Works in BMC Genomics, 2019, Vol 20, Issue 1

Results: 916

Methylome and transcriptome analyses of apple fruit somatic mutations reveal the difference of red phenotype.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5499-2

By:

Jiang, Sheng-Hui;
Sun, Qing-Guo;
Chen, Min;
Wang, Nan;
Xu, Hai-Feng;
Fang, Hong-Cheng;
Wang, Yi-Cheng;
Zhang, Zong-Ying;
Chen, Xue-Sen

Publication type:

Article

The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5485-8

By:

Masonbrink, Rick;
Maier, Tom R.;
Muppirala, Usha;
Seetharam, Arun S.;
Lord, Etienne;
Juvale, Parijat S.;
Schmutz, Jeremy;
Johnson, Nathan T.;
Korkin, Dmitry;
Mitchum, Melissa G.;
Mimee, Benjamin;
den Akker, Sebastian Eves-van;
Hudson, Matthew;
Severin, Andrew J.;
Baum, Thomas J.

Publication type:

Article

Phylogenomic analysis of cytochrome P450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5483-x

By:

Vasav, A. P.;
Barvkar, V. T.

Publication type:

Article

Molecular characterization of carbendazim resistance of Fusarium species complex that causes sugarcane pokkah boeng disease.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5479-6

By:

Xu, Shiqiang;
Wang, Jihua;
Wang, Haixuan;
Bao, Yixue;
Li, Yisha;
Govindaraju, Muralidharan;
Yao, Wei;
Chen, Baoshan;
Zhang, Muqing

Publication type:

Article

In silico characterization of multiple genes encoding the GP63 virulence protein from Leishmania braziliensis: identification of sources of variation and putative roles in immune evasion.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5465-z

By:

Castro Neto, Artur L.;
Brito, Adriana N. A. L. M.;
Rezende, Antonio M.;
Magalhães, Franklin B.;
de Melo Neto, Osvaldo P.

Publication type:

Article

Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5399-x

By:

Olarte, Rodrigo A.;
Menke, Jon;
Zhang, Ying;
Sullivan, Shawn;
Slot, Jason C.;
Huang, Yinyin;
Badalamenti, Jonathan P.;
Quandt, Alisha C.;
Spatafora, Joseph W.;
Bushley, Kathryn E.

Publication type:

Article

Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum).

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5500-0

By:

Liu, Moyang;
Ma, Zhaotang;
Sun, Wenjun;
Huang, Li;
Wu, Qi;
Tang, Zizhong;
Bu, Tongliang;
Li, Chenglei;
Chen, Hui

Publication type:

Article

Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5492-9

By:

Kampfraath, A. A.;
Klasson, L.;
Anvar, S. Y.;
Vossen, R. H. A. M.;
Roelofs, D.;
Kraaijeveld, K.;
Ellers, J.

Publication type:

Article

De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5486-7

By:

Vergara-Pulgar, Cristian;
Rothkegel, Karin;
González-Agüero, Mauricio;
Pedreschi, Romina;
Campos-Vargas, Reinaldo;
Defilippi, Bruno G.;
Meneses, Claudio

Publication type:

Article

Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5481-z

By:

Gonçalves, Luana P.;
Boscariol Camargo, Raquel L.;
Takita, Marco Aurélio;
Machado, Marcos A.;
dos Soares Filho, Walter S.;
Costa, Marcio G. C.

Publication type:

Article

Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5480-0

By:

Boettcher, Michael;
Covarrubias, Sergio;
Biton, Anne;
Blau, James;
Wang, Haopeng;
Zaitlen, Noah;
McManus, Michael T.

Publication type:

Article

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5464-0

By:

Mura, Marzena;
Jaksik, Roman;
Lalik, Anna;
Biernacki, Krzysztof;
Kimmel, Marek;
Rzeszowska-Wolny, Joanna;
Fujarewicz, Krzysztof

Publication type:

Article

Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5456-0

By:

Détrée, Camille;
Haddad, Iman;
Demey-Thomas, Emmanuelle;
Vinh, Joëlle;
Lallier, François H.;
Tanguy, Arnaud;
Mary, Jean

Publication type:

Article

Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5443-5

By:

Le Luyer, J.;
Auffret, P.;
Quillien, V.;
Leclerc, N.;
Reisser, C.;
Vidal-Dupiol, J.;
Ky, C.-L.

Publication type:

Article

Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5427-5

By:

Naoumkina, Marina;
Thyssen, Gregory N.;
Fang, David D.;
Jenkins, Johnie N.;
McCarty, Jack C.;
Florane, Christopher B.

