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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

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
Hamandi Khalid
Tommy Stodberg
Ching Ching Ng Danielle Andrade Marte Roa Syvertsen Elena Gardella Alessandro Orsini Choong Yi Fong Jana Zarubova Michaela Kajsov 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

Method

RECOMBINE identifies recurrent composite markers of cell types and states

Xubin Li
Justin Nguyen
Anil Korkut

First Published May 20, 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

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

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

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

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

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

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

Method

Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie

Krzysztof H. Banecki
Haoxi Chai
Yijun Ruan
Dariusz Plewczynski

First Published April 8, 2026

Method

Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer

Junhai Qi
Zhidong Yang
Ting Yu
Guojun Li

First Published April 8, 2026

Method

Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes

Xuyan Liu
Lin Xia
Yixin Qiao
Yang Li
Yan Huang
Bingyan Yue Xi Liang Xin Yang Honghui Zhang
... [+4 authors] ...,
Jiaxun Zhang
Xiao Chen
Dan Xie
Jifeng Liu

First Published April 8, 2026

Method

Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses

Xiuhao Fu
Chao Yang
Chunyan Cui
Aoyun Geng
Yidi Sun
Chao Zha Feifei Cui
... [+2 authors] ...,
Leyi Wei
Quan Zou
Xin Gao
Zilong Zhang

First Published March 26, 2026

Method

High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND

Kehan Lang
Chenyang Jia
Siyu Li
Yi Guo
Dingjun Hu
Shengquan Chen

First Published March 26, 2026

Method

Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End

Lucinda C. Xiao
Ayush Semwal
Brianna St John
Kathleen Zeglinski
Shian Su
James Lancaster Shifeng Xue Bruno Reversade
... [+3 authors] ...,
Matthew E. Ritchie
Frédérique Magdinier
Marnie E. Blewitt
Quentin Gouil

First Published March 23, 2026

Method

k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants" > k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants

Pengju Zhao
Jiayi He
Chen Peng
Yuelang Zhang
Chong Wang
Dongyou Yu
Lingzhao Fang
Zhengguang Wang

First Published March 23, 2026

Method

High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map

Sheila Lutz
Megan Lawler
Samuel Amidon
Frank W. Albert

First Published March 23, 2026

Method

Restoring the potency of a neutralizing antibody via guided hypermutation with hyper-antibody editor HAE1

Yuhong Wang
Yuefeng Guo
Qiuyu Lu
Xinyi Liu
Haoqi Xu
Jiayi Chen Ruiqi Pi Shaopeng Yuan Ziting Yang
... [+4 authors] ...,
Rusen Lu
Fei-Long Meng
Tingting Gan
Jiazhi Hu

First Published March 19, 2026

Method

Parallel analysis of replication timing, gene expression, and copy number with PARTAGE

Lakshana Sruthi Sadu Murari
Quinn Dickinson
Silvia Meyer-Nava
Juan Carlos Rivera-Mulia

First Published March 19, 2026

Method

Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet

Yidi Deng
Jiadong Mao
Jarny Choi
Kim-Anh Lê Cao

First Published March 5, 2026

Method

Minimizing reference bias with an imputed personalized reference

Kavya Vaddadi
Mao-Jan Lin
Sina Majidian
Taher Mun
Ben Langmead

First Published March 5, 2026

Method

Automated interpretable artificial intelligence genomic prediction with AIGP

Lei Wei
Ziqin Jiang
Baoliang Fan
Yidan Yan
Zhenqiang Xu
Xiaoxiang Hu
Yuzhe Wang

First Published March 5, 2026

Method

Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution

Paul Ashford
Alexander M. Frankell
Zofia Piszka
Camilla S.M. Pang
Mahnaz Abbasian
Maise Al Bakir
... [+1 authors] ...,
Mariam Jamal-Hanjani
Nicholas McGranahan
Charles Swanton
Christine A. Orengo

First Published February 19, 2026

Method

Robust and efficient annotation of cell states through gene signature scoring

Laure Ciernik
Agnieszka Kraft
Florian Barkmann
Josephine Yates
Valentina Boeva

First Published February 18, 2026

Method

N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles" > EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles

Shuyu Zhang
Quan Zou
Mengting Niu
Zhibin Lv
Antony Stalin
Ximei Luo

First Published February 17, 2026

Method

Mapping and quantifying nascent transcript start sites using TT-TSS-seq

Eleanor Elgood Hunt
Claudia Vivori
Richard Mitter
Vedis Agnadottir
Folkert J. van Werven

First Published February 17, 2026

Method

Analysis of coding gene expression from small RNA sequencing

Aygun Azadova
Anthonia Ekperuoh
Greg N. Brooke
Antonio Marco

First Published February 10, 2026

Method

spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model

Tianyu Liu
Tinglin Huang
Wengong Jin
Tinyi Chu
Rex Ying
Hongyu Zhao

First Published February 3, 2026

Method

scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment

Zhitao Huang
Ruiqing Zheng
Pengzhen Jia
Xuhua Yan
Jinmiao Chen
Min Li

First Published January 20, 2026

Method

Autoencoders for genomic variation analysis

Margarita Geleta
Daniel Mas Montserrat
Xavier Giro-i-Nieto
Alexander G. Ioannidis

First Published January 20, 2026

Method

cis-regulatory elements" > A scalable computational framework for predicting gene expression from candidate cis-regulatory elements

Qinhu Zhang
Siguo Wang
Zhipeng Li
Wenzheng Bao
Wenjian Liu
De-Shuang Huang

First Published January 16, 2026

Method

Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit

David R. Lougheed
Tomi Pastinen
Guillaume Bourque

First Published January 15, 2026

Method

Quantifying pathological progression from single-cell transcriptomic data with scPSS

Samin Rahman Khan
M Saifur Rahman
M. Sohel Rahman
Md Abul Hassan Samee

First Published January 14, 2026

Method

Strain-level metagenomic profiling using pangenome graphs with PanTax

Wenhai Zhang
Yuansheng Liu
Guangyi Li
Jialu Xu
Enlian Chen
Alexander Schönhuth
Xiao Luo

First Published January 14, 2026

Method

Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation

Sophia N. Lee
Erin C. Banda
Lu Qiao
Sarah L. Thompson
Karan Singh
Ryan A. Hagenson
Teresa Davoli
Stefan F. Pinter
Jason M. Sheltzer

First Published January 12, 2026

Method

Early feature extraction drives model performance in high-resolution chromatin accessibility prediction

Aayush Grover
Till Muser
Liine Kasak
Lin Zhang
Ekaterina Krymova
Valentina Boeva

First Published January 12, 2026

Method

A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis

Ruhollah Shemirani
Gillian M. Belbin
Sinead Cullina
Christa Caggiano
Christopher R. Gignoux
Noah Zaitlen
Eimear E. Kenny

First Published December 23, 2025

Method

Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations

Yuwei Cao
Lauren Patel
Lauren Alcoser
Eric Mendenhall
Christopher Benner
Sven Heinz
Alon Goren

First Published December 12, 2025

Method

The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects

Maureen Pittman
Kihyun Lee
Franco Felix
Yu Huang
Adrienne Lam
Mauro W. Costa
Deepak Srivastava
Katherine S. Pollard

First Published December 12, 2025

Method

6A demethylation in mRNAs" > A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs

Panagiotis G. Adamopoulos
Konstantina Athanasopoulou
Andreas Scorilas

First Published December 11, 2025

Method

Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates

Marian F. Laughery
Bastian Stark
Benjamin Morledge-Hampton
Steven A. Roberts
John J. Wyrick

First Published December 9, 2025

Method

ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage

Xiran Liu
Lorin Crawford
Sohini Ramachandran

First Published November 19, 2025

Method

Integration of high-throughput proteomic data and complementary omics layers with PriOmics

Robin Kosch
Katharina Limm
Annette M. Staiger
Nadine S. Kurz
Nicole Seifert
Bence Oláh Stefan Solbrig Viola Poeschel Gerhard Held Marita Ziepert Norbert Schmitz Emil Chteinberg Reiner Siebert Rainer Spang
... [+9 authors] ...,
Helena U. Zacharias
German Ott
Peter J. Oefner
Michael Altenbuchinger

