Works in BMC Genomics, 2015, Vol 16, Issue 1

Results: 1005

Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membraneassociated and secreted proteome.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1980-8

By:

Sangal, Vartul;
Blom, Jochen;
Sutcliffe, Iain C.;
von Hunolstein, Christina;
Burkovski, Andreas;
Hoskisson, Paul A.

Publication type:

Article

Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1977-3

By:

Metzger, Julia;
Karwath, Matthias;
Tonda, Raul;
Beltran, Sergi;
Águeda, Lídia;
Gut, Marta;
Gut, Ivo Glynne;
Distl, Ottmar

Publication type:

Article

Transcriptome profile of liver at different physiological stages reveals potential mode for lipid metabolism in laying hens.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1943-0

By:

Hong Li;
Taian Wang;
Chunlin Xu;
Dandan Wang;
Junxiao Ren;
Yanmin Li;
Yadong Tian;
Yanbin Wang;
Yuping Jiao;
Xiangtao Kang;
Xiaojun Liu

Publication type:

Article

A transcriptome approach towards understanding the development of ripening capacity in 'Bartlett' pears (Pyrus communis L.).

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1939-9

By:

Nham, Ngoc T.;
de Freitas, Sergio Tonetto;
Macnish, Andrew J.;
Carr, Kevin M.;
Kietikul, Trisha;
Guilatco, Angelo J.;
Cai-Zhong Jiang;
Zakharov, Florence;
Mitcham, Elizabeth J.

Publication type:

Article

A nonsensemutation in B3GALNT2 is concordant with hydrocephalus in Friesian horses.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1936-z

By:

Ducro, Bart J.;
Schurink, Anouk;
Bastiaansen, John W. M.;
Boegheim, Iris J. M.;
van Steenbeek, Frank G.;
Vos-Loohuis, Manon;
Nijman, Isaac J.;
Monroe, Glen R.;
Hellinga, Ids;
Dibbits, Bert W.;
Back, Willem;
Leegwater, Peter A. J.

Publication type:

Article

The impact of PPARα activation on whole genome gene expression in human precision cut liver slices.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1969-3

By:

Janssen, Aafke W. F.;
Betzel, Bark;
Stoopen, Geert;
Berends, Frits J.;
Janssen, Ignace M.;
Peijnenburg, Ad A.;
Kersten, Sander

Publication type:

Article

The genome of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV) reveals novel genetic connection between baculoviruses infecting moths of the Lymantriidae family.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1963-9

By:

Krejmer, Martyna;
Skrzecz, Iwona;
Wasag, Bartosz;
Szewczyk, Boguslaw;
Rabalski, Lukasz

Publication type:

Article

Capsular profiling of the Cronobacter genus and the association of specific Cronobacter sakazakii and C. malonaticus capsule types with neonatal meningitis and necrotizing enterocolitis.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1960-z

By:

Ogrodzki, P.;
Forsythe, S.

Publication type:

Article

Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1955-9

By:

Sant'Anna, F. H.;
Lebedinsky, A. V.;
Sokolova, T. G.;
Robb, F. T.;
Gonzalez, J. M.

Publication type:

Article

Transcriptomic analyses of regenerating adult feathers in chicken.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1966-6

By:

Chen Siang Ng;
Chih-Kuan Chen;
Wen-Lang Fan;
Ping Wu;
Siao-Man Wu;
Jiun-Jie Chen;
Yu-Ting Lai;
Chi-Tang Mao;
Mei-Yeh Jade Lu;
Di-Rong Chen;
Ze-Shiang Lin;
Kai-Jung Yang;
Yuan-An Sha;
Tsung-Che Tu;
Chih-Feng Chen;
Cheng-Ming Chuong;
Wen-Hsiung Li

Publication type:

Article

Development of ListeriaBase and comparative analysis of Listeria monocytogenes.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1959-5

By:

