Works in Genome Biology, 2024, Vol 25, Issue 1

Results: 301

Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03465-7

By:

Wang, Dingyue;
Xiao, Suxin;
Shu, Jiayue;
Luo, Lingxiao;
Yang, Minqi;
Calonje, Myriam;
He, Hang;
Song, Baoxing;
Zhou, Yue

Publication type:

Article

Molecular dependencies and genomic consequences of a global DNA damage tolerance defect.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03451-z

By:

de Groot, Daniel;
Spanjaard, Aldo;
Shah, Ronak;
Kreft, Maaike;
Morris, Ben;
Lieftink, Cor;
Catsman, Joyce J. I.;
Ormel, Shirley;
Ayidah, Matilda;
Pilzecker, Bas;
Buoninfante, Olimpia Alessandra;
van den Berk, Paul C. M.;
Beijersbergen, Roderick L.;
Jacobs, Heinz

Publication type:

Article

Chromatin-based memory as a self-stabilizing influence on cell identity.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03461-x

By:

Bell, Charles C.;
Faulkner, Geoffrey J.;
Gilan, Omer

Publication type:

Article

Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03458-6

By:

Chen, Xiaoyang;
Li, Keyi;
Wu, Xiaoqing;
Li, Zhen;
Jiang, Qun;
Cui, Xuejian;
Gao, Zijing;
Wu, Yanhong;
Jiang, Rui

Publication type:

Article

vmrseq: probabilistic modeling of single-cell methylation heterogeneity.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03457-7

By:

Shen, Ning;
Korthauer, Keegan

Publication type:

Article

Multi-omics approaches reveal that diffuse midline gliomas present altered DNA replication and are susceptible to replication stress therapy.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03460-y

By:

Hains, Anastasia E.;
Chetal, Kashish;
Nakatani, Tsunetoshi;
Marques, Joana G.;
Ettinger, Andreas;
Junior, Carlos A. O. Biagi;
Gonzalez-Sandoval, Adriana;
Pillai, Renjitha;
Filbin, Mariella G.;
Torres-Padilla, Maria-Elena;
Sadreyev, Ruslan I.;
Van Rechem, Capucine

Publication type:

Article

GenomeDelta: detecting recent transposable element invasions without repeat library.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03459-5

By:

Pianezza, Riccardo;
Haider, Anna;
Kofler, Robert

Publication type:

Article

Cas12f1 gene drives propagate efficiently in herpesviruses and induce minimal resistance.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03455-9

By:

Lin, Zhuangjie;
Yao, Qiaorui;
Lai, Keyuan;
Jiao, Kehua;
Zeng, Xianying;
Lei, Guanxiong;
Zhang, Tongwen;
Dai, Hongsheng

Publication type:

Article

Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03454-w

By:

Jiao, Wu;
Wang, Mangmang;
Guan, Yijian;
Guo, Wei;
Zhang, Chang;
Wei, Yuanchun;
Zhao, Zhenwei;
Ma, Hongyu;
Wang, Longfei;
Jiang, Xinyu;
Ye, Wenxue;
Cao, Dong;
Song, Qingxin

Publication type:

Article

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03452-y

By:

Sarashetti, Prasad;
Lipovac, Josipa;
Tomas, Filip;
Šikić, Mile;
Liu, Jianjun

Publication type:

Article

HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03450-0

By:

Otoničar, Jan;
Lazareva, Olga;
Mallm, Jan-Philipp;
Simovic-Lorenz, Milena;
Philippos, George;
Sant, Pooja;
Parekh, Urja;
Hammann, Linda;
Li, Albert;
Yildiz, Umut;
Marttinen, Mikael;
Zaugg, Judith;
Noh, Kyung Min;
Stegle, Oliver;
Ernst, Aurélie

Publication type:

Article

EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03449-7

By:

Gao, Zijing;
Liu, Qiao;
Zeng, Wanwen;
Jiang, Rui;
Wong, Wing Hung

Publication type:

Article

SQUiD: ultra-secure storage and analysis of genetic data for the advancement of precision medicine.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03447-9

By:

Blindenbach, Jacob;
Kang, Jiayi;
Hong, Seungwan;
Karam, Caline;
Lehner, Thomas;
Gürsoy, Gamze