First Published November 18, 2025

Method

Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms

Hongyu Zheng
Hirak Sarkar
Benjamin J. Raphael

First Published November 17, 2025

Method

OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities

Siavash Raeisi Dehkordi
Zhaoyang Jia
Joey Estabrook
Jen Hauenstein
Neil Miller
Naz Güleray-Lafci Jürgen Neesen Alex Hastie
... [+3 authors] ...,
Alka Chaubey
Andy Wing Chun Pang
Paul Dremsek
Vineet Bafna

First Published November 14, 2025

Method

Graph-based deep reinforcement learning for haplotype assembly with Ralphi

Enzo Battistella
Anant Maheshwari
Barış Ekim
Bonnie Berger
Victoria Popic

First Published November 14, 2025

Method

Unified integration of spatial transcriptomics across platforms with LLOKI

Ellie Haber
Ajinkya Deshpande
Jian Ma
Spencer Krieger

First Published November 13, 2025

Method

Secure phasing of private genomes in a trusted execution environment with TX-Phase

Natnatee Dokmai
Kaiyuan Zhu
S. Cenk Sahinalp
Hyunghoon Cho

First Published November 12, 2025

Method

Statistically rigorous and computationally efficient chromatin stripe detection with Quagga

Fan Feng
Sean Moran
Anders S. Hansen
Xiaotian Zhang
Jie Liu

First Published November 12, 2025

Method

Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover

An Wang
Stephanie Hicks
Donald Geman
Laurent Younes

First Published November 12, 2025

Method

Partitioned multi-MUM finding for scalable pangenomics with MumemtoM

Vikram S. Shivakumar
Ben Langmead

First Published November 7, 2025

Method

Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize

Shuai Wang
Merritt Khaipho-Burch
Lynn C. Johnson
Zachary R. Miller
Peter J. Bradbury
Doug Speed William J. Allen M. Cinta Romay
... [+3 authors] ...,
Jiquan Xue
Edward S. Buckler
Guillaume P. Ramstein
Baoxing Song

First Published October 31, 2025

Method

Real-time analysis and visualization of nanopore metagenomic samples with MARTi

Ned Peel
Samuel Martin
Darren Heavens
Douglas W. Yu
Matthew D. Clark
Richard M. Leggett

First Published October 27, 2025

Method

BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations

Antonio Nappi
Liubov Shilova
Theofanis Karaletsos
Na Cai
Francesco Paolo Casale

First Published October 24, 2025

Method

Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method

Quanyou Cai
Lihui Lin
Xin Liu
Jiekai Chen

First Published October 22, 2025

Method

Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates

Haiyue Liu
Lea H. Gregersen

First Published October 22, 2025

Method

Iterative improvement of deep learning models using synthetic regulatory genomics

André M. Ribeiro-dos-Santos
Matthew T. Maurano

First Published October 22, 2025

Method

Interpretable phenotype decoding from multicondition sequencing data with ALPINE

Wei-Hao Lee
Lechuan Li
Ruth Dannenfelser
Vicky Yao

First Published October 22, 2025

Method

PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing

Gianluca Mattei
Marta Baragli
Barbara Gega
Alessandra Mingrino
Martina Chieca
Tommaso Ducci Gianmaria Frigè Luca Mazzarella Romina D'Aurizio
... [+4 authors] ...,
Francesco De Logu
Romina Nassini
Pier Giuseppe Pelicci
Alberto Magi

First Published October 20, 2025

Method

c-separated cell types with SepSolve" > Optimal marker genes for c-separated cell types with SepSolve

Bartol Borozan
Tomislav Prusina
Luka Borozan
Domagoj Ševerdija
Francisca Rojas Ringeling
Domagoj Matijević
Stefan Canzar

First Published October 9, 2025

Method

Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN

Wenhao Zhang
Lan Cao
Xiaoxuan Gu
Yongyu Long
Ying Wang

First Published October 9, 2025

Method

Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS

Qunlun Shen
Shuqin Zhang
Shihua Zhang

First Published October 1, 2025

Method

Long-read reconstruction of many diverse haplotypes with devider

Jim Shaw
Christina Boucher
Yun William Yu
Noelle Noyes
Heng Li

First Published September 23, 2025

Method

Deep structural clustering reveals hidden systematic biases in RNA sequencing data

