Works matching IS 14747596 AND DT 2019 AND VI 20 AND IP 1

Results: 300

RADAR: differential analysis of MeRIP-seq data with a random effect model.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1915-9

By:

Zhang, Zijie;
Zhan, Qi;
Eckert, Mark;
Zhu, Allen;
Chryplewicz, Agnieszka;
De Jesus, Dario F.;
Ren, Decheng;
Kulkarni, Rohit N.;
Lengyel, Ernst;
He, Chuan;
Chen, Mengjie

Publication type:

Article

mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1901-2

By:

Waldron, Joseph A.;
Tack, David C.;
Ritchey, Laura E.;
Gillen, Sarah L.;
Wilczynska, Ania;
Turro, Ernest;
Bevilacqua, Philip C.;
Assmann, Sarah M.;
Bushell, Martin;
Le Quesne, John

Publication type:

Article

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1923-9

By:

Manara, Serena;
Asnicar, Francesco;
Beghini, Francesco;
Bazzani, Davide;
Cumbo, Fabio;
Zolfo, Moreno;
Nigro, Eleonora;
Karcher, Nicolai;
Manghi, Paolo;
Metzger, Marisa Isabell;
Pasolli, Edoardo;
Segata, Nicola

Publication type:

Article

The somatic mutation landscape of the human body.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1919-5

By:

García-Nieto, Pablo E.;
Morrison, Ashby J.;
Fraser, Hunter B.

Publication type:

Article

A comparison framework and guideline of clustering methods for mass cytometry data.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1917-7

By:

Liu, Xiao;
Song, Weichen;
Wong, Brandon Y.;
Zhang, Ting;
Yu, Shunying;
Lin, Guan Ning;
Ding, Xianting

Publication type:

Article

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1874-1

By:

Hafemeister, Christoph;
Satija, Rahul

Publication type:

Article

tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1871-4

By:

Liao, Tianhua;
Wei, Yuchen;
Luo, Mingjing;
Zhao, Guo-Ping;
Zhou, Haokui

Publication type:

Article

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1861-6

By:

Townes, F. William;
Hicks, Stephanie C.;
Aryee, Martin J.;
Irizarry, Rafael A.

Publication type:

Article

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1880-3

By:

Fang, Jingwen;
Ma, Qing;
Chu, Ci;
Huang, Beibei;
Li, Lingjie;
Cai, Pengfei;
Batista, Pedro J.;
Tolentino, Karen Erisse Martin;
Xu, Jin;
Li, Rui;
Du, Pengcheng;
Qu, Kun;
Chang, Howard Y.

Publication type:

Article

Paragraph: a graph-based structural variant genotyper for short-read sequence data.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1909-7

By:

Chen, Sai;
Krusche, Peter;
Dolzhenko, Egor;
Sherman, Rachel M.;
Petrovski, Roman;
Schlesinger, Felix;
Kirsche, Melanie;
Bentley, David R.;
Schatz, Michael C.;
Sedlazeck, Fritz J.;
Eberle, Michael A.

Publication type:

Article

What is the question?

Published in:

2019

By:

Yanai, Itai;
Lercher, Martin

Publication type:

Editorial

Genotype-free demultiplexing of pooled single-cell RNA-seq.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1852-7

By:

Xu, Jun;
Falconer, Caitlin;
Nguyen, Quan;
Crawford, Joanna;
McKinnon, Brett D.;
Mortlock, Sally;
Senabouth, Anne;
Andersen, Stacey;
Chiu, Han Sheng;
Jiang, Longda;
Palpant, Nathan J.;
Yang, Jian;
Mueller, Michael D.;
Hewitt, Alex W.;
Pébay, Alice;
Montgomery, Grant W.;
Powell, Joseph E.;
Coin, Lachlan J.M

Publication type:

Article

Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1914-x

By:

Pightling, Arthur W.;
Pettengill, James B.;
Wang, Yu;
Rand, Hugh;
Strain, Errol

Publication type:

Article

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1899-5

By:

Monat, Cécile;
Padmarasu, Sudharsan;
Lux, Thomas;
Wicker, Thomas;
Gundlach, Heidrun;
Himmelbach, Axel;
Ens, Jennifer;
Li, Chengdao;
Muehlbauer, Gary J.;
Schulman, Alan H.;
Waugh, Robbie;
Braumann, Ilka;
Pozniak, Curtis;
Scholz, Uwe;
Mayer, Klaus F. X.;
Spannagl, Manuel;
Stein, Nils;
Mascher, Martin

Publication type:

Article

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1892-z

By:

Franco, Irene;
Helgadottir, Hafdis T.;
Moggio, Aldo;
Larsson, Malin;
Vrtačnik, Peter;
Johansson, Anna;
Norgren, Nina;
Lundin, Pär;
Mas-Ponte, David;
Nordström, Johan;
Lundgren, Torbjörn;
Stenvinkel, Peter;
Wennberg, Lars;
Supek, Fran;
Eriksson, Maria

Publication type:

Article

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1883-0

By:

Tung, Laura H.;
Shao, Mingfu;
Kingsford, Carl

Publication type:

Article

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1893-y

By:

An, Lin;
Yang, Tao;
Yang, Jiahao;
Nuebler, Johannes;
Xiang, Guanjue;
Hardison, Ross C.;
Li, Qunhua;
Zhang, Yu

Publication type:

Article

Systematic underestimation of the epigenetic clock and age acceleration in older subjects.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1810-4

By:

El Khoury, Louis Y.;
Gorrie-Stone, Tyler;
Smart, Melissa;
Hughes, Amanda;
Bao, Yanchun;
Andrayas, Alexandria;
Burrage, Joe;
Hannon, Eilis;
Kumari, Meena;
Mill, Jonathan;
Schalkwyk, Leonard C.

