Works in BMC Genomics, 2016, Vol 17

Results: 1045

Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2815-y

By:

Troell, Karin;
Hallström, Björn;
Divne, Anna-Maria;
Alsmark, Cecilia;
Arrighi, Romanico;
Huss, Mikael;
Beser, Jessica;
Bertilsson, Stefan

Publication type:

Article

Negative selection maintains transcription factor binding motifs in human cancer.

Published in:

BMC Genomics, 2016, v. 17, p. 263, doi. 10.1186/s12864-016-2728-9

By:

Vorontsov, Ilya E.;
Khimulya, Grigory;
Lukianova, Elena N.;
Nikolaeva, Daria D.;
Eliseeva, Irina A.;
Kulakovskiy, Ivan V.;
Makeev, Vsevolod J.

Publication type:

Article

Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types.

Published in:

BMC Genomics, 2016, v. 17, p. 249, doi. 10.1186/s12864-016-2727-x

By:

Tenghui Chen;
Zixing Wang;
Wanding Zhou;
Zechen Chong;
Meric-Bernstam, Funda;
Mills, Gordon B.;
Ken Chen

Publication type:

Article

Large scale analysis of protein stability in OMIM disease related human protein variants.

Published in:

BMC Genomics, 2016, v. 17, p. 239, doi. 10.1186/s12864-016-2726-y

By:

Martelli, Pier Luigi;
Fariselli, Piero;
Savojardo, Castrense;
Babbi, Giulia;
Aggazio, Francesco;
Casadio, Rita

Publication type:

Article

A loss of function variant in CASP7 protects against Alzheimer's disease in homozygous APOE ε4 allele carriers.

Published in:

BMC Genomics, 2016, v. 17, p. 229, doi. 10.1186/s12864-016-2725-z

By:

Ayers, Kristin L.;
Mirshahi, Uyenlinh L.;
Wardeh, Amr H.;
Murray, Michael F.;
Ke Hao;
Glicksberg, Benjamin S.;
Shuyu Li;
Carey, David J.;
Rong Chen

Publication type:

Article

Establishing and validating regulatory regions for variant annotation and expression analysis.

Published in:

BMC Genomics, 2016, v. 17, p. 219, doi. 10.1186/s12864-016-2724-0

By:

Kaplun, Alexander;
Krull, Mathias;
Lakshman, Karthick;
Matys, Volker;
Lewicki, Birgit;
Hogan, Jennifer D.

Publication type:

Article

KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily.

Published in:

BMC Genomics, 2016, v. 17, p. 207, doi. 10.1186/s12864-016-2723-1

By:

Pons, Tirso;
Vazquez, Miguel;
Matey-Hernandez, María Luisa;
Brunak, Søren;
Valencia, Alfonso;
Izarzugaza, Jose M. G.

Publication type:

Article

VarElect: the phenotype-based variation prioritizer of the GeneCards Suite.

Published in:

BMC Genomics, 2016, v. 17, p. 195, doi. 10.1186/s12864-016-2722-2

By:

Stelzer, Gil;
Plaschkes, Inbar;
Oz-Levi, Danit;
Alkelai, Anna;
Olender, Tsviya;
Zimmerman, Shahar;
Twik, Michal;
Belinky, Frida;
Fishilevich, Simon;
Nudel, Ron;
Guan-Golan, Yaron;
Warshawsky, David;
Dahary, Dvir;
Kohn, Asher;
Mazor, Yaron;
Kaplan, Sergey;
Stein, Tsippi Iny;
Baris, Hagit N.;
Rappaport, Noa;
Safran, Marilyn

Publication type:

Article

VarI-SIG 2015: methods for personalized medicine - the role of variant interpretation in research and diagnostics.

Published in:

2016

By:

Bromberg, Yana;
Capriotti, Emidio;
Carter, Hannah

Publication type:

Proceeding

An evaluation of processing methods for HumanMethylation450 BeadChip data.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2819-7

By:

Jie Liu;
Siegmund, Kimberly D.

