Works matching IS 14747596 AND DT 2021 AND VI 22

Results: 381

Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02255-1

By:

Silvestre-Ryan, Jordi;
Holmes, Ian

Publication type:

Article

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02220-y

By:

Williams, Justin;
Xu, Beisi;
Putnam, Daniel;
Thrasher, Andrew;
Li, Chunliang;
Yang, Jun;
Chen, Xiang

Publication type:

Article

Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02258-y

By:

Martín, Guiomar;
Márquez, Yamile;
Mantica, Federica;
Duque, Paula;
Irimia, Manuel

Publication type:

Article

SPIN reveals genome-wide landscape of nuclear compartmentalization.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02253-3

By:

Wang, Yuchuan;
Zhang, Yang;
Zhang, Ruochi;
van Schaik, Tom;
Zhang, Liguo;
Sasaki, Takayo;
Peric-Hupkes, Daniel;
Chen, Yu;
Gilbert, David M.;
van Steensel, Bas;
Belmont, Andrew S.;
Ma, Jian

Publication type:

Article

A novel protein encoded by circular SMO RNA is essential for Hedgehog signaling activation and glioblastoma tumorigenicity.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02250-6

By:

Wu, Xujia;
Xiao, Songhua;
Zhang, Maolei;
Yang, Lixuan;
Zhong, Jian;
Li, Bo;
Li, Fanying;
Xia, Xin;
Li, Xixi;
Zhou, Huangkai;
Liu, Dawei;
Huang, Nunu;
Yang, Xuesong;
Xiao, Feizhe;
Zhang, Nu

Publication type:

Article

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02245-3

By:

Chia, Minghao;
Li, Cai;
Marques, Sueli;
Pelechano, Vicente;
Luscombe, Nicholas M.;
van Werven, Folkert J.

Publication type:

Article

The variant call format provides efficient and robust storage of GWAS summary statistics.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02248-0

By:

Lyon, Matthew S.;
Andrews, Shea J.;
Elsworth, Ben;
Gaunt, Tom R.;
Hemani, Gibran;
Marcora, Edoardo

Publication type:

Article

Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02247-1

By:

Ross, Caroline Jane;
Rom, Aviv;
Spinrad, Amit;
Gelbard-Solodkin, Dikla;
Degani, Neta;
Ulitsky, Igor

Publication type:

Article

BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02237-3

By:

Luhmann, Nina;
Holley, Guillaume;
Achtman, Mark

Publication type:

Article

Half a century of the reverse transcriptase—happy birthday!

Published in:

2021

By:

Moelling, Karin

Publication type:

Editorial

Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02217-7

By:

Zhang, Kaixuan;
He, Ming;
Fan, Yu;
Zhao, Hui;
Gao, Bin;
Yang, Keli;
Li, Faliang;
Tang, Yu;
Gao, Qiang;
Lin, Tao;
Quinet, Muriel;
Janovská, Dagmar;
Meglič, Vladimir;
Kwiatkowski, Jacek;
Romanova, Olga;
Chrungoo, Nikhil;
Suzuki, Tatsuro;
Luthar, Zlata;
Germ, Mateja;
Woo, Sun-Hee

Publication type:

Article

A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02272-8

By:

Li, Li;
Ugalde, Alejandro P.;
Scheele, Colinda L. G. J.;
Dieter, Sebastian M.;
Nagel, Remco;
Ma, Jin;
Pataskar, Abhijeet;
Korkmaz, Gozde;
Elkon, Ran;
Chien, Miao-Ping;
You, Li;
Su, Pin-Rui;
Bleijerveld, Onno B.;
Altelaar, Maarten;
Momchev, Lyubomir;
Manber, Zohar;
Han, Ruiqi;
van Breugel, Pieter C.;
Lopes, Rui;
ten Dijke, Peter

Publication type:

Article

My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02269-3

By:

Zhou, Yadi;
Zhao, Junfei;
Fang, Jiansong;
Martin, William;
Li, Lang;
Nussinov, Ruth;
Chan, Timothy A.;
Eng, Charis;
Cheng, Feixiong

Publication type:

Article

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02261-x

By:

Huang, Kie Kyon;
Huang, Jiawen;
Wu, Jeanie Kar Leng;
Lee, Minghui;
Tay, Su Ting;
Kumar, Vikrant;
Ramnarayanan, Kalpana;
Padmanabhan, Nisha;
Xu, Chang;
Tan, Angie Lay Keng;
Chan, Charlene;
Kappei, Dennis;
Göke, Jonathan;
Tan, Patrick

Publication type:

Article

Evolutionary conservation and divergence of the human brain transcriptome.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02257-z

By:

Pembroke, William G.;
Hartl, Christopher L.;
Geschwind, Daniel H.

