Works in BMC Genomics, 2016, Vol 17

Results: 1045

A de novo transcriptome analysis shows that modulation of the JAK-STAT signaling pathway by salmonid alphavirus subtype 3 favors virus replication in macrophage/dendritic-like TO-cells.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2739-6

By:

Cheng Xu;
Evensen, Øystein;
Mweemba Munang'andu, Hetron

Publication type:

Article

RNA-seq analysis of virR and revR mutants of Clostridium perfringens.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2706-2

By:

Lee-Yean Low;
Harrison, Paul F.;
Ya-Hsun Lin;
Boyce, John D.;
Rood, Julian I.;
Cheung, Jackie K.

Publication type:

Article

De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2633-2

By:

Shanshan Nie;
Chao Li;
Liang Xu;
Yan Wang;
Danqiong Huang;
Muleke, Everlyne M.;
Xiaochuan Sun;
Yang Xie;
Liwang Liu

Publication type:

Article

A systematic, large-scale comparison of transcription factor binding site models.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2729-8

By:

Hombach, Daniela;
Schwarz, Jana Marie;
Robinson, Peter N.;
Schuelke, Markus;
Seelow, Dominik

Publication type:

Article

Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2716-0

By:

Yadong Huang;
Lin Li;
Smith, Kevin P.;
Muehlbauer, Gary J.

Publication type:

Article

Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2735-x

By:

De Maayer, Pieter;
Cowan, Don A.

Publication type:

Article

Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae).

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2732-0

By:

Yan Luo;
Jin-Yong Hu;
Lu Li;
Yin-Ling Luo;
Peng-Fei Wang;
Bao-Hua Song

Publication type:

Article

Identification and functional characterization of the sulfate transporter gene GmSULTR1;2b in soybean.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2705-3

By:

Yiqiong Ding;
Xiaoqiong Zhou;
Li Zuo;
Hui Wang;
Deyue Yu

Publication type:

Article

Genome-wide characterization of soybean P1B-ATPases gene family provides functional implications in cadmium responses.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2730-2

By:

Xiaolong Fang;
Lei Wang;
Xiaojuan Deng;
Peng Wang;
Qibin Ma;
Hai Nian;
Yingxiang Wang;
Cunyi Yang

Publication type:

Article

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2720-4

By:

Wilkinson, Jamie M.;
Bao, Hua;
Ladinig, Andrea;
Hong, Linjun;
Stothard, Paul;
Lunney, Joan K.;
Plastow, Graham S.;
Harding, John C. S.

Publication type:

Article

Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2717-z

By:

Kasuga, Takao;
Bui, Mai;
Bernhardt, Elizabeth;
Swiecki, Tedmund;
Aram, Kamyar;
Cano, Liliana M.;
Webber, Joan;
Brasier, Clive;
Press, Caroline;
Grünwald, Niklaus J.;
Rizzo, David M.;
Garbelotto, Matteo

Publication type:

Article

The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2707-1

By:

Wysocki, William P.;
Ruiz-Sanchez, Eduardo;
Yin, Yanbin;
Duvall, Melvin R.

Publication type:

Article

Genome-wide alteration of 5- hydroxymenthylcytosine in a mouse model of Alzheimer's disease.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2731-1

By:

Liqi Shu;
Wenjia Sun;
Liping Li;
Zihui Xu;
Li Lin;
Pei Xie;
Hui Shen;
Luoxiu Huang;
Qi Xu;
Peng Jin;
Xuekun Li

Publication type:

Article

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2704-4

By:

Voutsina, Nikol;
Payne, Adrienne C.;
Hancock, Robert D.;
Clarkson, Graham J. J.;
Rothwell, Steve D.;
Chapman, Mark A.;
Taylor, Gail

Publication type:

Article

Genome-wide patterns of copy number variation in the Chinese yak genome.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2702-6

By:

Xiao Zhang;
Kun Wang;
Lizhong Wang;
Yongzhi Yang;
Zhengqiang Ni;
Xiuyue Xie;
Xuemin Shao;
Jin Han;
Dongshi Wan;
Qiang Qiu

Publication type:

Article

Inference of kinship using spatial distributions of SNPs for genome-wide association studies.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2696-0

By:

Hyokyeong Lee;
Liang Chen

Publication type:

Article

ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2687-1

By:

Lang, Kathrin;
Wagner, Ines;
Schöne, Bianca;
Birkner, Kerstin;
Hofmann, Jan A.;
Sauter, Jürgen;
Pingel, Julia;
Böhme, Irina;
Schmidt, Alexander H.;
Lange, Vinzenz

Publication type:

Article

Transcriptome analysis revealed the drought-responsive genes in Tibetan hulless barley.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2685-3

By:

Xingquan Zeng;
Lijun Bai;
Zexiu Wei;
Hongjun Yuan;
Yulin Wang;
Qijun Xu;
Yawei Tang;
Tashi Nyima

Publication type:

Article

The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2684-4

By:

Dobon, Albor;
Bunting, Daniel C. E.;
Cabrera-Quio, Luis Enrique;
Uauy, Cristobal;
Saunders, Diane G. O.