Publication type:

Article

Genomic analysis of nontypeable pneumococci causing invasive pneumococcal disease in South Africa, 2003-2013.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2808-x

By:

Mohale, Thabo;
Wolter, Nicole;
Allam, Mushal;
Ndlangisa, Kedibone;
Crowther-Gibson, Penny;
du Plessis, Mignon;
von Gottberg, Anne

Publication type:

Article

Genome-wide association analyses using a Bayesian approach for litter size and piglet mortality in Danish Landrace and Yorkshire pigs.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2806-z

By:

Xiangyu Guo;
Guosheng Su;
Fredslund Christensen, Ole;
Janss, Luc;
Sandø Lund, Mogens

Publication type:

Article

EventPointer: an effective identification of alternative splicing events using junction arrays.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2816-x

By:

Romero, Juan P.;
Muniategui, Ander;
De Miguel, Fernando J.;
Aramburu, Ander;
Montuenga, Luis;
Pio, Ruben;
Rubio, Angel

Publication type:

Article

Construction of a high-density, high-quality genetic map of cultivated lotus (Nelumbo nucifera) using next-generation sequencing.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2781-4

By:

Zhengwei Liu;
Honglian Zhu;
Yuping Liu;
Jing Kuang;
Kai Zhou;
Fan Liang;
Zhenhua Liu;
Depeng Wang;
Weidong Ke

Publication type:

Article

A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2814-z

By:

Schiöth, Helgi B.;
Boström, Adrian;
Murphy, Susan K.;
Erhart, Wiebke;
Hampe, Jochen;
Moylan, Cynthia;
Mwinyi, Jessica

Publication type:

Article

RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2810-3

By:

Aifu Yang;
Zunchun Zhou;
Yongjia Pan;
Jingwei Jiang;
Ying Dong;
Xiaoyan Guan;
Hongjuan Sun;
Shan Gao;
Zhong Chen

Publication type:

Article

Genome-wide characterization of human L1 antisense promoter-driven transcripts.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2800-5

By:

Criscione, Steven W.;
Theodosakis, Nicholas;
Micevic, Goran;
Cornish, Toby C.;
Burns, Kathleen H.;
Neretti, Nicola;
Rodić, Nemanja

Publication type:

Article

Comparative analysis of the GBLUP, emBayesB, and GWAS algorithms to predict genetic values in large yellow croaker (Larimichthys crocea).

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2756-5

By:

Linsong Dong;
Shijun Xiao;
Qiurong Wang;
Zhiyong Wang

Publication type:

Article

High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq).

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2669-3

By:

Preston, Jessica L.;
Royall, Ariel E.;
Randel, Melissa A.;
Sikkink, Kristin L.;
Phillips, Patrick C.;
Johnson, Eric A.

Publication type:

Article

Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2643-0

By:

Forde, Taya;
Biek, Roman;
Zadoks, Ruth;
Workentine, Matthew L.;
De Buck, Jeroen;
Kutz, Susan;
Opriessnig, Tanja;
Trewby, Hannah;
van der Meer, Frank;
Orsel, Karin

Publication type:

Article

Outlier analysis of functional genomic profiles enriches for oncology targets and enables precision medicine.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2807-y

By:

Zhou Zhu;
Ihle, Nathan T.;
Rejto, Paul A.;
Zarrinkar, Patrick P.

Publication type:

Article

Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2804-1

By:

Balasubramanian, Mukundh N.;
Panserat, Stephane;
Dupont-Nivet, Mathilde;
Quillet, Edwige;
Montfort, Jerome;
Le Cam, Aurelie;
Medale, Francoise;
Kaushik, Sadasivam J.;
Geurden, Inge

Publication type:

Article

Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2803-2

By:

Hoffmann, Robert D.;
Palmgren, Michael

Publication type:

Article

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2802-3

By:

Covarrubias-Pazaran, Giovanny;
Diaz-Garcia, Luis;
Schlautman, Brandon;
Deutsch, Joseph;
Salazar, Walter;
Hernandez-Ochoa, Miguel;
Grygleski, Edward;
Steffan, Shawn;
Iorizzo, Massimo;
Polashock, James;
Vorsa, Nicholi;
Zalapa, Juan

Publication type:

Article

RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2801-4

By:

Corley, Susan M.;
Canales, Cesar P.;
Carmona-Mora, Paulina;
Mendoza-Reinosa, Veronica;
Beverdam, Annemiek;
Hardeman, Edna C.;
Wilkins, Marc R.;
Palmer, Stephen J.