Qiang Su
Yi Long
Deming Gou
Junmin Quan
Xiaoming Zhou
Qizhou Lian

First Published September 19, 2025

Method

Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes

Philipp Rentzsch
Aaron Kollotzek
Kaushik Ram Ganapathy
Pejman Mohammadi
Tuuli Lappalainen

First Published September 17, 2025

Method

ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search

Haotian Zhang
Yiming Zhang
Teng Gao
Yufeng Wu

First Published September 3, 2025

Method

Robust 16S rRNA classification based on a compressed LCA index

Omar Ahmed
Christina Boucher
Ben Langmead

First Published August 25, 2025

Method

Estimating the size of long tandem repeat expansions from short reads with ScatTR

Rashid Al-Abri
Gamze Gürsoy

First Published August 21, 2025

Method

Tree-based differential testing using inferential uncertainty for RNA-seq

Noor Pratap Singh
Euphy Y. Wu
Jason Fan
Michael I. Love
Rob Patro

First Published August 21, 2025

Method

Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP

Lin Li
Xianbin Su
Ze-Guang Han

First Published August 21, 2025

Method

Pangenome-based genome inference using integer programming

Ghanshyam Chandra
Md Helal Hossen
Stephan Scholz
Alexander T. Dilthey
Daniel Gibney
Chirag Jain

First Published August 21, 2025

Method

Accurate detection of tandem repeats from error-prone sequences with EquiRep

Zhezheng Song
Tasfia Zahin
Xiang Li
Mingfu Shao

First Published August 21, 2025

Method

Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus

Mari B. Gornitzka
Egil Røsjø
Uddalok Jana
Easton E. Ford
Alan Tourancheau
William D. Lees
... [+1 authors] ...,
Zachary Vanwinkle
Melissa L. Smith
Corey T. Watson
Andreas Lossius

First Published August 21, 2025

Method

Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA

Han Shu
Jing Chen
Chang Xu
Jialu Hu
Yongtian Wang
Jiajie Peng
Qinghua Jiang
Xuequn Shang
Tao Wang

First Published August 14, 2025

Method

Multicondition and multimodal temporal profile inference during mouse embryonic development

Ran Zhang
Chengxiang Qiu
Galina N. Filippova
Gang Li
Jay Shendure
Jean-Philippe Vert
Xinxian Deng
William Stafford Noble
Christine M. Disteche

First Published August 14, 2025

Method

Unveiling the functional fate of duplicated genes through expression profiling and structural analysis

Alex Warwick Vesztrocy
Natasha Glover
Paul D. Thomas
Christophe Dessimoz
Irene Julca

First Published August 14, 2025

Method

FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data

Can Luo
Zimeng Jamie Zhou
Yichen Henry Liu
Xin Maizie Zhou

First Published August 13, 2025

Method

ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies

Jordan H. Little
Guillermo Hoffmann Meyer
Aakash Grover
Alex Michael Francette
Raghavendran Partha
Karen M. Arndt
Martin Smith
Nathan Clark
Maria Chikina

First Published August 7, 2025

Method

BRCA1 and BRCA2 splice isoforms" > The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms

Daffodil M. Canson
Michael T. Parsons
Gemma Moir-Meyer
Troy Dumenil
Gemma Montalban
Erica Lin Terri P. McVeigh Aimee L. Davidson
... [+3 authors] ...,
Shaun M. Bouckaert
Matt Trau
Darren Korbie
Amanda B. Spurdle

First Published August 6, 2025

Method

Genotyping of selected germline adaptive immune system loci using short-read sequencing data

Michael K.B. Ford
Ananth Hari
Meredith Yeager
Lisa Mirabello
Stephen Chanock
Ibrahim Numanagić
S. Cenk Sahinalp

First Published August 5, 2025

Method

3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors

Jacob Stewart-Ornstein
Matthew J. Irby
Marina K. Lilieholm
Dylan Laprise
Maria D. Collier
Thomas Aunins
... [+1 authors] ...,
Dewi Harjanto
Aaron N. Chang
Deepak Reyon
Jeremy S. Duffield