Mui Fern Tan;
Cheuk Chuen Siow;
Dutta, Avirup;
Mutha, Naresh V. R.;
Wei Yee Wee;
Heydari, Hamed;
Shi Yang Tan;
Mia Yang Ang;
Guat Jah Wong;
Siew Woh Choo

Publication type:

Article

Evolutionary divergence of core and post-translational circadian clock genes in the pitcher-plant mosquito, Wyeomyia smithii.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1937-y

By:

Tormey, Duncan;
Colbourne, John K.;
Mockaitis, Keithanne;
Jeong-Hyeon Choi;
Lopez, Jacqueline;
Burkhart, Joshua;
Bradshaw, William;
Holzapfel, Christina

Publication type:

Article

Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1935-0

By:

Aramburu, Ander;
Zudaire, Isabel;
Pajares, María J.;
Agorreta, Jackeline;
Orta, Alberto;
Lozano, María D.;
Gúrpide, Alfonso;
Gómez-Román, Javier;
Martinez-Climent, Jose A.;
Jassem, Jacek;
Skrzypski, Marcin;
Suraokar, Milind;
Behrens, Carmen;
Wistuba, Ignacio I.;
Pio, Ruben;
Rubio, Angel;
Montuenga, Luis M.

Publication type:

Article

De novo transcriptome sequencing and comprehensive analysis of the drought-responsive genes in the desert plant Cynanchum komarovii.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1873-x

By:

Xiaowen Ma;
Ping Wang;
Sihong Zhou;
Yun Sun;
Nana Liu;
Xiaoning Li;
Yuxia Hou

Publication type:

Article

Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1961-y

By:

Masood, Naqash;
Moore, Karen;
Farbos, Audrey;
Paszkiewicz, Konrad;
Dickins, Ben;
McNally, Alan;
Forsythe, Stephen

Publication type:

Article

Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1953-y

By:

Huamei Xiao;
Zhuting Yuan;
Dianhao Guo;
Bofeng Hou;
Chuanlin Yin;
Wenqing Zhang;
Fei Li

Publication type:

Article

Functional development of the adult ovine mammary gland—insights from gene expression profiling.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1947-9

By:

Paten, Amy M.;
Duncan, Elizabeth J.;
Pain, Sarah J.;
Peterson, Sam W.;
Kenyon, Paul R.;
Blair, Hugh T.;
Dearden, Peter K.

Publication type:

Article

A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1946-x

By:

Rui Sun;
Yuansheng Chang;
Fengqiu Yang;
Yi Wang;
Hui Li;
Yongbo Zhao;
Dongmei Chen;
Ting Wu;
Xinzhong Zhang;
Zhenhai Han

Publication type:

Article

Genome-wide association study dissects genetic architecture underlying longitudinal egg weights in chickens.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1945-y

By:

Guoqiang Yi;
Manman Shen;
Jingwei Yuan;
Congjiao Sun;
Zhongyi Duan;
Liang Qu;
Taocun Dou;
Meng Ma;
Jian Lu;
Jun Guo;
Sirui Chen;
Lujiang Qu;
Kehua Wang;
Ning Yang

Publication type:

Article

Identifying binary protein-protein interactions from affinity purification mass spectrometry data.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1944-z

By:

Xiao-Fei Zhang;
Le Ou-Yang;
Xiaohua Hu;
Dao-Qing Dai

Publication type:

Article

Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1942-1

By:

Staton, Margaret;
Zhebentyayeva, Tetyana;
Olukolu, Bode;
Guang Chen Fang;
Nelson, Dana;
Carlson, John E.;
Abbott, Albert G.

Publication type:

Article

Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1938-x

By:

Schachtschneider, Kyle M.;
Madsen, Ole;
Chankyu Park;
Rund, Laurie A.;
Groenen, Martien A. M.;
Schook, Lawrence B.