Publication type:

Article

Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5484-9

By:

Velie, Brandon D.;
Lillie, Mette;
Fegraeus, Kim Jäderkvist;
Rosengren, Maria K.;
Solé, Marina;
Wiklund, Maja;
Ihler, Carl-Fredrik;
Strand, Eric;
Lindgren, Gabriella

Publication type:

Article

CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5439-1

By:

McDonald, Nathan D.;
Regmi, Abish;
Morreale, Daniel P.;
Borowski, Joseph D.;
Fidelma Boyd, E.

Publication type:

Article

Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5373-7

By:

Pei, Guangsheng;
Sun, Hua;
Dai, Yulin;
Liu, Xiaoming;
Zhao, Zhongming;
Jia, Peilin

Publication type:

Article

NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5372-8

By:

Liu, Qian;
Georgieva, Daniela C.;
Egli, Dieter;
Wang, Kai

Publication type:

Article

CeL-ID: cell line identification using RNA-seq data.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5371-9

By:

Mohammad, Tabrez A.;
Tsai, Yun S.;
Ameer, Safwa;
Chen, Hung-I Harry;
Chiu, Yu-Chiao;
Chen, Yidong

Publication type:

Article

Gene2vec: distributed representation of genes based on co-expression.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5370-x

By:

Du, Jingcheng;
Jia, Peilin;
Dai, Yulin;
Tao, Cui;
Zhao, Zhongming;
Zhi, Degui

Publication type:

Article

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5369-3

By:

Wu, Zhijin;
Yan, Jingwen;
Wang, Kai;
Liu, Xiaoming;
Guo, Yan;
Zhi, Degui;
Ruan, Jianhua;
Zhao, Zhongming

Publication type:

Article

Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.).

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5455-1

By:

Han, Zhisheng;
Liu, Yanlin;
Deng, Xiong;
Liu, Dongmiao;
Liu, Yue;
Hu, Yingkao;
Yan, Yueming

Publication type:

Article

Probing transcription factor combinatorics in different promoter classes and in enhancers.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5408-0

By:

Vandel, Jimmy;
Cassan, Océane;
Lèbre, Sophie;
Lecellier, Charles-Henri;
Bréhélin, Laurent

Publication type:

Article

CpG traffic lights are markers of regulatory regions in human genome.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5387-1

By:

Lioznova, Anna V.;
Khamis, Abdullah M.;
Artemov, Artem V.;
Besedina, Elizaveta;
Ramensky, Vasily;
Bajic, Vladimir B.;
Kulakovskiy, Ivan V.;
Medvedeva, Yulia A.

Publication type:

Article

A genome-wide analysis of coatomer protein (COP) subunits of apicomplexan parasites and their evolutionary relationships.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5463-1

By:

Kibria, K. M. Kaderi;
Ferdous, Jannatul;
Sardar, Rahila;
Panda, Ashutosh;
Gupta, Dinesh;
Mohmmed, Asif;
Malhotra, Pawan

Publication type:

Article

Conserved regulation of RNA processing in somatic cell reprogramming.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5438-2

By:

Kanitz, Alexander;
Syed, Afzal Pasha;
Kaji, Keisuke;
Zavolan, Mihaela

Publication type:

Article

Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5352-z

By:

Giner-Lamia, Joaquín;
Vinuesa, Pablo;
Betancor, Laura;
Silva, Claudia;
Bisio, Julieta;
Soleto, Lorena;
Chabalgoity, José A.;
Puente, José Luis;
García-del Portillo, Francisco

Publication type:

Article

Correction to: Identification of new signalling peptides through a genome-wide survey of 250 fungal secretomes.

Published in:

2019

By:

Le Marquer, Morgane;
Clemente, Hélène San;
Roux, Christophe;
Savelli, Bruno;
dit Frey, Nicolas Frei

Publication type:

Correction Notice

Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5462-2

By:

Shen, Manman;
Li, Tingting;
Zhang, Genxi;
Wu, Pengfei;
Chen, Fuxiang;
Lou, Qiuhong;
Chen, Lan;
Yin, Xuemei;
Zhang, Tao;
Wang, Jinyu

Publication type:

Article

Comparison of splenocyte microRNA expression profiles of pigs during acute and chronic toxoplasmosis.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5458-y

By:

Hou, Zhaofeng;
Liu, Dandan;
Su, Shijie;
Wang, Lele;
Zhao, Zhenxing;
Ma, Yifei;
Li, Qiaoqiao;
Jia, Chuanli;
Xu, Jinjun;
Zhou, Yonghua;
Tao, Jianping

Publication type:

Article

Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5452-4

By:

Wilhelmsson, Per K. I.;
Chandler, Jake O.;
Fernandez-Pozo, Noe;
Graeber, Kai;
Ullrich, Kristian K.;
Arshad, Waheed;
Khan, Safina;
Hofberger, Johannes A.;
Buchta, Karl;
Edger, Patrick P.;
Pires, J. Chris;
Schranz, M. Eric;
Leubner-Metzger, Gerhard;
Rensing, Stefan A.