Publication type:

Article

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1911-0

By:

Goel, Manish;
Sun, Hequan;
Jiao, Wen-Biao;
Schneeberger, Korbinian

Publication type:

Article

Transcriptome assembly from long-read RNA-seq alignments with StringTie2.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1910-1

By:

Kovaka, Sam;
Zimin, Aleksey V.;
Pertea, Geo M.;
Razaghi, Roham;
Salzberg, Steven L.;
Pertea, Mihaela

Publication type:

Article

Curing hemophilia A by NHEJ-mediated ectopic F8 insertion in the mouse.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1907-9

By:

Zhang, Jian-Ping;
Cheng, Xin-Xin;
Zhao, Mei;
Li, Guo-Hua;
Xu, Jing;
Zhang, Feng;
Yin, Meng-Di;
Meng, Fei-Ying;
Dai, Xin-Yue;
Fu, Ya-Wen;
Yang, Zhi-Xue;
Arakaki, Cameron;
Su, Ruijun Jeanna;
Wen, Wei;
Wang, Wen-Tian;
Chen, Wanqiu;
Choi, Hannah;
Wang, Charles;
Gao, Guangping;
Zhang, Lei

Publication type:

Article

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1905-y

By:

Ou, Shujun;
Su, Weija;
Liao, Yi;
Chougule, Kapeel;
Agda, Jireh R. A.;
Hellinga, Adam J.;
Lugo, Carlos Santiago Blanco;
Elliott, Tyler A.;
Ware, Doreen;
Peterson, Thomas;
Jiang, Ning;
Hirsch, Candice N.;
Hufford, Matthew B.

Publication type:

Article

HOPS: automated detection and authentication of pathogen DNA in archaeological remains.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1903-0

By:

Hübler, Ron;
Key, Felix M.;
Warinner, Christina;
Bos, Kirsten I.;
Krause, Johannes;
Herbig, Alexander

Publication type:

Article

PASTMUS: mapping functional elements at single amino acid resolution in human cells.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1897-7

By:

Zhang, Xinyi;
Yue, Di;
Wang, Yinan;
Zhou, Yuexin;
Liu, Ying;
Qiu, Yeting;
Tian, Feng;
Yu, Ying;
Zhou, Zhuo;
Wei, Wensheng

Publication type:

Article

deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1895-9

By:

Liu, Bo;
Liu, Yadong;
Li, Junyi;
Guo, Hongzhe;
Zang, Tianyi;
Wang, Yadong

Publication type:

Article

Guidelines for benchmarking of optimization-based approaches for fitting mathematical models.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1887-9

By:

Kreutz, Clemens

Publication type:

Article

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1865-2

By:

Huang, Yuanhua;
McCarthy, Davis J.;
Stegle, Oliver

Publication type:

Article

CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1896-8

By:

Llères, David;
Moindrot, Benoît;
Pathak, Rakesh;
Piras, Vincent;
Matelot, Mélody;
Pignard, Benoît;
Marchand, Alice;
Poncelet, Mallory;
Perrin, Aurélien;
Tellier, Virgile;
Feil, Robert;
Noordermeer, Daan

Publication type:

Article

From Hawaii to PECASE award: tips of success from a female bioinformatician.

Published in:

2019

By:

Garmire, Lana X.

Publication type:

Editorial

scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1862-5

By:

Alquicira-Hernandez, Jose;
Sathe, Anuja;
Ji, Hanlee P.;
Nguyen, Quan;
Powell, Joseph E.

Publication type:

Article

Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1898-6

By:

Sun, Shiquan;
Zhu, Jiaqiang;
Ma, Ying;
Zhou, Xiang

Publication type:

Article

The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1890-1

By:

Vasquez-Rifo, Alejandro;
Veksler-Lublinsky, Isana;
Cheng, Zhenyu;
Ausubel, Frederick M.;
Ambros, Victor

Publication type:

Article

The majority of A-to-I RNA editing is not required for mammalian homeostasis.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1873-2

By:

Chalk, Alistair M.;
Taylor, Scott;
Heraud-Farlow, Jacki E.;
Walkley, Carl R.