Publication type:

Article

VDJviz: a versatile browser for immunogenomics data.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2799-7

By:

Bagaev, Dmitriy V.;
Zvyagin, Ivan V.;
Putintseva, Ekaterina V.;
Izraelson, Mark;
Britanova, Olga V.;
Chudakov, Dmitriy M.;
Shugay, Mikhail

Publication type:

Article

Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2757-4

By:

Aigrain, Louise;
Yong Gu;
Quail, Michael A.

Publication type:

Article

Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2752-9

By:

da Silva, Joaquim Manoel;
Giachetto, Poliana Fernanda;
Otávio da Silva, Luiz;
Carrijo Cintra, Leandro;
Rezende Paiva, Samuel;
Beleza Yamagishi, Michel Eduardo;
Rodrigues Caetano, Alexandre

Publication type:

Article

Local transmission and global dissemination of New Delhi Metallo-Beta-Lactamase (NDM): a whole genome analysis.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2740-0

By:

Wei Xin Khong;
Eryu Xia;
Marimuthu, Kalisvar;
Wenting Xu;
Yik-Ying Teo;
Eng Lee Tan;
Shiyong Neo;
Unny Krishnan, Prabha;
Ang, Brenda S. P.;
Lye, David C. B.;
Chow, Angela L. P.;
Twee-Hee Ong4, Rick;
Oon Tek Ng

Publication type:

Article

Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2738-7

By:

Brown, Nathan M.;
Mueller, Ryan S.;
Shepardson, Jonathan W.;
Landry, Zachary C.;
Morré, Jeffrey T.;
Maier, Claudia S.;
Hardy, F. Joan;
Dreher, Theo W.

Publication type:

Article

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2777-0

By:

Mihai Pop;
Paulson, Joseph N.;
Chakraborty, Subhra;
Astrovskaya, Irina;
Lindsay, Brianna R.;
Shan Li;
Corrada Bravo, Héctor;
Harro, Clayton;
Parkhill, Julian;
Walker, Alan W.;
Walker, Richard I.;
Sack, David A.;
Stine, O. Colin

Publication type:

Article

Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2774-3

By:

Deakin, Janine E.;
Edwards, Melanie J.;
Patel, Hardip;
O'Meally, Denis;
Jinmin Lian;
Stenhouse, Rachael;
Ryan, Sam;
Livernois, Alexandra M.;
Azad, Bhumika;
Holleley, Clare E.;
Qiye Li;
Georges, Arthur

Publication type:

Article

Mapping the sex determination locus in the hāpuku (Polyprion oxygeneios) using ddRAD sequencing.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2773-4

By:

Brown, Jeremy K.;
Taggart, John B.;
Bekaert, Michaël;
Wehner, Stefanie;
Palaiokostas, Christos;
Setiawan, Alvin N.;
Symonds, Jane E.;
Penman, David J.

Publication type:

Article

Bivariate genome-wide association study identifies novel pleiotropic loci for lipids and inflammation.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2712-4

By:

Ligthart, Symen;
Vaez, Ahmad;
Yi-Hsiang Hsu;
Stolk, Ronald;
Uitterlinden, André G.;
Hofman, Albert;
Alizadeh, Behrooz Z.;
Franco, Oscar H.;
Dehghan, Abbas

Publication type:

Article

The stepwise evolution of the exome during acquisition of docetaxel resistance in breast cancer cells.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2749-4

By:

Hansen, Stine Ninel;
Ehlers, Natasja Spring;
Shida Zhu;
Houlberg Thomsen, Mathilde Borg;
Nielsen, Rikke Linnemann;
Dongbing Liu;
Guangbiao Wang;
Yong Hou;
Xiuqing Zhang;
Xun Xu;
Bolund, Lars;
Huanming Yang;
Jun Wang;
Moreira, Jose;
Ditzel, Henrik J.;
Brünner, Nils;
Schrohl, Anne-Sofie;
Stenvang, Jan;
Gupta, Ramneek

Publication type:

Article

Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2817-9

By:

Jisen Zhang;
Sharma, Anupma;
Qingyi Yu;
Jianping Wang;
Leiting Li;
Lin Zhu;
Xingtan Zhang;
Youqiang Chen;
Ming, Ray

Publication type:

Article

Copy number variants in the sheep genome detected using multiple approaches.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2754-7

By:

Jenkins, Gemma M.;
Goddard, Michael E.;
Black, Michael A.;
Brauning, Rudiger;
Auvray, Benoit;
Dodds, Ken G.;
Kijas, James W.;
Cockett, Noelle;
McEwan, John C.