Publication type:

Article

SyntheVAEiser: augmenting traditional machine learning methods with VAE-based gene expression sample generation for improved cancer subtype predictions.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03431-3

By:

Karlberg, Brian;
Kirchgaessner, Raphael;
Lee, Jordan;
Peterkort, Matthew;
Beckman, Liam;
Goecks, Jeremy;
Ellrott, Kyle

Publication type:

Article

Systemic evaluation of various CRISPR/Cas13 orthologs for knockdown of targeted transcripts in plants.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03448-8

By:

Yu, Lu;
Zou, Jiawei;
Hussain, Amjad;
Jia, Ruoyu;
Fan, Yibo;
Liu, Jinhang;
Nie, Xinhui;
Zhang, Xianlong;
Jin, Shuangxia

Publication type:

Article

Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03435-z

By:

Soupir, Alex C.;
Hayes, Mitchell T.;
Peak, Taylor C.;
Ospina, Oscar;
Chakiryan, Nicholas H.;
Berglund, Anders E.;
Stewart, Paul A.;
Nguyen, Jonathan;
Segura, Carlos Moran;
Francis, Natasha L.;
Echevarria, Paola M. Ramos;
Chahoud, Jad;
Li, Roger;
Tsai, Kenneth Y.;
Balasi, Jodi A.;
Peres, Yamila Caraballo;
Dhillon, Jasreman;
Martinez, Lindsey A.;
Gloria, Warren E.;
Schurman, Nathan

Publication type:

Article

EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03446-w

By:

Kelly, Katherine;
Scherer, Michael;
Braun, Martina Maria;
Lutsik, Pavlo;
Plass, Christoph

Publication type:

Article

Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03437-x

By:

Liu, Yanyan;
Xu, Xintong;
He, Chao;
Jin, Liujie;
Zhou, Ziru;
Gao, Jie;
Guo, Minrong;
Wang, Xin;
Chen, Chuanye;
Ayaad, Mohammed H.;
Li, Xingwang;
Yan, Wenhao

Publication type:

Article

HTAD: a human-in-the-loop framework for supervised chromatin domain detection.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03445-x

By:

Shen, Wei;
Zhang, Ping;
Jiang, Yiwei;
Tao, Hailin;
Zi, Zhike;
Li, Li

Publication type:

Article

MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03444-y

By:

Faure, Andre J.;
Lehner, Ben

Publication type:

Article

Functional screening reveals genetic dependencies and diverging cell cycle control in atypical teratoid rhabdoid tumors.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03438-w

By:

Merk, Daniel J.;
Tsiami, Foteini;
Hirsch, Sophie;
Walter, Bianca;
Haeusser, Lara A.;
Maile, Jens D.;
Stahl, Aaron;
Jarboui, Mohamed A.;
Lechado-Terradas, Anna;
Klose, Franziska;
Babaei, Sepideh;
Admard, Jakob;
Casadei, Nicolas;
Roggia, Cristiana;
Spohn, Michael;
Schittenhelm, Jens;
Singer, Stephan;
Schüller, Ulrich;
Piccioni, Federica;
Persky, Nicole S.

Publication type:

Article

Genetic-by-age interaction analyses on complex traits in UK Biobank and their potential to identify effects on longitudinal trait change.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03439-9

By:

Winkler, Thomas W.;
Wiegrebe, Simon;
Herold, Janina M.;
Stark, Klaus J.;
Küchenhoff, Helmut;
Heid, Iris M.

Publication type:

Article

Publisher Correction: Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing.

Published in:

2024

By:

Niu, Jianxia;
Wang, Wenxi;
Wang, Zihao;
Chen, Zhe;
Zhang, Xiaoyu;
Qin, Zhen;
Miao, Lingfeng;
Yang, Zhengzhao;
Xie, Chaojie;
Xin, Mingming;
Peng, Huiru;
Yao, Yingyin;
Liu, Jie;
Ni, Zhongfu;
Sun, Qixin;
Guo, Weilong

Publication type:

Correction Notice

Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03440-2

By:

Przytycki, Pawel F.;
Pollard, Katherine S.