Publication type:

Article

Pathogen-regulated genes in wheat isogenic lines differing in resistance to brown rust Puccinia triticina.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1932-3

By:

Dmochowska-Boguta, Marta;
Alaba, Sylwia;
Yanushevska, Yuliya;
Piechota, Urszula;
Lasota, Elzbieta;
Nadolska-Orczyk, Anna;
Karlowski, Wojciech M.;
Orczyk, Waclaw

Publication type:

Article

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1924-3

By:

Borges, Rui;
Khan, Imran;
Johnson, Warren E.;
Gilbert, M. Thomas P.;
Guojie Zhang;
Jarvis, Erich D.;
O'Brien, Stephen J.;
Antunes, Agostinho

Publication type:

Article

Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1904-7

By:

Sharma, Rahul;
Xiaojuan Xia;
Cano, Liliana M.;
Evangelisti, Edouard;
Kemen, Eric;
Judelson, Howard;
Oome, Stan;
Sambles, Christine;
van den Hoogen, D. Johan;
Kitner, Miloslav;
Klein, Joël;
Meijer, Harold J. G.;
Spring, Otmar;
Win, Joe;
Zipper, Reinhard;
Bode, Helge B.;
Govers, Francine;
Kamoun, Sophien;
Schornack, Sebastian;
Studholme, David J.

Publication type:

Article

MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1835-3

By:

Calla, Bernarda;
Geib, Scott M.

Publication type:

Article

Generation of a de novo transcriptome from equine lamellar tissue.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1948-8

By:

Holl, Heather M.;
Shan Gao;
Zhangjun Fei;
Andrews, Caroline;
Brooks, Samantha A.

Publication type:

Article

Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.).

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1887-4

By:

Yuanyuan Xu;
Xiaogang Li;
Jing Lin;
Zhonghua Wang;
Qingsong Yang;
Youhong Chang

Publication type:

Article

Diverse regulatory factors associate with flowering time and yield responses in winter-type Brassica napus.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1950-1

By:

Schiessl, Sarah;
Iniguez-Luy, Federico;
Wei Qian;
Snowdon, Rod J.

Publication type:

Article

The idiopathic preterm delivery methylation profile in umbilical cord blood DNA.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1915-4

By:

Fernando, Febilla;
Keijser, Remco;
Henneman, Peter;
van der Kevie-Kersemaekers, Anne-Marie F.;
Mannens, Marcel M. A. M.;
van der Post, Joris A. M.;
Afink, Gijs B.;
Ris-Stalpers, Carrie

Publication type:

Article

Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1526-0

By:

Lichius, Alexander;
Bidard, Frédérique;
Buchholz, Franziska;
Le Crom, Stéphane;
Martin, Joel;
Schackwitz, Wendy;
Austerlitz, Tina;
Grigoriev, Igor V.;
Baker, Scott E.;
Margeot, Antoine;
Seiboth, Bernhard;
Kubicek, Christian P.

Publication type:

Article

Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1934-1

By:

Shuang Yin;
Rusconi, Brigida;
Sanjar, Fatemeh;
Goswami, Kakolie;
Lingzi Xiaoli;
Eppinger, Mark;
Dudley, Edward G.

Publication type:

Article

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1911-8

By:

Shelton, Jennifer M.;
Coleman, Michelle C.;
Herndon, Nic;
Nanyan Lu;
Lam, Ernest T.;
Anantharaman, Thomas;
Sheth, Palak;
Brown, Susan J.

Publication type:

Article

Next generation sequencing profiling identifies miR-574-3p and miR-660-5p as potential novel prognostic markers for breast cancer.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1899-0

By:

Krishnan, Preethi;
Ghosh, Sunita;
Bo Wang;
Dongping Li;
Narasimhan, Ashok;
Berendt, Richard;
Graham, Kathryn;
Mackey, John R.;
Kovalchuk, Olga;
Damaraju, Sambasivarao

Publication type:

Article

Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1919-0

By:

Nan Hu;
Chaoyu Wang;
Clifford, Robert J.;
Yang, Howard H.;
Hua Su;
Lemin Wang;
Yuan Wang;
Yi Xu;
Ze-Zhong Tang;
Ti Ding;
Tongwu Zhang;
Goldstein, Alisa M.;
Giffen, Carol;
Lee, Maxwell P.;
Philip R. Taylor

Publication type:

Article

Glutamine rapidly induces the expression of key transcription factor genes involved in nitrogen and stress responses in rice roots.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1892-7

By:

Chia-Cheng Kan;
Tsui-Yun Chung;
Yan-An Juo;
Ming-Hsiun Hsieh

Publication type:

Article

Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1877-6

By:

Yunxia Zhang;
Chunyan Cheng;
Ji Li;
Shuqiong Yang;
Yunzhu Wang;
Ziang Li;
Jinfeng Chen;
Qunfeng Lou

Publication type:

Article

Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1407-6

By:

Mikalsen, Theresa;
Pedersen, Torunn;
Willems, Rob;
Coque, Teresa M.;
Werner, Guido;
Sadowy, Ewa;
van Schaik, Willem;
Jensen, Lars Bogø;
Sundsfjord, Arnfinn;
Hegstad, Kristin

Publication type:

Article

The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1910-9

By:

Norling, Martin;
Bishop, Richard P.;
Pelle, Roger;
Weihong Qi;
Henson, Sonal;
Drábek, Elliott F.;
Tretina, Kyle;
Odongo, David;
Mwaura, Stephen;
Njoroge, Thomas;
Bongcam-Rudloff, Erik;
Daubenberger, Claudia A.;
Silva, Joana C.

Publication type:

Article

Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1931-4

By:

Yufang Guo;
Wiegert-Rininger, Krystle E.;
Vallejo, Veronica A.;
Barry, Cornelius S.;
Warner, Ryan M.

Publication type:

Article

Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1929-y

By:

Yan Guo;
Bosompem, Amma;
Mohan, Sanjay;
Erdogan, Begum;
Fei Ye;
Vickers, Kasey C.;
Quanhu Sheng;
Shilin Zhao;
Chung-I Li;
Pei-Fang Su;
Jagasia, Madan;
Strickland, Stephen A.;
Griffiths, Elizabeth A.;
Kim, Annette S.

Publication type:

Article

RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1817-5

By:

Moreira, Rebeca;
Pereiro, Patricia;
Canchaya, Carlos;
Posada, David;
Figueras, Antonio;
Novoa, Beatriz

Publication type:

Article

An improved genome reference for the African cichlid, Metriaclima zebra.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1930-5

By:

Conte, Matthew A.;
Kocher, Thomas D.

Publication type:

Article

TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1921-6

By:

Mwangi, Sarah;
Attardo, Geoffrey;
Suzuki, Yutaka;
Aksoy, Serap;
Christoffels, Alan

Publication type:

Article

Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype.

Published in:: 2015
Publication type:: Correction Notice

De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea).

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1908-3

By:

Muriira, Nkatha G.;
Wei Xu;
Muchugi, Alice;
Jianchu Xu;
Aizhong Liu

Publication type:

Article

Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1914-5

By:

Xiang Jia Min;
Powell, Brian;
Braessler, Jonathan;
Meinken, John;
Feng Yu;
Sablok, Gaurav

Publication type:

Article

Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1907-4

By:

Poupardin, Rodolphe;
Schöttner, Konrad;
Korbelová, Jaroslava;
Provazník, Jan;
Doležel, David;
Pavlinic, Dinko;
Beneš, Vladimír;
Koštál, Vladimír

Publication type:

Article

Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1903-8

By:

Pastor-Flores, Daniel;
Ferrer-Dalmau, Jofre;
Bahí, Anna;
Boleda, Martí;
Biondi, Ricardo M.;
Casamayor, Antonio

Publication type:

Article

Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici).

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1895-4

By:

Mueth, Nicholas A.;
Ramachandran, Sowmya R.;
Hulbert, Scot H.

Publication type:

Article