Works matching IS 14747596 AND DT 2021 AND VI 22 AND IP 1

Results: 371

Heterochromatin: did H3K9 methylation evolve to tame transposons?

Published in:

2021

By:

Kabi, Manisha;
Filion, Guillaume J.

Publication type:

Editorial

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02279-1

By:

Przytycki, Pawel F.;
Pollard, Katherine S.

Publication type:

Article

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02559-w

By:

Wang, Zheng;
Usyk, Mykhaylo;
Vázquez-Baeza, Yoshiki;
Chen, Guo-Chong;
Isasi, Carmen R.;
Williams-Nguyen, Jessica S.;
Hua, Simin;
McDonald, Daniel;
Thyagarajan, Bharat;
Daviglus, Martha L.;
Cai, Jianwen;
North, Kari E.;
Wang, Tao;
Knight, Rob;
Burk, Robert D.;
Kaplan, Robert C.;
Qi, Qibin

Publication type:

Article

Roadblock: improved annotations do not necessarily translate into new functional insights.

Published in:

2021

By:

Hall, Nicola A. L.;
Carlyle, Becky C.;
Haerty, Wilfried;
Tunbridge, Elizabeth M.

Publication type:

Editorial

Malignancy and NF-κB signalling strengthen coordination between expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02541-6

By:

Perez, Marcos Francisco;
Sarkies, Peter

Publication type:

Article

Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02538-1

By:

Louadi, Zakaria;
Elkjaer, Maria L.;
Klug, Melissa;
Lio, Chit Tong;
Fenn, Amit;
Illes, Zsolt;
Bongiovanni, Dario;
Baumbach, Jan;
Kacprowski, Tim;
List, Markus;
Tsoy, Olga

Publication type:

Article

Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02555-0

By:

Rezaei-Lotfi, Saba;
Vujovic, Filip;
Simonian, Mary;
Hunter, Neil;
Farahani, Ramin M.

Publication type:

Article

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02557-y

By:

Huang, Sihao;
Zhang, Wen;
Katanski, Christopher D.;
Dersh, Devin;
Dai, Qing;
Lolans, Karen;
Yewdell, Jonathan;
Eren, A. Murat;
Pan, Tao

Publication type:

Article

Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02554-1

By:

Kim, Heon Seok;
Grimes, Susan M.;
Hooker, Anna C.;
Lau, Billy T.;
Ji, Hanlee P.

Publication type:

Article

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02548-z

By:

Missarova, Alsu;
Jain, Jaison;
Butler, Andrew;
Ghazanfar, Shila;
Stuart, Tim;
Brusko, Maigan;
Wasserfall, Clive;
Nick, Harry;
Brusko, Todd;
Atkinson, Mark;
Satija, Rahul;
Marioni, John C.

Publication type:

Article

The SEQC2 epigenomics quality control (EpiQC) study.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02529-2

By:

Foox, Jonathan;
Nordlund, Jessica;
Lalancette, Claudia;
Gong, Ting;
Lacey, Michelle;
Lent, Samantha;
Langhorst, Bradley W.;
Ponnaluri, V. K. Chaithanya;
Williams, Louise;
Padmanabhan, Karthik Ramaswamy;
Cavalcante, Raymond;
Lundmark, Anders;
Butler, Daniel;
Mozsary, Christopher;
Gurvitch, Justin;
Greally, John M.;
Suzuki, Masako;
Menor, Mark;
Nasu, Masaki;
Alonso, Alicia

Publication type:

Article

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02449-1

By:

Thirunavukarasu, Deepak;
Cheng, Lauren Y.;
Song, Ping;
Chen, Sherry X.;
Borad, Mitesh J.;
Kwong, Lawrence;
James, Phillip;
Turner, Daniel J.;
Zhang, David Yu

Publication type:

Article

Heterochromatin: did H3K9 methylation evolve to tame transposons?

Published in:

2021

By:

Kabi, Manisha;
Filion, Guillaume J.