Publication type:

Article

In vitro infectivity and differential gene expression of Leishmania infantum metacyclic promastigotes: negative selection with peanut agglutinin in culture versus isolation from the stomodeal valve of Phlebotomus perniciosus.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2672-8

By:

Alcolea, Pedro J.;
Alonso, Ana;
Degayón, María A.;
Moreno-Paz, Mercedes;
Jiménez, Maribel;
Larraga, Vicente;
Molina, Ricardo

Publication type:

Article

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2709-z

By:

Pasquier, Jeremy;
Cabau, Cédric;
Nguyen, Thaovi;
Jouanno, Elodie;
Severac, Dany;
Braasch, Ingo;
Journot, Laurent;
Pontarotti, Pierre;
Klopp, Christophe;
Postlethwait, John H.;
Guiguen, Yann;
Bobe, Julien

Publication type:

Article

Seasonal immunoregulation in a naturallyoccurring vertebrate.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2701-7

By:

Brown, Martha;
Hablützel, Pascal;
Friberg, Ida M.;
Thomason, Anna G.;
Stewart, Alexander;
Pachebat, Justin A.;
Jackson, Joseph A.

Publication type:

Article

Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2690-6

By:

Kentaro Yoshida;
Saunders, Diane G. O.;
Chikako Mitsuoka;
Satoshi Natsume;
Shunichi Kosugi;
Hiromasa Saitoh;
Yoshihiro Inoue;
Izumi Chuma;
Yukio Tosa;
Cano, Liliana M.;
Kamoun, Sophien;
Ryohei Terauchi

Publication type:

Article

Bone-associated gene evolution and the origin of flight in birds.

Published in:

BMC Genomics, 2016, v. 17, p. 2, doi. 10.1186/s12864-016-2681-7

By:

Machado, João Paulo;
Johnson, Warren E.;
Gilbert, M. Thomas P.;
Guojie Zhang;
Jarvis, Erich D.;
O'Brien, Stephen J.;
Antunes, Agostinho

Publication type:

Article

Small RNA sequencing and degradome analysis of developing fibers of short fiber mutants Ligon-lintles-1 (Li1) and -2 (Li2) revealed a role for miRNAs and their targets in cotton fiber elongation.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2715-1

By:

Naoumkina, Marina;
Thyssen, Gregory N.;
Fang, David D.;
Hinchliffe, Doug J.;
Florane, Christopher B.;
Jenkins, Johnie N.

Publication type:

Article

Molecular profile of dissociative drug ketamine in relation to its rapid antidepressant action.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2713-3

By:

Ficek, Joanna;
Zygmunt, Magdalena;
Piechota, Marcin;
Hoinkis, Dzesika;
Parkitna, Jan Rodriguez;
Przewlocki, Ryszard;
Korostynski, Michal

Publication type:

Article

Genome sequence and comparative analysis of clavicipitaceous insect-pathogenic fungus Aschersonia badia with Metarhizium spp.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2710-6

By:

Agrawal, Yamini;
Narwani, Tarun;
Subramanian, Srikrishna

Publication type:

Article

Transcriptome analysis reveals selfincompatibility in the tea plant (Camellia sinensis) might be under gametophytic control.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2703-5

By:

Cheng-Cai Zhang;
Li-Yuan Wang;
Kang Wei;
Li-Yun Wu;
Hai-Lin Li;
Fen Zhang;
Hao Cheng;
De-Jiang Ni

Publication type:

Article

Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2697-z

By:

Kneitz, Susanne;
Mishra, Rasmi R.;
Chalopin, Domitille;
Postlethwait, John;
Warren, Wesley C.;
Walter, Ronald B.;
Schartl, Manfred

Publication type:

Article

Improving microRNA target prediction with gene expression profiles.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2695-1

By:

Ovando-Vázquez, Cesaré;
Lepe-Soltero, Daniel;
Abreu-Goodger, Cei

Publication type:

Article

RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2694-2

By:

Pellegrino, Maurizio;
Sciambi, Adam;
Yates, Jamie L.;
Mast, Joshua D.;
Silver, Charles;
Eastburn, Dennis J.

Publication type:

Article

Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2693-3

By:

Fister, Andrew S.;
Mejia, Luis C.;
Yufan Zhang;
Herre, Edward Allen;
Maximova, Siela N.;
Guiltinan, Mark J.

