Works matching IS 14747596 AND DT 2022 AND VI 23 AND IP 1

Results: 302

METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02819-3

By:

Hsu, Kai-Wen;
Lai, Joseph Chieh-Yu;
Chang, Jeng-Shou;
Peng, Pei-Hua;
Huang, Ching-Hui;
Lee, Der-Yen;
Tsai, Yu-Cheng;
Chung, Chi-Jung;
Chang, Han;
Chang, Chao-Hsiang;
Chen, Ji-Lin;
Pang, See-Tong;
Hao, Ziyang;
Cui, Xiao-Long;
He, Chuan;
Wu, Kou-Juey

Publication type:

Article

SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02813-9

By:

Kang, Senbai;
Borgsmüller, Nico;
Valecha, Monica;
Kuipers, Jack;
Alves, Joao M.;
Prado-López, Sonia;
Chantada, Débora;
Beerenwinkel, Niko;
Posada, David;
Szczurek, Ewa

Publication type:

Article

Deciphering the impact of genetic variation on human polyadenylation using APARENT2.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02799-4

By:

Linder, Johannes;
Koplik, Samantha E.;
Kundaje, Anshul;
Seelig, Georg

Publication type:

Article

Statistics or biology: the zero-inflation controversy about scRNA-seq data.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02601-5

By:

Jiang, Ruochen;
Sun, Tianyi;
Song, Dongyuan;
Li, Jingyi Jessica

Publication type:

Article

A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-021-02595-6

By:

Li, Gaoyang;
Fu, Shaliu;
Wang, Shuguang;
Zhu, Chenyu;
Duan, Bin;
Tang, Chen;
Chen, Xiaohan;
Chuai, Guohui;
Wang, Ping;
Liu, Qi

Publication type:

Article

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02815-7

By:

Rossini, Roberto;
Kumar, Vipin;
Mathelier, Anthony;
Rognes, Torbjørn;
Paulsen, Jonas

Publication type:

Article

SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02813-9

By:

Kang, Senbai;
Borgsmüller, Nico;
Valecha, Monica;
Kuipers, Jack;
Alves, Joao M.;
Prado-López, Sonia;
Chantada, Débora;
Beerenwinkel, Niko;
Posada, David;
Szczurek, Ewa

Publication type:

Article

Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02812-w

By:

Jiang, Yongpeng;
Huang, Jie;
Tian, Kai;
Yi, Xiao;
Zheng, Haonan;
Zhu, Yi;
Guo, Tiannan;
Ji, Xiong

Publication type:

Article

m<sup>6</sup>A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02814-8

By:

Wang, Ling;
Zhuang, Haiyan;
Fan, Wenwen;
Zhang, Xia;
Dong, Haihong;
Yang, Hongxing;
Cho, Jungnam

Publication type:

Article

The genetic and biochemical determinants of mRNA degradation rates in mammals.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02811-x

By:

Agarwal, Vikram;
Kelley, David R.

Publication type:

Article

Parallel evolution of amphioxus and vertebrate small-scale gene duplications.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02808-6

By:

Brasó-Vives, Marina;
Marlétaz, Ferdinand;
Echchiki, Amina;
Mantica, Federica;
Acemel, Rafael D.;
Gómez-Skarmeta, José L.;
Hartasánchez, Diego A.;
Le Targa, Lorlane;
Pontarotti, Pierre;
Tena, Juan J.;
Maeso, Ignacio;
Escriva, Hector;
Irimia, Manuel;
Robinson-Rechavi, Marc

Publication type:

Article

metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02810-y

By:

Lai, Senying;
Pan, Shaojun;
Sun, Chuqing;
Coelho, Luis Pedro;
Chen, Wei-Hua;
Zhao, Xing-Ming

Publication type:

Article

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02794-9

By:

Kaufmann, Tom L.;
Petkovic, Marina;
Watkins, Thomas B. K.;
Colliver, Emma C.;
Laskina, Sofya;
Thapa, Nisha;
Minussi, Darlan C.;
Navin, Nicholas;
Swanton, Charles;
Van Loo, Peter;
Haase, Kerstin;
Tarabichi, Maxime;
Schwarz, Roland F.