Publication type:

Editorial

DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02547-0

By:

Muskovic, Walter;
Powell, Joseph E.

Publication type:

Article

Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02549-y

By:

Yang, Xiaofei;
Yu, Haopeng;
Sun, Wenqing;
Ding, Ling;
Li, Ji;
Cheema, Jitender;
Ramirez-Gonzalez, Ricardo;
Zhao, Xuebo;
Martín, Azahara C.;
Lu, Fei;
Liu, Bao;
Uauy, Cristobal;
Ding, Yiliang;
Zhang, Huakun

Publication type:

Article

recount3: summaries and queries for large-scale RNA-seq expression and splicing.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02533-6

By:

Wilks, Christopher;
Zheng, Shijie C.;
Chen, Feng Yong;
Charles, Rone;
Solomon, Brad;
Ling, Jonathan P.;
Imada, Eddie Luidy;
Zhang, David;
Joseph, Lance;
Leek, Jeffrey T.;
Jaffe, Andrew E.;
Nellore, Abhinav;
Collado-Torres, Leonardo;
Hansen, Kasper D.;
Langmead, Ben

Publication type:

Article

Feature selection revisited in the single-cell era.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02544-3

By:

Yang, Pengyi;
Huang, Hao;
Liu, Chunlei

Publication type:

Article

phasebook: haplotype-aware de novo assembly of diploid genomes from long reads.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02512-x

By:

Luo, Xiao;
Kang, Xiongbin;
Schönhuth, Alexander

Publication type:

Article

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02543-4

By:

Mo, Weipeng;
Liu, Bo;
Zhang, Hong;
Jin, Xianhao;
Lu, Dongdong;
Yu, Yiming;
Liu, Yuelin;
Jia, Jinbu;
Long, Yanping;
Deng, Xian;
Cao, Xiaofeng;
Guo, Hongwei;
Zhai, Jixian

Publication type:

Article

treekoR: identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02526-5

By:

Chan, Adam;
Jiang, Wei;
Blyth, Emily;
Yang, Jean;
Patrick, Ellis

Publication type:

Article

Transcriptional landscape of highly lignified poplar stems at single-cell resolution.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02537-2

By:

Chen, Yang;
Tong, Shaofei;
Jiang, Yuanzhong;
Ai, Fandi;
Feng, Yanlin;
Zhang, Junlin;
Gong, Jue;
Qin, Jiajia;
Zhang, Yuanyuan;
Zhu, Yingying;
Liu, Jianquan;
Ma, Tao

Publication type:

Article

Correction: Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist.

Published in:

2021

By:

Mei, Hong;
Zha, Zhao;
Wang, Wei;
Xie, Yusang;
Huang, Yuege;
Li, Wenping;
Wei, Dong;
Zhang, Xinxin;
Qu, Jieming;
Liu, Jia

Publication type:

Correction Notice

SquiggleNet: real-time, direct classification of nanopore signals.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02511-y

By:

Bao, Yuwei;
Wadden, Jack;
Erb-Downward, John R.;
Ranjan, Piyush;
Zhou, Weichen;
McDonald, Torrin L.;
Mills, Ryan E.;
Boyle, Alan P.;
Dickson, Robert P.;
Blaauw, David;
Welch, Joshua D.

Publication type:

Article

Promotech: a general tool for bacterial promoter recognition.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02514-9

By:

Chevez-Guardado, Ruben;
Peña-Castillo, Lourdes

Publication type:

Article

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02525-6

By:

Tian, Luyi;
Jabbari, Jafar S.;
Thijssen, Rachel;
Gouil, Quentin;
Amarasinghe, Shanika L.;
Voogd, Oliver;
Kariyawasam, Hasaru;
Du, Mei R. M.;
Schuster, Jakob;
Wang, Changqing;
Su, Shian;
Dong, Xueyi;
Law, Charity W.;
Lucattini, Alexis;
Prawer, Yair David Joseph;
Collar-Fernández, Coralina;
Chung, Jin D.;
Naim, Timur;
Chan, Audrey;
Ly, Chi Hai

Publication type:

Article

Lamin C is required to establish genome organization after mitosis.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02516-7

By:

Wong, Xianrong;
Hoskins, Victoria E.;
Melendez-Perez, Ashley J.;
Harr, Jennifer C.;
Gordon, Molly;
Reddy, Karen L.

