carella
  • Joseph F. Walker
  • First Published May 19, 2026
Method

Deep learning the TF regulatory code for gene expression

  • Yuanyuan Li
  • Xiaohui Huang
  • Yixuan Qi
  • Zheng Zhang
  • Hui Ding
  • Quan Zou
  • Li Liu
  • First Published May 15, 2026
Review

Building genomic data structures from compressed representations using prefix-free parsing

  • Rahul Varki
  • Christina Boucher
  • First Published May 15, 2026
Method

Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics

  • John Vollmers
  • Maximiano Correa Cassal
  • Anne-Kristin Kaster
  • First Published May 15, 2026
Research

N-ethyl-N-nitrosourea" > Evidence for negative selection against somatic mutations induced in normal fibroblasts by N-ethyl-N-nitrosourea

  • Cutler Ronald
  • Heid Johanna
  • Sun Shixiang
  • Lee Moonsook
  • Maslov Alex
  • Zhang Lei
  • Sidoli Simone
  • Dong Xiao
  • Vijg Jan
  • First Published May 15, 2026
Research

Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources

  • Xiaoyu Zhuo
  • Chad Tomlinson
  • Edward A. Belter
  • Prashant Kumar Kuntala
  • Wesley N. Saintilnord
  • Juan Jiang Tina Lindsay Juan F. Macias-Velasco Robert S. Fulton Ting Wang Derek Albracht Ivan A. Alexandrov Jamie Allen Alawi A. Alsheikh-Ali Nicolas Altemose Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Floris P. Barthel Edward A. Belter Halle D. Bender Andrew P. Blair Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Silvia Buonaiuto Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Mark J.P. Chaisson Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Hiram Clawson Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Danilo Dubocanin Richard Durbin Jana Ebler Evan E. Eichler Jordan M. Eizenga Parsa Eskandar Eddie Ferro Anna-Sophie Fiston-Lavier Sarah M. Ford Willard W. Ford Giulio Formenti Adam Frankish Mallory A. Freeberg Qichen Fu Stephanie M. Fullerton Robert S. Fulton Yan Gao Gage H. Garcia Obed A. Garcia Joshua M.V. Gardner Shilpa Garg Erik Garrison Nanibaa’ A. Garrison John E. Garza Margarita Geleta Mohammadmersad Ghorbani Tina A. Graves-Lindsay Richard E. Green Cristian Groza Bida Gu Andrea Guarracino Melissa Gymrek Maximilian Haeussler Leanne Haggerty Ira M. Hall Nancy F. Hansen Yue Hao Mohammad Amiruddin Hashmi David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Alexander G. Ioannidis Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Maryam Jehangir Juan Jiang Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Charles H. Langley Ben Langmead Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Jonathan LoTempio Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Walfred Ma Juan F. Macias-Velasco Kateryna D. Makova Maximillian G. Marin Christopher Markovic Tobias Marschall Franco L. Marsico Fergal J. Martin Mira Mastoras Capucine Mayoud Brandy McNulty Jack A. Medico Julian M. Menendez Karen H. Miga Anna Minkina Matthew W. Mitchell Saswat K. Mohanty Younes Mokrab Jean Monlong Shabir Moosa Avelina Moreno-Ochando Shinichi Morishita Jonathan M. Mudge Katherine M. Munson Njagi Mwaniki Nasna Nassir Chiara Natali Shloka Negi Lingbin Ni Adam M. Novak Pilar N. Ossorio Chie Owa Sadye Paez Benedict Paten Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan T. Rhyker Ranallo-Benavidez Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Fedor Ryabov Samuel Sacco Farnaz Salehi Michael C. Schatz Laura B. Scheinfeldt Aarushi Sehgal William E. Seligmann Mahsa Shabani Kishwar Shafin Shadi Shahatit Ruhollah Shemirani Vikram S. Shivakumar Swati Sinha Jouni Sirén Linnéa Smeds Steven J. Solar Marco Sollitto Nicole Soranzo Andrew B. Stergachis Marie-Marthe Suner Yoshihiko Suzuki Arda Söylev Ahmad Abou Tayoun Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Ivo Violich Mitchell R. Vollger Brian P. Walenz Charles Wang Lisa E. Wang Ting Wang Aaron M. Wenger Conor V. Whelan Zilan Xin Zheng Xu Kai Ye DongAhn Yoo
  • ... [+208 authors] ...,
  • Wenjin Zhang
  • Ying Zhou
  • Xiaoyu Zhuo
  • Giulia Zunino
  • First Published May 14, 2026
Research

DNA conformational flexibility descriptors improve transcription factor binding prediction across diverse transcription factor families

  • Upalabdha Dey
  • Venkata Rajesh Yella
  • Aditya Kumar
  • First Published May 14, 2026
Method

Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining

  • Kevin An
  • Sebastian Prillo
  • Wilson Wu
  • Ivan Kristanto
  • Matthew G. Jones
  • Yun S. Song
  • Nir Yosef
  • First Published May 14, 2026
Research

Allele-specific splicing modulates protein isoforms and Alzheimer's disease risk

  • Alison J. King
  • Kofi Amoah
  • Laixing Zhang
  • Jae Hoon Bahn
  • Ryan M. Barney
  • Giovanni Quinones-Valdez
  • Xinshu Xiao
  • First Published May 14, 2026
Research

Single-cell transcriptomics reveals rapid divergence of genes guiding meiosis and spermiogenesis in two passerine birds

  • J. Carolina Segami
  • Marie Sémon
  • Catarina Cunha
  • Claudia Bergin
  • Carina F. Mugal
  • Anna Qvarnström
  • First Published May 14, 2026
Research