Publication type:

Article

Survey of the binding preferences of RNA-binding proteins to RNA editing events.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02741-8

By:

Hu, Xiaolin;
Zou, Qin;
Yao, Li;
Yang, Xuerui

Publication type:

Article

A benchmark study of deep learning-based multi-omics data fusion methods for cancer.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02739-2

By:

Leng, Dongjin;
Zheng, Linyi;
Wen, Yuqi;
Zhang, Yunhao;
Wu, Lianlian;
Wang, Jing;
Wang, Meihong;
Zhang, Zhongnan;
He, Song;
Bo, Xiaochen

Publication type:

Article

Evolution and function of developmentally dynamic pseudogenes in mammals.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02802-y

By:

Qian, Sheng Hu;
Chen, Lu;
Xiong, Yu-Li;
Chen, Zhen-Xia

Publication type:

Article

Differential richness inference for 16S rRNA marker gene surveys.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02722-x

By:

Kumar, M. Senthil;
Slud, Eric V.;
Hehnly, Christine;
Zhang, Lijun;
Broach, James;
Irizarry, Rafael A.;
Schiff, Steven J.;
Paulson, Joseph N.

Publication type:

Article

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02789-6

By:

David, Julianne K.;
Maden, Sean K.;
Wood, Mary A.;
Thompson, Reid F.;
Nellore, Abhinav

Publication type:

Article

Gene flow and introgression are pervasive forces shaping the evolution of bacterial species.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02809-5

By:

Diop, Awa;
Torrance, Ellis L.;
Stott, Caroline M.;
Bobay, Louis-Marie

Publication type:

Article

Towards accurate and reliable resolution of structural variants for clinical diagnosis.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02636-8

By:

Liu, Zhichao;
Roberts, Ruth;
Mercer, Timothy R.;
Xu, Joshua;
Sedlazeck, Fritz J.;
Tong, Weida

Publication type:

Article

Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02728-5

By:

de Mendoza, Alex;
Nguyen, Trung Viet;
Ford, Ethan;
Poppe, Daniel;
Buckberry, Sam;
Pflueger, Jahnvi;
Grimmer, Matthew R.;
Stolzenburg, Sabine;
Bogdanovic, Ozren;
Oshlack, Alicia;
Farnham, Peggy J.;
Blancafort, Pilar;
Lister, Ryan

Publication type:

Article

Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02801-z

By:

Tan, Zengdong;
Peng, Yan;
Xiong, Yao;
Xiong, Feng;
Zhang, Yuting;
Guo, Ning;
Tu, Zhuo;
Zong, Zhanxiang;
Wu, Xiaokun;
Ye, Jiang;
Xia, Chunjiao;
Zhu, Tao;
Liu, Yinmeng;
Lou, Hongxiang;
Liu, Dongxu;
Lu, Shaoping;
Yao, Xuan;
Liu, Kede;
Snowdon, Rod J.;
Golicz, Agnieszka A.

Publication type:

Article

Folliculin-interacting protein FNIP2 impacts on overweight and obesity through a polymorphism in a conserved 3′ untranslated region.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02798-5

By:

Fernández, Lara P.;
Deleyto-Seldas, Nerea;
Colmenarejo, Gonzalo;
Sanz, Alba;
Wagner, Sonia;
Plata-Gómez, Ana Belén;
Gómez-Patiño, Mónica;
Molina, Susana;
Espinosa-Salinas, Isabel;
Aguilar-Aguilar, Elena;
Ortega, Sagrario;
Graña-Castro, Osvaldo;
Loria-Kohen, Viviana;
Fernández-Marcos, Pablo J.;
Efeyan, Alejo;
Ramírez de Molina, Ana

Publication type:

Article

Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02640-y

By:

Sen, Arko;
Huo, Yuchen;
Elster, Jennifer;
Zage, Peter E.;
McVicker, Graham

Publication type:

Article

Mapping responsive genomic elements to heat stress in a maize diversity panel.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02807-7

By:

Liang, Zhikai;
Myers, Zachary A.;
Petrella, Dominic;
Engelhorn, Julia;
Hartwig, Thomas;
Springer, Nathan M.