Publication type:

Article

A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02531-8

By:

Wang, Runze;
Xue, Yongsong;
Fan, Jing;
Yao, Jia-Long;
Qin, Mengfan;
Lin, Tao;
Lian, Qun;
Zhang, Mingyue;
Li, Xiaolong;
Li, Jiaming;
Sun, Manyi;
Song, Bobo;
Zhang, Jiaying;
Zhao, Kejiao;
Chen, Xu;
Hu, Hongju;
Fei, Zhangjun;
Xue, Cheng;
Wu, Jun

Publication type:

Article

Accurate long-read de novo assembly evaluation with Inspector.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02527-4

By:

Chen, Yu;
Zhang, Yixin;
Wang, Amy Y.;
Gao, Min;
Chong, Zechen

Publication type:

Article

ATRX regulates glial identity and the tumor microenvironment in IDH-mutant glioma.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02535-4

By:

Babikir, Husam;
Wang, Lin;
Shamardani, Karin;
Catalan, Francisca;
Sudhir, Sweta;
Aghi, Manish K.;
Raleigh, David R.;
Phillips, Joanna J.;
Diaz, Aaron A.

Publication type:

Article

An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02532-7

By:

Wolfe, Jareth C.;
Mikheeva, Liudmila A.;
Hagras, Hani;
Zabet, Nicolae Radu

Publication type:

Article

The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine.

Published in:

2021

By:

Mercer, Tim R.;
Xu, Joshua;
Mason, Christopher E.;
Tong, Weida

Publication type:

Editorial

TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02523-8

By:

Cheng, Yubao;
Liu, Miao;
Hu, Mengwei;
Wang, Siyuan

Publication type:

Article

Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02518-5

By:

Talon, Irene;
Janiszewski, Adrian;
Theeuwes, Bart;
Lefevre, Thomas;
Song, Juan;
Bervoets, Greet;
Vanheer, Lotte;
De Geest, Natalie;
Poovathingal, Suresh;
Allsop, Ryan;
Marine, Jean-Christophe;
Rambow, Florian;
Voet, Thierry;
Pasque, Vincent

Publication type:

Article

High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02522-9

By:

Wang, Shouchuang;
Xiao, Yong;
Zhou, Zhi-Wei;
Yuan, Jiaqing;
Guo, Hao;
Yang, Zhuang;
Yang, Jun;
Sun, Pengchuan;
Sun, Lisong;
Deng, Yuan;
Xie, Wen-Zhao;
Song, Jia-Ming;
Qamar, Muhammad Tahir ul;
Xia, Wei;
Liu, Rui;
Gong, Shufang;
Wang, Yong;
Wang, Fuyou;
Liu, Xianqing;
Fernie, Alisdair R.

Publication type:

Article

IRFinder-S: a comprehensive suite to discover and explore intron retention.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02515-8

By:

Lorenzi, Claudio;
Barriere, Sylvain;
Arnold, Katharina;
Luco, Reini F.;
Oldfield, Andrew J.;
Ritchie, William

Publication type:

Article

Sex without crossing over in the yeast Saccharomycodes ludwigii.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02521-w

By:

Papaioannou, Ioannis A.;
Dutreux, Fabien;
Peltier, France A.;
Maekawa, Hiromi;
Delhomme, Nicolas;
Bardhan, Amit;
Friedrich, Anne;
Schacherer, Joseph;
Knop, Michael

Publication type:

Article

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02519-4

By:

Zappia, Luke;
Theis, Fabian J.