Publication type:

Article

Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1889-7

By:

Fan, Huizhong;
Wu, Qi;
Wei, Fuwen;
Yang, Fengtang;
Ng, Bee Ling;
Hu, Yibo

Publication type:

Article

Dashing: fast and accurate genomic distances with HyperLogLog.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1875-0

By:

Baker, Daniel N.;
Langmead, Ben

Publication type:

Article

Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1872-3

By:

Tang, Kujin;
Ren, Jie;
Sun, Fengzhu

Publication type:

Article

CRISPR-Cas13d mediates robust RNA virus interference in plants.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1881-2

By:

Mahas, Ahmed;
Aman, Rashid;
Mahfouz, Magdy

Publication type:

Article

eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5′UTR.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1857-2

By:

Wilczynska, Ania;
Gillen, Sarah L.;
Schmidt, Tobias;
Meijer, Hedda A.;
Jukes-Jones, Rebekah;
Langlais, Claudia;
Kopra, Kari;
Lu, Wei-Ting;
Godfrey, Jack D.;
Hawley, Benjamin R.;
Hodge, Kelly;
Zanivan, Sara;
Cain, Kelvin;
Le Quesne, John;
Bushell, Martin

Publication type:

Article

Common DNA sequence variation influences 3-dimensional conformation of the human genome.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1855-4

By:

Gorkin, David U.;
Qiu, Yunjiang;
Hu, Ming;
Fletez-Brant, Kipper;
Liu, Tristin;
Schmitt, Anthony D.;
Noor, Amina;
Chiou, Joshua;
Gaulton, Kyle J.;
Sebat, Jonathan;
Li, Yun;
Hansen, Kasper D.;
Ren, Bing

Publication type:

Article

ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1884-z

By:

Ruiz-Reche, Angel;
Srivastava, Akanksha;
Indi, Joel A.;
de la Rubia, Ivan;
Eyras, Eduardo

Publication type:

Article

methylCC: technology-independent estimation of cell type composition using differentially methylated regions.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1827-8

By:

Hicks, Stephanie C.;
Irizarry, Rafael A.

Publication type:

Article

Improved metagenomic analysis with Kraken 2.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1891-0

By:

Wood, Derrick E.;
Lu, Jennifer;
Langmead, Ben

Publication type:

Article

The Aquilegia genome reveals a hybrid origin of core eudicots.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1888-8

By:

Aköz, Gökçe;
Nordborg, Magnus

Publication type:

Article

547 transcriptomes from 44 brain areas reveal features of the aging brain in non-human primates.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1866-1

By:

Li, Ming-Li;
Wu, Shi-Hao;
Zhang, Jin-Jin;
Tian, Hang-Yu;
Shao, Yong;
Wang, Zheng-Bo;
Irwin, David M.;
Li, Jia-Li;
Hu, Xin-Tian;
Wu, Dong-Dong

Publication type:

Article

Characterizing the interplay between gene nucleotide composition bias and splicing.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1869-y

By:

Lemaire, Sébastien;
Fontrodona, Nicolas;
Aubé, Fabien;
Claude, Jean-Baptiste;
Polvèche, Hélène;
Modolo, Laurent;
Bourgeois, Cyril F.;
Mortreux, Franck;
Auboeuf, Didier

Publication type:

Article

RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1847-4

By:

Lin, Hai;
Hargreaves, Katherine A.;
Li, Rudong;
Reiter, Jill L.;
Wang, Yue;
Mort, Matthew;
Cooper, David N.;
Zhou, Yaoqi;
Zhang, Chi;
Eadon, Michael T.;
Dolan, M. Eileen;
Ipe, Joseph;
Skaar, Todd C.;
Liu, Yunlong

Publication type:

Article

Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1848-3

By:

Sa, Jason K.;
Hwang, Jae Ryoung;
Cho, Young-Jae;
Ryu, Ji-Yoon;
Choi, Jung-Joo;
Jeong, Soo Young;
Kim, Jihye;
Kim, Myeong Seon;
Paik, E. Sun;
Lee, Yoo-Young;
Choi, Chel Hun;
Kim, Tae-Joong;
Kim, Byoung-Gie;
Bae, Duk-Soo;
Lee, Yeri;
Her, Nam-Gu;
Shin, Yong Jae;
Cho, Hee Jin;
Kim, Ja Yeon;
Seo, Yun Jee

Publication type:

Article

Gut-derived Enterococcus faecium from ulcerative colitis patients promotes colitis in a genetically susceptible mouse host.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1879-9

By:

Seishima, Jun;
Iida, Noriho;
Kitamura, Kazuya;
Yutani, Masahiro;
Wang, Ziyu;
Seki, Akihiro;
Yamashita, Taro;
Sakai, Yoshio;
Honda, Masao;
Yamashita, Tatsuya;
Kagaya, Takashi;
Shirota, Yukihiro;
Fujinaga, Yukako;
Mizukoshi, Eishiro;
Kaneko, Shuichi

Publication type:

Article

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1868-z

By:

Kim, Minji;
Zheng, Meizhen;
Tian, Simon Zhongyuan;
Lee, Byoungkoo;
Chuang, Jeffrey H.;
Ruan, Yijun

Publication type:

Article

Crowdfunding science.

Published in:

2019

By:

Wilson, Melissa A.

Publication type:

Editorial