Drosophila" > Structural variants are enriched in deleterious visible phenotypes in Drosophila

  • Alejandra Samano
  • Matthew Musat
  • Mihir Junaghare
  • Asad Ahmad
  • Mehlum Ali
  • Sebastian Alves Sreeram Pasupuleti Jelisha Perera Omar Saada
  • ... [+4 authors] ...,
  • Brady Sabido
  • Trevor Smith
  • Sophie Walz
  • Mahul Chakraborty
  • First Published May 14, 2026
Method

Accurate delineation of cellular niches via integrated spatial transcriptomics and histological imaging with SYMOL

  • Daoyuan Wang
  • Fengyi Zhou
  • Wenlan Chen
  • Cheng Liang
  • Fei Guo
  • First Published May 14, 2026
Research

6A reprogramming unveils vitamin-driven post-transcriptional regulation in mice" > Tissue-specific mRNA m6A reprogramming unveils vitamin-driven post-transcriptional regulation in mice

  • Jia Li
  • Anrui Liu
  • Runzhou Liu
  • Zihe Xu
  • Meng Yang
  • Xiaoqi Zheng Ye Tian Shengjun Wen Kaixin Cao
  • ... [+4 authors] ...,
  • Daoqiang Lu
  • Chen Huang
  • Tong-Meng Yan
  • Xiaoyun Wang
  • First Published May 11, 2026
Research

Single-cell template strand sequencing reveals culture-induced chromosomal instability in a gibbon cell line

  • Alessia Daponte
  • Gerardina Chirico
  • Annalisa Paparella
  • Annalaura Montanari
  • Caterina Manzari
  • Martina Macino Oliver Dionisi Dyck Francesco De Leonardis Flavia Angela Maria Maggiolini Alberto L'Abbate Francesco Montinaro Sandra Louzada
  • ... [+7 authors] ...,
  • Mario Ventura
  • Ashley D. Sanders
  • Francesca Antonacci
  • Claudia Rita Catacchio
  • First Published May 4, 2026
Research

Dynamic body size evolution during speciation of predatory cichlid fishes in the Lake Malawi superradiation

  • Liandong Yang
  • Holly Scott
  • Benjamin P. Ngatunga
  • Asilatu H. Shechonge
  • George F. Turner
  • Martin J. Genner
  • First Published May 4, 2026
Review

Hash functions in nucleotide sequence analysis

  • Ke Chen
  • Xiang Li
  • Qian Shi
  • Mingfu Shao
  • Paul Medvedev
  • First Published May 4, 2026
Research

R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation

  • Chun-Hao Chao
  • Thomas G. Fazzio
  • First Published May 4, 2026
Method

Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution

  • Yolanda Andres-Lopez
  • Alice Santambrogio
  • Ioannis Kafetzopoulos
  • Christopher D. Todd
  • Carla El Khouri-Gonzalez
  • J-Elliot Gonzalez-Alvarez
  • ... [+1 authors] ...,
  • Celia Alda-Catalinas
  • Stephen J. Clark
  • Wolf Reik
  • Irene Hernando-Herraez
  • First Published May 1, 2026
Method

Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity

  • Xinxin Wang
  • Ryan Christ
  • Erica Young
  • Chul Joo Kang
  • Indraniel Das
  • Edward A. Belter Markku Laakso
  • ... [+2 authors] ...,
  • Louis J.M. Aslett
  • David Steinsaltz
  • Nathan O. Stitziel
  • Ira M. Hall
  • First Published April 16, 2026
Method

Balancing Gene Ontology annotation specificity in protein function prediction based on the protein sequence large graph

  • Jiangyi Shao
  • Shutao Chen
  • Ziwen Wang
  • Zixu Chen
  • Bin Liu
  • First Published April 15, 2026
Research

Age-dependent mutational loads in human tRNA genes are tumor-specific and result in chimeric tRNA sequences that could disrupt the genetic code

  • Marina Murillo
  • Marina Salvadores
  • Aina Vaquer Picó
  • Lina Tsapanou
  • Adrian Gabriel Torres
  • Fran Supek
  • Lluis Ribas de Pouplana
  • First Published April 15, 2026
Method

Highly efficient and scarless genome editing via essential-gene-coupled homology-directed repair

  • Joo Hye Yeo
  • Hyongbum Henry Kim
  • Sang Ho Oh
  • Jinu Lee
  • First Published April 15, 2026
Research

Drosophila innate immune response" > A genome-wide survey reveals that a diverse array of enhancers coordinates the Drosophila innate immune response

  • Lianne B. Cohen
  • Tamara Hadzic
  • Caitlin Sauer
  • Julia R. Gibbs
  • Zeba Wunderlich
  • First Published April 15, 2026
Research

Epigenetic characterization of pseudogenes across human tissues

  • Yunzhe Jiang
  • Beatrice Borsari
  • Mark Gerstein
  • First Published April 15, 2026
Method

Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation

  • Richa Rashmi
  • Abhinaya Muruganandham
  • Pranita Borkar
  • Sumana Mallick
  • Taylor Hubbs
  • Ari Aviles
  • Daniel Chung
  • Irtisha Singh
  • First Published April 13, 2026
Resource

Lignature provides a curated resource of ligand-induced transcriptomic signatures for signaling inference

  • Ying Xin
  • Md Amanullah
  • Cheng Qian
  • Chingmo Zhou
  • Jiang Qian
  • First Published April 8, 2026
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