Publication type:

Article

Tejaas: reverse regression increases power for detecting trans-eQTLs.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02361-8

By:

Banerjee, Saikat;
Simonetti, Franco L.;
Detrois, Kira E.;
Kaphle, Anubhav;
Mitra, Raktim;
Nagial, Rahul;
Söding, Johannes

Publication type:

Article

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02507-8

By:

Cmero, Marek;
Schmidt, Breon;
Majewski, Ian J.;
Ekert, Paul G.;
Oshlack, Alicia;
Davidson, Nadia M.

Publication type:

Article

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02507-8

By:

Cmero, Marek;
Schmidt, Breon;
Majewski, Ian J.;
Ekert, Paul G.;
Oshlack, Alicia;
Davidson, Nadia M.

Publication type:

Article

Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02414-y

By:

Barile, Melania;
Imaz-Rosshandler, Ivan;
Inzani, Isabella;
Ghazanfar, Shila;
Nichols, Jennifer;
Marioni, John C.;
Guibentif, Carolina;
Göttgens, Berthold

Publication type:

Article

A generalization of t-SNE and UMAP to single-cell multimodal omics.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02356-5

By:

Do, Van Hoan;
Canzar, Stefan

Publication type:

Article

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02517-6

By:

Ji, Feiyang;
Ma, Qingguo;
Zhang, Wenting;
Liu, Jie;
Feng, Yu;
Zhao, Peng;
Song, Xiaobo;
Chen, Jiaxin;
Zhang, Junpei;
Wei, Xin;
Zhou, Ye;
Chang, Yingying;
Zhang, Pu;
Huang, Xuehui;
Qiu, Jie;
Pei, Dong

Publication type:

Article

Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02513-w

By:

Mei, Hong;
Zha, Zhao;
Wang, Wei;
Xie, Yusang;
Huang, Yuege;
Li, Wenping;
Wei, Dong;
Zhang, Xinxin;
Qu, Jieming;
Liu, Jia

Publication type:

Article

SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02497-7

By:

Rabin, Avigayel;
Zaffagni, Michela;
Ashwal-Fluss, Reut;
Patop, Ines Lucia;
Jajoo, Aarti;
Shenzis, Shlomo;
Carmel, Liran;
Kadener, Sebastian

Publication type:

Article

Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02503-y

By:

Patel, Zain M.;
Hughes, Timothy R.

Publication type:

Article

Clipper: p-value-free FDR control on high-throughput data from two conditions.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02506-9

By:

Ge, Xinzhou;
Chen, Yiling Elaine;
Song, Dongyuan;
McDermott, MeiLu;
Woyshner, Kyla;
Manousopoulou, Antigoni;
Wang, Ning;
Li, Wei;
Wang, Leo D.;
Li, Jingyi Jessica

Publication type:

Article

DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02510-z

By:

Liu, Yang;
Rosikiewicz, Wojciech;
Pan, Ziwei;
Jillette, Nathaniel;
Wang, Ping;
Taghbalout, Aziz;
Foox, Jonathan;
Mason, Christopher;
Carroll, Martin;
Cheng, Albert;
Li, Sheng

Publication type:

Article

Kras<sup>G12D</sup> induces changes in chromatin territories that differentially impact early nuclear reprogramming in pancreatic cells.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02498-6

By:

Mathison, Angela J.;
Kerketta, Romica;
de Assuncao, Thiago Milech;
Leverence, Elise;
Zeighami, Atefeh;
Urrutia, Guillermo;
Stodola, Timothy J.;
di Magliano, Marina Pasca;
Iovanna, Juan L.;
Zimmermann, Michael T.;
Lomberk, Gwen;
Urrutia, Raul

Publication type:

Article

Effects of sequence motifs in the yeast 3′ untranslated region determined from massively parallel assays of random sequences.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02509-6

By:

Savinov, Andrew;
Brandsen, Benjamin M.;
Angell, Brooke E.;
Cuperus, Josh T.;
Fields, Stanley

Publication type:

Article