Publication type:

Article

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2692-4

By:

Trotta, Edoardo

Publication type:

Article

Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2689-z

By:

Daisuke Hagiwara;
Hiroki Takahashi;
Yoko Kusuya;
Susumu Kawamoto;
Katsuhiko Kamei;
Tohru Gonoi

Publication type:

Article

A novel RNAseq-assisted method for MHC class I genotyping in a non-model species applied to a lethal vaccination-induced alloimmune disease.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2688-0

By:

Demasius, Wiebke;
Weikard, Rosemarie;
Hadlich, Frieder;
Buitkamp, Johannes;
Kühn, Christa

Publication type:

Article

CRISPRDetect: A flexible algorithm to define CRISPR arrays.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2627-0

By:

Biswas, Ambarish;
Staals, Raymond H. J.;
Morales, Sergio E.;
Fineran, Peter C.;
Brown, Chris M.

Publication type:

Article

Transcriptome analysis of Sporisorium scitamineum reveals critical environmental signals for fungal sexual mating and filamentous growth.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2691-5

By:

Meixin Yan;
Weijun Dai;
Enping Cai;
Yi Zhen Deng;
Changqing Chang;
Zide Jiang;
Lian-Hui Zhang

Publication type:

Article

LOGIQA: a database dedicated to long-range genome interactions quality assessment.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2642-1

By:

Mendoza-Parra, Marco-Antonio;
Blum, Matthias;
Malysheva, Valeriya;
Cholley, Pierre-Etienne;
Gronemeyer, Hinrich

Publication type:

Article

Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2662-x

By:

Xinhui Nie;
Cong Huang;
Chunyuan You;
Wu Li;
Wenxia Zhao;
Chao Shen;
Beibei Zhang;
Hantao Wang;
Zhenhua Yan;
Baoshen Dai;
Maojun Wang;
Xianlong Zhang;
Zhongxu Lin

Publication type:

Article

Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2644-z

By:

Ferrarini, Mariana G.;
Siqueira, Franciele M.;
Mucha, Scheila G.;
Palama, Tony L.;
Jobard, Élodie;
Elena-Herrmann, Bénédicte;
Vasconcelos, Ana T. R.;
Tardy, Florence;
Schrank, Irene S.;
Zaha, Arnaldo;
Sagot, Marie-France

Publication type:

Article

Mapping genetic determinants of host susceptibility to Pseudomonas aeruginosa lung infection in mice.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2676-4

By:

De Simone, Maura;
Spagnuolo, Lorenza;
Lorè, Nicola Ivan;
Cigana, Cristina;
De Fino, Ida;
Broman, Karl W.;
Iraqi, Fuad A.;
Bragonzi, Alessandra

Publication type:

Article

Transcriptome analysis of sweet orange trees infected with 'Candidatus Liberibacter asiaticus' and two strains of Citrus Tristeza Virus.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2663-9

By:

Shimin Fu;
Shao, Jonathan;
Changyong Zhou;
Hartung, John S.

Publication type:

Article

Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.).

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2650-1

By:

Yuanda Lv;
Zhikai Liang;
Min Ge;
Weicong Qi;
Tifu Zhang;
Feng Lin;
Zhaohua Peng;
Han Zhao

Publication type:

Article

Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2682-6

By:

Nettling, Martin;
Treutler, Hendrik;
Cerquides, Jesus;
Grosse, Ivo

Publication type:

Article

Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.).

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2677-3

By:

Hong Yue;
Meng Wang;
Siyan Liu;
Xianghong Du;
Weining Song;
Xiaojun Nie

Publication type:

Article

Next-generation sequencing-based detection of germline L1-mediated transductions.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2670-x

By:

Tica, Jelena;
Eunjung Lee;
Untergasser, Andreas;
Meiers, Sascha;
Garfield, David A.;
Gokcumen, Omer;
Furlong, Eileen E. M.;
Park, Peter J.;
Stütz, Adrian M.;
Korbel, Jan O.

Publication type:

Article

The Tetrahymena metallothionein gene family: twenty-one new cDNAs, molecular characterization, phylogenetic study and comparative analysis of the gene expression under different abiotic stressors.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2658-6

By:

de Francisco, Patricia;
Melgar, Laura María;
Díaz, Silvia;
Martín-González, Ana;
Gutiérrez, Juan Carlos

Publication type:

Article

Time-resolved pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2657-7

By:

Seunghwan Kim;
Yong-Joon Cho;
Eun-Sung Song;
Sang Hee Lee;
Jeong-Gu Kim;
Lin-Woo Kang

Publication type:

Article

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2648-8

By:

Rius, Nuria;
Guillén, Yolanda;
Delprat, Alejandra;
Kapusta, Aurélie;
Feschotte, Cédric;
Ruiz, Alfredo

Publication type:

Article

Erratum to: 'Reference-free inference of tumor phylogenies from single-cell sequencing data'.

Published in:

2016

By:

Subramanian, Ayshwarya;
Schwartz, Russell

Publication type:

Correction Notice