Publication type:

Article

The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02633-x

By:

Ma, Xiaokai;
Yu, Li'ang;
Fatima, Mahpara;
Wadlington, William H.;
Hulse-Kemp, Amanda M.;
Zhang, Xingtan;
Zhang, Shengcheng;
Xu, Xindan;
Wang, Jingjing;
Huang, Huaxing;
Lin, Jing;
Deng, Ban;
Liao, Zhenyang;
Yang, Zhenhui;
Ma, Yanhong;
Tang, Haibao;
Van Deynze, Allen;
Ming, Ray

Publication type:

Article

HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02627-9

By:

Chen, Haojie;
Tu, Shiqi;
Yuan, Chongze;
Tian, Feng;
Zhang, Yijing;
Sun, Yihua;
Shao, Zhen

Publication type:

Article

IDEAS: individual level differential expression analysis for single-cell RNA-seq data.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02605-1

By:

Zhang, Mengqi;
Liu, Si;
Miao, Zhen;
Han, Fang;
Gottardo, Raphael;
Sun, Wei

Publication type:

Article

Strainline: full-length de novo viral haplotype reconstruction from noisy long reads.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-021-02587-6

By:

Luo, Xiao;
Kang, Xiongbin;
Schönhuth, Alexander

Publication type:

Article

Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02803-x

By:

Xiao, Chunlin;
Chen, Zhong;
Chen, Wanqiu;
Padilla, Cory;
Colgan, Michael;
Wu, Wenjun;
Fang, Li-Tai;
Liu, Tiantian;
Yang, Yibin;
Schneider, Valerie;
Wang, Charles;
Xiao, Wenming

Publication type:

Article

A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02790-z

By:

Lohia, Ruchi;
Fox, Nathan;
Gillis, Jesse

Publication type:

Article

Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02805-9

By:

Baaijens, Jasmijn A.;
Zulli, Alessandro;
Ott, Isabel M.;
Nika, Ioanna;
van der Lugt, Mart J.;
Petrone, Mary E.;
Alpert, Tara;
Fauver, Joseph R.;
Kalinich, Chaney C.;
Vogels, Chantal B. F.;
Breban, Mallery I.;
Duvallet, Claire;
McElroy, Kyle A.;
Ghaeli, Newsha;
Imakaev, Maxim;
Mckenzie-Bennett, Malaika F.;
Robison, Keith;
Plocik, Alex;
Schilling, Rebecca;
Pierson, Martha

Publication type:

Article

Evolution and function of developmentally dynamic pseudogenes in mammals.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02802-y

By:

Qian, Sheng Hu;
Chen, Lu;
Xiong, Yu-Li;
Chen, Zhen-Xia

Publication type:

Article

Mapping responsive genomic elements to heat stress in a maize diversity panel.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02807-7

By:

Liang, Zhikai;
Myers, Zachary A.;
Petrella, Dominic;
Engelhorn, Julia;
Hartwig, Thomas;
Springer, Nathan M.

Publication type:

Article

Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02801-z

By:

Tan, Zengdong;
Peng, Yan;
Xiong, Yao;
Xiong, Feng;
Zhang, Yuting;
Guo, Ning;
Tu, Zhuo;
Zong, Zhanxiang;
Wu, Xiaokun;
Ye, Jiang;
Xia, Chunjiao;
Zhu, Tao;
Liu, Yinmeng;
Lou, Hongxiang;
Liu, Dongxu;
Lu, Shaoping;
Yao, Xuan;
Liu, Kede;
Snowdon, Rod J.;
Golicz, Agnieszka A.

Publication type:

Article

Deciphering the impact of genetic variation on human polyadenylation using APARENT2.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02799-4

By:

Linder, Johannes;
Koplik, Samantha E.;
Kundaje, Anshul;
Seelig, Georg

Publication type:

Article

Folliculin-interacting protein FNIP2 impacts on overweight and obesity through a polymorphism in a conserved 3′ untranslated region.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02798-5

By:

Fernández, Lara P.;
Deleyto-Seldas, Nerea;
Colmenarejo, Gonzalo;
Sanz, Alba;
Wagner, Sonia;
Plata-Gómez, Ana Belén;
Gómez-Patiño, Mónica;
Molina, Susana;
Espinosa-Salinas, Isabel;
Aguilar-Aguilar, Elena;
Ortega, Sagrario;
Graña-Castro, Osvaldo;
Loria-Kohen, Viviana;
Fernández-Marcos, Pablo J.;
Efeyan, Alejo;
Ramírez de Molina, Ana

Publication type:

Article

scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02796-7

By:

Bianchi, Agostina;
Scherer, Michael;
Zaurin, Roser;
Quililan, Kimberly;
Velten, Lars;
Beekman, Renée

Publication type:

Article

ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02795-8

By:

Meyer, Elisabeth;
Chaung, Kaitlin;
Dehghannasiri, Roozbeh;
Salzman, Julia

Publication type:

Article

CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02779-8

By:

Tanaka, Masayuki;
Yokoyama, Keiko;
Hayashi, Hideki;
Isaki, Sanae;
Kitatani, Kanae;
Wang, Ting;
Kawata, Hisako;
Matsuzawa, Hideyuki;
Gurumurthy, Channabasavaiah B.;
Miura, Hiromi;
Ohtsuka, Masato

Publication type:

Article

INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02778-9

By:

Ivančić, Dimitrije;
Mir-Pedrol, Júlia;
Jaraba-Wallace, Jessica;
Rafel, Núria;
Sanchez-Mejias, Avencia;
Güell, Marc

Publication type:

Article

Significant variation in the performance of DNA methylation predictors across data preprocessing and normalization strategies.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02793-w

By:

Ori, Anil P. S.;
Lu, Ake T.;
Horvath, Steve;
Ophoff, Roel A.

Publication type:

Article

Author Correction: Pooled extracellular receptor-ligand interaction screening using CRISPR activation.

Published in:

2022

By:

Chong, Zheng-Shan;
Ohnishi, Shuhei;
Yusa, Kosuke;
Wright, Gavin J.

Publication type:

Correction Notice

Multi-omics analysis dissects the genetic architecture of seed coat content in Brassica napus.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02647-5

By:

Zhang, Yuting;
Zhang, Hui;
Zhao, Hu;
Xia, Yefan;
Zheng, Xiangbo;
Fan, Ruyi;
Tan, Zengdong;
Duan, Chenhua;
Fu, Yansong;
Li, Long;
Ye, Jiang;
Tang, Shan;
Hu, Honghong;
Xie, Weibo;
Yao, Xuan;
Guo, Liang

Publication type:

Article

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02626-w

By:

Du, Yuxuan;
Sun, Fengzhu

Publication type:

Article

Enhanced protein isoform characterization through long-read proteogenomics.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02624-y

By:

Miller, Rachel M.;
Jordan, Ben T.;
Mehlferber, Madison M.;
Jeffery, Erin D.;
Chatzipantsiou, Christina;
Kaur, Simi;
Millikin, Robert J.;
Dai, Yunxiang;
Tiberi, Simone;
Castaldi, Peter J.;
Shortreed, Michael R.;
Luckey, Chance John;
Conesa, Ana;
Smith, Lloyd M.;
Deslattes Mays, Anne;
Sheynkman, Gloria M.

Publication type:

Article

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02623-z

By:

Fitzgerald, Tomas;
Brettell, Ian;
Leger, Adrien;
Wolf, Nadeshda;
Kusminski, Natalja;
Monahan, Jack;
Barton, Carl;
Herder, Cathrin;
Aadepu, Narendar;
Gierten, Jakob;
Becker, Clara;
Hammouda, Omar T.;
Hasel, Eva;
Lischik, Colin;
Lust, Katharina;
Sokolova, Natalia;
Suzuki, Risa;
Tsingos, Erika;
Tavhelidse, Tinatini;
Thumberger, Thomas

Publication type:

Article

Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02781-0

By:

Shaikh, Nadeem;
Mazzagatti, Alice;
De Angelis, Simone;
Johnson, Sarah C.;
Bakker, Bjorn;
Spierings, Diana C. J.;
Wardenaar, René;
Maniati, Eleni;
Wang, Jun;
Boemo, Michael A.;
Foijer, Floris;
McClelland, Sarah E.

Publication type:

Article

JAFFAL: detecting fusion genes with long-read transcriptome sequencing.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-021-02588-5

By:

Davidson, Nadia M.;
Chen, Ying;
Sadras, Teresa;
Ryland, Georgina L.;
Blombery, Piers;
Ekert, Paul G.;
Göke, Jonathan;
Oshlack, Alicia

Publication type:

Article

A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02792-x

By:

Hansen, Jeffrey L.;
Cohen, Barak A.

Publication type:

Article