Publication type:

Article

Half a century of the reverse transcriptase—happy birthday!

Published in:

2021

By:

Moelling, Karin

Publication type:

Editorial

Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02244-4

By:

Holley, Guillaume;
Beyter, Doruk;
Ingimundardottir, Helga;
Møller, Peter L.;
Kristmundsdottir, Snædis;
Eggertsson, Hannes P.;
Halldorsson, Bjarni V.

Publication type:

Article

Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02225-7

By:

Jia, Jizeng;
Xie, Yilin;
Cheng, Jingfei;
Kong, Chuizheng;
Wang, Meiyue;
Gao, Lifeng;
Zhao, Fei;
Guo, Jingyu;
Wang, Kai;
Li, Guangwei;
Cui, Dangqun;
Hu, Tiezhu;
Zhao, Guangyao;
Wang, Daowen;
Ru, Zhengang;
Zhang, Yijing

Publication type:

Article

Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02221-x

By:

Wang, Chen;
Lin, Haifan

Publication type:

Article

Evolution of regulatory networks associated with traits under selection in cichlids.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02208-8

By:

Mehta, Tarang K.;
Koch, Christopher;
Nash, Will;
Knaack, Sara A.;
Sudhakar, Padhmanand;
Olbei, Marton;
Bastkowski, Sarah;
Penso-Dolfin, Luca;
Korcsmaros, Tamas;
Haerty, Wilfried;
Roy, Sushmita;
Di-Palma, Federica

Publication type:

Article

Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02241-7

By:

Gao, Yubang;
Liu, Xuqing;
Wu, Bizhi;
Wang, Huihui;
Xi, Feihu;
Kohnen, Markus V.;
Reddy, Anireddy S. N.;
Gu, Lianfeng

Publication type:

Article

Reference flow: reducing reference bias using multiple population genomes.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. N.PAG, doi. 10.1186/s13059-020-02229-3

By:

Chen, Nae-Chyun;
Solomon, Brad;
Mun, Taher;
Iyer, Sheila;
Langmead, Ben

Publication type:

Article

HiDeF: identifying persistent structures in multiscale 'omics data.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02228-4

By:

Zheng, Fan;
Zhang, She;
Churas, Christopher;
Pratt, Dexter;
Bahar, Ivet;
Ideker, Trey

Publication type:

Article

An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02218-6

By:

Srivastava, Divyanshi;
Aydin, Begüm;
Mazzoni, Esteban O.;
Mahony, Shaun

Publication type:

Article

An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02213-x

By:

Ghaffari, Saba;
Hanson, Casey;
Schmidt, Remington E.;
Bouchonville, Kelly J.;
Offer, Steven M.;
Sinha, Saurabh

Publication type:

Article

Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02256-0

By:

Zhao, Taolan;
Chen, Yan-Ming;
Li, Yu;
Wang, Jia;
Chen, Siyu;
Gao, Ning;
Qian, Wenfeng

Publication type:

Article

Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02251-5

By:

Medina-Muñoz, Santiago Gerardo;
Kushawah, Gopal;
Castellano, Luciana Andrea;
Diez, Michay;
DeVore, Michelle Lynn;
Salazar, María José Blanco;
Bazzini, Ariel Alejandro

Publication type:

Article

N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer's disease.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02249-z

By:

Shafik, Andrew M.;
Zhang, Feiran;
Guo, Zhenxing;
Dai, Qing;
Pajdzik, Kinga;
Li, Yangping;
Kang, Yunhee;
Yao, Bing;
Wu, Hao;
He, Chuan;
Allen, Emily G.;
Duan, Ranhui;
Jin, Peng

Publication type:

Article

Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02242-6

By:

Yang, Xiaoyu;
You, Chenjiang;
Wang, Xufeng;
Gao, Lei;
Mo, Beixin;
Liu, Lin;
Chen, Xuemei

Publication type:

Article

Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02239-1

By:

Guan, Jiantao;
Xu, Yaoguang;
Yu, Yang;
Fu, Jun;
Ren, Fei;
Guo, Jiying;
Zhao, Jianbo;
Jiang, Quan;
Wei, Jianhua;
Xie, Hua

Publication type:

Article

Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02223-9

By:

Planterose Jiménez, Benjamin;
Liu, Fan;
Caliebe, Amke;
Montiel González, Diego;
Bell, Jordana T.;
Kayser, Manfred;
Vidaki, Athina

