Works matching IS 14747596 AND DT 2021 AND VI 22

Results: 381

Cobolt: integrative analysis of multimodal single-cell sequencing data.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02556-z

By:

Gong, Boying;
Zhou, Yun;
Purdom, Elizabeth

Publication type:

Article

Author Correction: The SEQC2 epigenomics quality control (EpiQC) study.

Published in:

2021

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:

Correction Notice

An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02536-3

By:

Perez-Sepulveda, Blanca M.;
Heavens, Darren;
Pulford, Caisey V.;
Predeus, Alexander V.;
Low, Ross;
Webster, Hermione;
Dykes, Gregory F.;
Schudoma, Christian;
Rowe, Will;
Lipscombe, James;
Watkins, Chris;
Kumwenda, Benjamin;
Shearer, Neil;
Costigan, Karl;
Baker, Kate S.;
Feasey, Nicholas A.;
Hinton, Jay C. D.;
Hall, Neil;
The 10KSG consortium;
Acuña, María Teresa

Publication type:

Article

Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02574-x

By:

Waters, Colin T.;
Gisselbrecht, Stephen S.;
Sytnikova, Yuliya A.;
Cafarelli, Tiziana M.;
Hill, David E.;
Bulyk, Martha L.

Publication type:

Article

The economics of organellar gene loss and endosymbiotic gene transfer.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02567-w

By:

Kelly, Steven

Publication type:

Article

MultiMAP: dimensionality reduction and integration of multimodal data.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02565-y

By:

Jain, Mika Sarkin;
Polanski, Krzysztof;
Conde, Cecilia Dominguez;
Chen, Xi;
Park, Jongeun;
Mamanova, Lira;
Knights, Andrew;
Botting, Rachel A.;
Stephenson, Emily;
Haniffa, Muzlifah;
Lamacraft, Austen;
Efremova, Mirjana;
Teichmann, Sarah A.

Publication type:

Article

Hidden biases in germline structural variant detection.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02558-x

By:

Khayat, Michael M.;
Sahraeian, Sayed Mohammad Ebrahim;
Zarate, Samantha;
Carroll, Andrew;
Hong, Huixiao;
Pan, Bohu;
Shi, Leming;
Gibbs, Richard A.;
Mohiyuddin, Marghoob;
Zheng, Yuanting;
Sedlazeck, Fritz J.

Publication type:

Article

SCEPTRE improves calibration and sensitivity in single-cell CRISPR screen analysis.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02545-2

By:

Barry, Timothy;
Wang, Xuran;
Morris, John A.;
Roeder, Kathryn;
Katsevich, Eugene

Publication type:

Article

Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02540-7

By:

Dempster, Joshua M.;
Boyle, Isabella;
Vazquez, Francisca;
Root, David E.;
Boehm, Jesse S.;
Hahn, William C.;
Tsherniak, Aviad;
McFarland, James M.

Publication type:

Article

An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02536-3

By:

Perez-Sepulveda, Blanca M.;
Heavens, Darren;
Pulford, Caisey V.;
Predeus, Alexander V.;
Low, Ross;
Webster, Hermione;
Dykes, Gregory F.;
Schudoma, Christian;
Rowe, Will;
Lipscombe, James;
Watkins, Chris;
Kumwenda, Benjamin;
Shearer, Neil;
Costigan, Karl;
Baker, Kate S.;
Feasey, Nicholas A.;
Hinton, Jay C. D.;
Hall, Neil;
The 10KSG consortium;
Acuña, María Teresa

Publication type:

Article

Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02564-z

By:

Annacondia, Maria Luz;
Martinez, German

Publication type:

Article

A benchmark of structural variation detection by long reads through a realistic simulated model.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02551-4

By:

Dierckxsens, Nicolas;
Li, Tong;
Vermeesch, Joris R.;
Xie, Zhi

Publication type:

Article

splatPop: simulating population scale single-cell RNA sequencing data.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02546-1

By:

Azodi, Christina B.;
Zappia, Luke;
Oshlack, Alicia;
McCarthy, Davis J.

Publication type:

Article

Heterochromatin: did H3K9 methylation evolve to tame transposons?

Published in:

2021

By:

Kabi, Manisha;
Filion, Guillaume J.

Publication type:

Editorial

Benchmarking UMI-based single-cell RNA-seq preprocessing workflows.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02552-3

By:

You, Yue;
Tian, Luyi;
Su, Shian;
Dong, Xueyi;
Jabbari, Jafar S.;
Hickey, Peter F.;
Ritchie, Matthew E.

Publication type:

Article

A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02539-0

By:

Nim, Hieu T.;
Dang, Louis;
Thiyagarajah, Harshini;
Bakopoulos, Daniel;
See, Michael;
Charitakis, Natalie;
Sibbritt, Tennille;
Eichenlaub, Michael P.;
Archer, Stuart K.;
Fossat, Nicolas;
Burke, Richard E.;
Tam, Patrick P. L.;
Warr, Coral G.;
Johnson, Travis K.;
Ramialison, Mirana

Publication type:

Article

CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02561-2

By:

Hu, Zhiyuan;
Ahmed, Ahmed A.;
Yau, Christopher

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

Flimma: a federated and privacy-aware tool for differential gene expression analysis.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02553-2

By:

Zolotareva, Olga;
Nasirigerdeh, Reza;
Matschinske, Julian;
Torkzadehmahani, Reihaneh;
Bakhtiari, Mohammad;
Frisch, Tobias;
Späth, Julian;
Blumenthal, David B.;
Abbasinejad, Amir;
Tieri, Paolo;
Kaissis, Georgios;
Rückert, Daniel;
Wenke, Nina K.;
List, Markus;
Baumbach, Jan

Publication type:

Article

Heterochromatin: did H3K9 methylation evolve to tame transposons?

Published in:

2021

By:

Kabi, Manisha;
Filion, Guillaume J.

Publication type:

Editorial

scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02367-2

By:

Sun, Tianyi;
Song, Dongyuan;
Li, Wei Vivian;
Li, Jingyi Jessica

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations.

Published in:

Genome Biology, 2021, v. 22, p. 1, doi. 10.1186/s13059-021-02520-x

By:

Xingguo Zhang;
Pandey, Manish K.;
Jianping Wang;
Kunkun Zhao;
Xingli Ma;
Zhongfeng Li;
Kai Zhao;
Fangping Gong;
Baozhu Guo;
Varshney, Rajeev K.;
Dongmei Yin

Publication type:

Article

NMD abnormalities during brain development in the Fmr1-knockout mouse model of fragile X syndrome.

Published in:

Genome Biology, 2021, v. 22, p. 1, doi. 10.1186/s13059-021-02530-9

By:

Tatsuaki Kurosaki;
Hitomi Sakano;
Pröschel, Christoph;
Wheeler, Jason;
Hewko, Alexander;
Maquat, Lynne E.

Publication type:

Article

Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity.

Published in:

Genome Biology, 2021, v. 22, p. 1, doi. 10.1186/s13059-021-02524-7

By:

Wei Hu;
Changmian Ji;
Zhe Liang;
Jianqiu Ye;
Wenjun Ou;
Zehong Ding;
Gang Zhou;
Weiwei Tie;
Yan Yan;
Jinghao Yang;
Liming Ma;
Xiaoying Yang;
Yunxie Wei;
Zhiqiang Jin;
Jianghui Xie;
Ming Peng;
Wenquan Wang;
Anping Guo;
Biyu Xu;
Jianchun Guo

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

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

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

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