Publication type:

Article

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03436-y

By:

Guo, Wenbo;
Li, Xinqi;
Wang, Dongfang;
Yan, Nan;
Hu, Qifan;
Yang, Fan;
Zhang, Xuegong;
Yao, Jianhua;
Gu, Jin

Publication type:

Article

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03436-y

By:

Guo, Wenbo;
Li, Xinqi;
Wang, Dongfang;
Yan, Nan;
Hu, Qifan;
Yang, Fan;
Zhang, Xuegong;
Yao, Jianhua;
Gu, Jin

Publication type:

Article

The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03430-4

By:

Ravasini, Francesco;
Kabral, Helja;
Solnik, Anu;
de Gennaro, Luciana;
Montinaro, Francesco;
Hui, Ruoyun;
Delpino, Chiara;
Finocchi, Stefano;
Giroldini, Pierluigi;
Mei, Oscar;
Beck De Lotto, Michael Allen;
Cilli, Elisabetta;
Hajiesmaeil, Mogge;
Pistacchia, Letizia;
Risi, Flavia;
Giacometti, Chiara;
Scheib, Christiana Lyn;
Tambets, Kristiina;
Metspalu, Mait;
Cruciani, Fulvio

Publication type:

Article

Considerations in the search for epistasis.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03427-z

By:

Balvert, Marleen;
Cooper-Knock, Johnathan;
Stamp, Julian;
Byrne, Ross P.;
Mourragui, Soufiane;
van Gils, Juami;
Benonisdottir, Stefania;
Schlüter, Johannes;
Kenna, Kevin;
Abeln, Sanne;
Iacoangeli, Alfredo;
Daub, Joséphine T.;
Browning, Brian L.;
Taş, Gizem;
Hu, Jiajing;
Wang, Yan;
Alhathli, Elham;
Harvey, Calum;
Pianesi, Luna;
Schulte, Sara C.

Publication type:

Article

Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03433-1

By:

Chabot, B. J.;
Sun, R.;
Amjad, A.;
Hoyt, S. J.;
Ouyang, L.;
Courret, C.;
Drennan, R.;
Leo, L.;
Larracuente, A. M.;
Core, L. J.;
O'Neill, R. J.;
Mellone, B. G.

Publication type:

Article

VI-VS: calibrated identification of feature dependencies in single-cell multiomics.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03419-z

By:

Boyeau, Pierre;
Bates, Stephen;
Ergen, Can;
Jordan, Michael I.;
Yosef, Nir

Publication type:

Article

Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03432-2

By:

Yuan, Tianyu;
Yan, Hao;
Li, Kevin C.;
Surovtsev, Ivan;
King, Megan C.;
Mochrie, Simon G. J.

Publication type:

Article

Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03434-0

By:

Wu, Leilei;
Jiang, Shutan;
Shi, Meisong;
Yuan, Tanglong;
Li, Yaqin;
Huang, Pinzheng;
Li, Yingqi;
Zuo, Erwei;
Zhou, Changyang;
Sun, Yidi

Publication type:

Article

scDOT: optimal transport for mapping senescent cells in spatial transcriptomics.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03426-0

By:

Nguyen, Nam D.;
Rosas, Lorena;
Khaliullin, Timur;
Jiang, Peiran;
Hasanaj, Euxhen;
Ovando-Ricardez, Jose A.;
Bueno, Marta;
Rahman, Irfan;
Pryhuber, Gloria S.;
Li, Dongmei;
Ma, Qin;
Finkel, Toren;
Königshoff, Melanie;
Eickelberg, Oliver;
Rojas, Mauricio;
Mora, Ana L.;
Lugo-Martinez, Jose;
Bar-Joseph, Ziv

Publication type:

Article

GraphPCA: a fast and interpretable dimension reduction algorithm for spatial transcriptomics data.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03429-x

By:

Yang, Jiyuan;
Wang, Lu;
Liu, Lin;
Zheng, Xiaoqi

Publication type:

Article

TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03423-3

By:

Qi, Junhai;
Li, Zhengyi;
Zhang, Yao-zhong;
Li, Guojun;
Gao, Xin;
Han, Renmin

Publication type:

Article

CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03417-1

By:

Oksza-Orzechowski, Kazimierz;
Quinten, Edwin;
Shafighi, Shadi;
Kiełbasa, Szymon M.;
van Kessel, Hugo W.;
de Groen, Ruben A. L.;
Vermaat, Joost S. P.;
Sepúlveda Yáñez, Julieta H.;
Navarrete, Marcelo A.;
Veelken, Hendrik;
van Bergen, Cornelis A. M.;
Szczurek, Ewa

Publication type:

Article

Measuring, visualizing, and diagnosing reference bias with biastools.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03240-8

By:

Mao‑Jan Lin;
Iyer, Sheila;
Nae‑Chyun Chen;
Langmead, Ben

Publication type:

Article

TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03423-3

By:

Qi, Junhai;
Li, Zhengyi;
Zhang, Yao-zhong;
Li, Guojun;
Gao, Xin;
Han, Renmin

Publication type:

Article

Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03424-2

By:

Li, Xiaoting;
Melo, Lucas A. N.;
Bussemaker, Harmen J.

Publication type:

Article

Response to "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and "Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples"

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03232-8

By:

Ge, Xinzhou;
Li, Yumei;
Li, Wei;
Li, Jingyi Jessica

Publication type:

Article

Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03231-9

By:

Hejblum, Boris P.;
Ba, Kalidou;
Thiébaut, Rodolphe;
Agniel, Denis

Publication type:

Article

Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03230-w

By:

Yang, Lu;
Zhang, Xianyang;
Chen, Jun

Publication type:

Article

pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03425-1

By:

De Bernardini, Nicola;
Zampieri, Guido;
Campanaro, Stefano;
Zimmermann, Johannes;
Waschina, Silvio;
Treu, Laura

Publication type:

Article

Plant conservation in the age of genome editing: opportunities and challenges.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03399-0

By:

Yin, Kangquan;
Chung, Mi Yoon;
Lan, Bo;
Du, Fang K.;
Chung, Myong Gi

Publication type:

Article

STASCAN deciphers fine-resolution cell distribution maps in spatial transcriptomics by deep learning.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03421-5

By:

Wu, Ying;
Zhou, Jia-Yi;
Yao, Bofei;
Cui, Guanshen;
Zhao, Yong-Liang;
Gao, Chun-Chun;
Yang, Ying;
Zhang, Shihua;
Yang, Yun-Gui

Publication type:

Article

Mapping lineage-traced cells across time points with moslin.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03422-4

By:

Lange, Marius;
Piran, Zoe;
Klein, Michal;
Spanjaard, Bastiaan;
Klein, Dominik;
Junker, Jan Philipp;
Theis, Fabian J.;
Nitzan, Mor

Publication type:

Article

A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03420-6

By:

Mustafa, Rima;
Mens, Michelle M. J.;
van Hilten, Arno;
Huang, Jian;
Roshchupkin, Gennady;
Huan, Tianxiao;
Broer, Linda;
van Meurs, Joyce B. J.;
Elliott, Paul;
Levy, Daniel;
Ikram, M. Arfan;
Evangelou, Marina;
Dehghan, Abbas;
Ghanbari, Mohsen

Publication type:

Article

Scalable identification of lineage-specific gene regulatory networks from metacells with NetID.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03418-0

By:

Wang, Weixu;
Wang, Yichen;
Lyu, Ruiqi;
Grün, Dominic

Publication type:

Article

MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03412-6

By:

Wade, Kristen J.;
Suseno, Rayo;
Kizer, Kerry;
Williams, Jacqueline;
Boquett, Juliano;
Caillier, Stacy;
Pollock, Nicholas R.;
Renschen, Adam;
Santaniello, Adam;
Oksenberg, Jorge R.;
Norman, Paul J.;
Augusto, Danillo G.;
Hollenbach, Jill A.

Publication type:

Article

HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03411-7

By:

Cheng, Youshu;
Cai, Biao;
Li, Hongyu;
Zhang, Xinyu;
D'Souza, Gypsyamber;
Shrestha, Sadeep;
Edmonds, Andrew;
Meyers, Jacquelyn;
Fischl, Margaret;
Kassaye, Seble;
Anastos, Kathryn;
Cohen, Mardge;
Aouizerat, Bradley E.;
Xu, Ke;
Zhao, Hongyu

Publication type:

Article