Publication type:

Article

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02240-8

By:

Oka, Miho;
Xu, Liu;
Suzuki, Toshihiro;
Yoshikawa, Toshiaki;
Sakamoto, Hiromi;
Uemura, Hayato;
Yoshizawa, Akiyasu C.;
Suzuki, Yutaka;
Nakatsura, Tetsuya;
Ishihama, Yasushi;
Suzuki, Ayako;
Seki, Masahide

Publication type:

Article

scMC learns biological variation through the alignment of multiple single-cell genomics datasets.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02238-2

By:

Zhang, Lihua;
Nie, Qing

Publication type:

Article

In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02236-4

By:

Liu, Zhenshan;
Liu, Qi;
Yang, Xiaofei;
Zhang, Yueying;
Norris, Matthew;
Chen, Xiaoxi;
Cheema, Jitender;
Zhang, Huakun;
Ding, Yiliang

Publication type:

Article

Compacting a synthetic yeast chromosome arm.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02232-8

By:

Luo, Zhouqing;
Yu, Kang;
Xie, Shangqian;
Monti, Marco;
Schindler, Daniel;
Fang, Yuan;
Zhao, Shijun;
Liang, Zhenzhen;
Jiang, Shuangying;
Luan, Meiwei;
Xiao, Chuanle;
Cai, Yizhi;
Dai, Junbiao

Publication type:

Article

SpRY greatly expands the genome editing scope in rice with highly flexible PAM recognition.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02231-9

By:

Xu, Ziyan;
Kuang, Yongjie;
Ren, Bin;
Yan, Daqi;
Yan, Fang;
Spetz, Carl;
Sun, Wenxian;
Wang, Guirong;
Zhou, Xueping;
Zhou, Huanbin

Publication type:

Article

Comprehensive integrative profiling of upper tract urothelial carcinomas.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02230-w

By:

Su, Xiaoping;
Lu, Xiaofan;
Bazai, Sehrish Khan;
Compérat, Eva;
Mouawad, Roger;
Yao, Hui;
Rouprêt, Morgan;
Spano, Jean-Philippe;
Khayat, David;
Davidson, Irwin;
Tannir, Nizar N.;
Yan, Fangrong;
Malouf, Gabriel G.

Publication type:

Article

Reference flow: reducing reference bias using multiple population genomes.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02229-3

By:

Chen, Nae-Chyun;
Solomon, Brad;
Mun, Taher;
Iyer, Sheila;
Langmead, Ben

Publication type:

Article

Mentorship is not co-authorship: a revisit to mentorship.

Published in:

2021

By:

Garmire, Lana X.

Publication type:

Editorial

How the pan-genome is changing crop genomics and improvement.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02224-8

By:

Della Coletta, Rafael;
Qiu, Yinjie;
Ou, Shujun;
Hufford, Matthew B.;
Hirsch, Candice N.

Publication type:

Article

Integrated genomic and transcriptomic analysis reveals unique characteristics of hepatic metastases and pro-metastatic role of complement C1q in pancreatic ductal adenocarcinoma.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02222-w

By:

Yang, Jianyu;
Lin, Ping;
Yang, Minwei;
Liu, Wei;
Fu, Xueliang;
Liu, Dejun;
Tao, Lingye;
Huo, Yanmiao;
Zhang, Junfeng;
Hua, Rong;
Zhang, Zhigang;
Li, Yixue;
Wang, Liwei;
Xue, Jing;
Li, Hong;
Sun, Yongwei

Publication type:

Article

Histone modifications during the life cycle of the brown alga Ectocarpus.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02216-8

By:

Bourdareau, Simon;
Tirichine, Leila;
Lombard, Bérangère;
Loew, Damarys;
Scornet, Delphine;
Wu, Yue;
Coelho, Susana M.;
Cock, J. Mark

Publication type:

Article

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02207-9

By:

Cousminer, Diana L.;
Wagley, Yadav;
Pippin, James A.;
Elhakeem, Ahmed;
Way, Gregory P.;
Pahl, Matthew C.;
McCormack, Shana E.;
Chesi, Alessandra;
Mitchell, Jonathan A.;
Kindler, Joseph M.;
Baird, Denis;
Hartley, April;
Howe, Laura;
Kalkwarf, Heidi J.;
Lappe, Joan M.;
Lu, Sumei;
Leonard, Michelle E.;
Johnson, Matthew E.;
Hakonarson, Hakon;
Gilsanz, Vicente

Publication type:

Article

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