First Published August 5, 2025

Method

High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow

Xue Dong
Mengzhu Hu
Xiaonan Cui
Wenjian Zhou
Jingtao Cai
Guangyao Mao
Weiyang Shi

First Published August 5, 2025

Method

Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks

Prashanthi Ravichandran
Princy Parsana
Rebecca Keener
Kasper D. Hansen
Alexis Battle

First Published July 17, 2025

Method

A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry

Meilin Zhang
Heng Du
Yu Zhang
Yue Zhuo
Zhen Liu
Yahui Xue
... [+1 authors] ...,
Lei Zhou
Sixuan Zhou
Wanying Li
Jian-Feng Liu

First Published July 15, 2025

Method

Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes

Rachel M. Petersen
Christopher M. Vockley
Amanda J. Lea

First Published July 14, 2025

Method

A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis

Daijun Zhang
Ren Qi
Xun Lan
Bin Liu

First Published July 14, 2025

Method

Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq

Yike Xie
Abbas Habibalahi
Ayad G. Anwer
Kanu Wahi
Jacqueline Bailey
Francis Lin Catherine Gatt Emma M.V. Johansson
... [+3 authors] ...,
Tatyana Chtanova
Jeff Holst
Ewa Goldys
Fabio Zanini

First Published July 8, 2025

Method

Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated

Sindri Emmanúel Antonsson
Páll Melsted

First Published July 7, 2025

Method

QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data

Xiaoyu Song
Yuqing Shang
Michelle E. Ehrlich
Panos Roussos
Guo-Cheng Yuan
Pei Wang

First Published June 23, 2025

Method

r-index-based pangenome indexing" > Accurate short-read alignment through r-index-based pangenome indexing

Rahul Varki
Massimiliano Rossi
Eddie Ferro
Marco Oliva
Erik Garrison
Ben Langmead
Christina Boucher

First Published June 12, 2025

Method

Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain

Jenna Kalleberg
Jacob Rissman
Robert D. Schnabel

First Published June 2, 2025

Method

Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs

Ziyan Rao
Min Zhang
Shaodong Huang
Chenyang Wu
Yuheng Zhou
Weijie Zhang
Xia Lin
Dongyu Zhao

First Published May 27, 2025

Method

Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies

Jianing Yao
Jinglun Yu
Brian Caffo
Stephanie C. Page
Keri Martinowich
Stephanie C. Hicks

First Published May 20, 2025

Method

Highly accurate assembly polishing with DeepPolisher

Mira Mastoras
Mobin Asri
Lucas Brambrink
Prajna Hebbar
Alexey Kolesnikov
Daniel E. Cook Maria Nattestad Julian Lucas Taylor S. Won Pi-Chuan Chang Andrew Carroll Benedict Paten Kishwar Shafin Ahmad Abou Tayoun Derek Albracht Jamie Allen Alawi A. Alsheikh-Ali Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Edward A. Belter Halle D. Bender Andrew P. Blair Silvia Buonaiuto Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong 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 Garza Mohammadmersad Ghorbani Tina Graves-Lindsay Richard E. Green Cristian Groza Andrea Guarracino Melissa Gymrek Leanne Haggerty Ira M. Hall Nancy F. Hansen Mohammad Amiruddin Hashmi Maximilian Haeussler David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Juan Jiang Jonathan LoTempio Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Ben Langmead Xiaoyu Zhuo Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Juan F. Macias-Velasco Maximillian G. Marin Franco L. Marsico Kateryna D. Makova Christopher Markovic Tobias Marschall 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 Chie Owa Sadye Paez Benedict Paten Hiram Clawson Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Farnaz Salehi Samuel Sacco 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 Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani 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
... [+196 authors] ...,
Wenjin Zhang
Ying Zhou
Ivo Violich
Giulia Zunino

First Published May 19, 2025

Method

Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

Dmitry Antipov
Mikko Rautiainen
Sergey Nurk
Brian P. Walenz
Steven J. Solar
Adam M. Phillippy
Sergey Koren

First Published May 19, 2025

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