Publication type:

Article

Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2772-5

By:

Gómez-Aix, Cristina;
Pascual, Laura;
Cañizares, Joaquín;
Sánchez-Pina, María Amelia;
Aranda, Miguel A.

Publication type:

Article

Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2637-y

By:

Yongyi Ge;
Yuchen Wang;
Yong Xiang Liu;
Yumei Tan;
Xiuxiu Ren;
Xinyu Zhang;
Hyde, Kevin D.;
Yongfeng Liu;
Zuoyi Liu

Publication type:

Article

Erratum to: Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis.

Published in:: 2016
Publication type:: Correction Notice

Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2746-7

By:

Peijie Lin;
Nicholls, Laura;
Assareh, Hassan;
Zhiming Fang;
Amos, Timothy G.;
Edwards, Richard J.;
Assareh, Amelia A.;
Voineagu, Irina

Publication type:

Article

Erratum to: Fusion transcript loci share many genomic features with non-fusion loci.

Published in:

BMC Genomics, 2016, v. 17, p. 424, doi. 10.1186/s12864-016-2751-x

By:

Lai, John;
An, Jiyuan;
Seim, Inge;
Walpole, Carina;
Hoffman, Andrea;
Moya, Leire;
Srinivasan, Srilakshmi;
Perry-Keene, Joanna L.;
Chenwei Wang;
Lehman, Melanie L.;
Nelson, Colleen C.;
Clements, Judith A.;
Batra, Jyotsna

Publication type:

Article

RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2686-2

By:

Catanese, Helen N.;
Brayton, Kelly A.;
Gebremedhin, Assefaw H.

Publication type:

Article

Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum).

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2591-8

By:

Hai-Yang Cheng;
Yan Wang;
Xiang Tao;
Yan-Fen Fan;
Ya Dai;
Hong Yang;
Xin-Rong Ma

Publication type:

Article

Erratum to: 'Ultra-precise detection of mutations by droplet-based amplification of circularized DNA'.

Published in:: 2016
Publication type:: Correction Notice

Genomic Clustering of differential DNA methylated regions (epimutations) associated with the epigenetic transgenerational inheritance of disease and phenotypic variation.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2748-5

By:

Haque, M. Muksitul;
Nilsson, Eric E.;
Holder, Lawrence B.;
Skinner, Michael K.

Publication type:

Article

Genomic survey sequencing for development and validation of single-locus SSR markers in peanut (Arachis hypogaea L.).

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2743-x

By:

Xiaojing Zhou;
Yang Dong;
Jiaojiao Zhao;
Li Huang;
Xiaoping Ren;
Yuning Chen;
Shunmou Huang;
Boshou Liao;
Yong Lei;
Liying Yan;
Huifang Jiang

Publication type:

Article

Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2747-6

By:

Grolmusz, Vince Kornél;
Tóth, Eszter Angéla;
Baghy, Kornélia;
Likó, István;
Darvasi, Ottó;
Kovalszky, Ilona;
Matkó, János;
Rácz, Károly;
Patócs, Attila

Publication type:

Article

Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2461-4

By:

Yang Zhou;
Utsunomiya, Yuri T.;
Lingyang Xu;
El Hamidi abdel Hay;
Bickhart, Derek M.;
Alexandre, Pamela Almeida;
Rosen, Benjamin D.;
Schroeder, Steven G.;
Carvalheiro, Roberto;
de Rezende Neves, Haroldo Henrique;
Sonstegard, Tad S.;
Van Tassell, Curtis P.;
Ferraz, José Bento Sterman;
Fukumasu, Heidge;
Garcia, Jose Fernando;
Liu, George E.

Publication type:

Article

Combined physiological, transcriptome, and cis-regulatory element analyses indicate that key aspects of ripening, metabolism, and transcriptional program in grapes (Vitis vinifera L.) are differentially modulated accordingly to fruit size.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2660-z

By:

Wong, D. C. J.;
Lopez Gutierrez, R.;
Dimopoulos, N.;
Gambetta, G. A.;
Castellarin, S. D.

Publication type:

Article