Publication type:

Article

Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5454-2

By:

Zhang, Wei;
Wang, Shenyun;
Yu, Fangwei;
Tang, Jun;
Shan, Xi;
Bao, Kan;
Yu, Li;
Wang, Hong;
Fei, Zhangjun;
Li, Jianbin

Publication type:

Article

Identification of lncRNAs involved in rice ovule development and female gametophyte abortion by genome-wide screening and functional analysis.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5442-6

By:

Liu, Helian;
Wang, Ruihua;
Mao, Bigang;
Zhao, Bingran;
Wang, Jianbo

Publication type:

Article

Proteomic dissection of the rice-Fusarium fujikuroi interaction and the correlation between the proteome and transcriptome under disease stress.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5435-5

By:

Ji, Zhijuan;
Zeng, Yuxiang;
Liang, Yan;
Qian, Qian;
Yang, Changdeng

Publication type:

Article

Comparative genomics of Bacteria commonly identified in the built environment.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5389-z

By:

Merino, Nancy;
Zhang, Shu;
Tomita, Masaru;
Suzuki, Haruo

Publication type:

Article

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5460-4

By:

Khan, Samiullah;
Wu, Shu-Biao;
Roberts, Juliet

Publication type:

Article

Sexual dimorphism in brain transcriptomes of Amami spiny rats (Tokudaia osimensis): a rodent species where males lack the Y chromosome.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5426-6

By:

Ortega, Madison T.;
Bivens, Nathan J.;
Jogahara, Takamichi;
Kuroiwa, Asato;
Givan, Scott A.;
Rosenfeld, Cheryl S.

Publication type:

Article

Sequence and structural properties of circular RNAs in the brain of nurse and forager honeybees (Apis mellifera).

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5402-6

By:

Thölken, Clemens;
Thamm, Markus;
Erbacher, Christoph;
Lechner, Marcus

Publication type:

Article

Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5453-3

By:

Gamboa, Maribet;
Watanabe, Kozo

Publication type:

Article

Transcriptome analysis of genes and metabolic pathways associated with nicotine degradation in Aspergillus oryzae 112822.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5446-2

By:

He, Chunjuan;
Huang, Yougui;
Liu, Peng;
Wei, Jianhuan;
Yang, Yirui;
Xu, Li;
Xiao, Min

Publication type:

Article

Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5437-3

By:

Wang, Yongjun;
Hua, Xiuting;
Xu, Jingsheng;
Chen, Zhichang;
Fan, Tianqu;
Zeng, Zhaohui;
Wang, Hengbo;
Hour, Ai-Ling;
Yu, Qingyi;
Ming, Ray;
Zhang, Jisen

Publication type:

Article

s ·nr: a visual analytics framework for contextual analyses of private and public RNA-seq data.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5396-0

By:

Klemm, Paul;
Frommolt, Peter;
Kornfeld, Jan-Wilhelm

Publication type:

Article

Fine mapping chromatin contacts in capture Hi-C data.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5314-5

By:

Eijsbouts, Christiaan Q;
Burren, Oliver S;
Newcombe, Paul J;
Wallace, Chris

Publication type:

Article

Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5450-6

By:

Denisenko, Elena;
Guler, Reto;
Mhlanga, Musa;
Suzuki, Harukazu;
Brombacher, Frank;
Schmeier, Sebastian

Publication type:

Article

Gene annotation errors are common in the mammalian mitochondrial genomes database.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5447-1

By:

Prada, Carlos F.;
Boore, Jeffrey L.

Publication type:

Article

Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5440-8

By:

Vendrami, David L. J.;
Forcada, Jaume;
Hoffman, Joseph I.

Publication type:

Article

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-019-5433-7

By:

Ye, Wenbin;
Long, Yuqi;
Ji, Guoli;
Su, Yaru;
Ye, Pengchao;
Fu, Hongjuan;
Wu, Xiaohui

Publication type:

Article

Characterization of G-protein coupled receptors from the blackback land crab Gecarcinus lateralis Y organ transcriptome over the molt cycle.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5363-9

By:

Tran, Nhut M.;
Mykles, Donald L.;
Elizur, Abigail;
Ventura, Tomer

Publication type:

Article

Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5317-2

By:

Lekklar, Chakkree;
Pongpanich, Monnat;
Suriya-arunroj, Duangjai;
Chinpongpanich, Aumnart;
Tsai, Helen;
Comai, Luca;
Chadchawan, Supachitra;
Buaboocha, Teerapong

Publication type:

Article