Comparative and evolutionary genomics

Section edited by Igor Rogozin

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

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  1. Research Article

    Genome-wide identification of genes probably relevant to the adaptation of schizothoracins (Teleostei: Cypriniformes) to the uplift of the Qinghai-Tibet Plateau

    Molecular adaptation to the severe environments present during the uplift of the Qinghai-Tibet Plateau has attracted the attention of researchers. The divergence of the three specialization groups of schizotho...

    Wei Chi, Xufa Ma, Jiangong Niu and Ming Zou

    BMC Genomics 2017 18:310

    Published on: 20 April 2017

  2. Research article

    Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals

    Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received l...

    Xiaotian Feng, Jicai Jiang, Abinash Padhi, Chao Ning, Jinluan Fu, Aiguo Wang, Raphael Mrode and Jian-Feng Liu

    BMC Genomics 2017 18:293

    Published on: 12 April 2017

  3. Research article

    Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

    Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play extensive roles in transcriptional regulation. In particular, we have reported that promoter-associated ncRNAs (pancRNAs) activa...

    Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima and Takuya Imamura

    BMC Genomics 2017 18:285

    Published on: 7 April 2017

  4. Research article

    Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome

    microRNAs (miRNAs) are endogenous small RNAs that play important regulatory functions in plant development. Genetic variations in miRNAs sequences or their target-binding sites (microRNA-target interaction sit...

    Jian Ling, Zhongqin Luo, Feng Liu, Zhenchuan Mao, Yuhong Yang and Bingyan Xie

    BMC Genomics 2017 18:275

    Published on: 4 April 2017

  5. Research article

    Widespread of horizontal gene transfer in the human genome

    A fundamental concept in biology is that heritable material is passed from parents to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene...

    Wenze Huang, Lillian Tsai, Yulong Li, Nan Hua, Chen Sun and Chaochun Wei

    BMC Genomics 2017 18:274

    Published on: 4 April 2017

  6. Methodology Article

    Positional bias in variant calls against draft reference assemblies

    Whole genome resequencing projects may implement variant calling using draft reference genomes assembled de novo from short-read libraries. Despite lower quality of such assemblies, they allowed researchers to...

    Roman V. Briskine and Kentaro K. Shimizu

    BMC Genomics 2017 18:263

    Published on: 28 March 2017

  7. Research article

    Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach

    Computational identification of non-coding RNAs (ncRNAs) is a challenging problem. We describe a genome-wide analysis using Bayesian segmentation to identify intronic elements highly conserved between three ev...

    Manjula Algama, Edward Tasker, Caitlin Williams, Adam C. Parslow, Robert J. Bryson-Richardson and Jonathan M. Keith

    BMC Genomics 2017 18:259

    Published on: 27 March 2017

  8. Research article

    Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients

    Although tumor-associated macrophages (TAMs) are essential for cancer progression, connections between different clinical outcomes and transcriptional networks have not been reported. We have addressed this is...

    Till Adhikary, Annika Wortmann, Florian Finkernagel, Sonja Lieber, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Sabine Müller-Brüsselbach, Silke Reinartz and Rolf Müller

    BMC Genomics 2017 18:243

    Published on: 21 March 2017

  9. Research article

    Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix

    Human papillomavirus (HPV) is the carcinogen of almost all invasive cervical cancer and a major cause of oral and other anogenital malignancies. HPV genotyping by dideoxy (Sanger) sequencing is currently the r...

    Jane Shen-Gunther, Yufeng Wang, Zhao Lai, Graham M. Poage, Luis Perez and Tim H. M. Huang

    BMC Genomics 2017 18:231

    Published on: 14 March 2017

  10. Research article

    Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans

    Segmental duplications are an abundant source for novel gene functions and evolutionary adaptations. This mechanism of generating novelty was very active during the evolution of primates particularly in the hu...

    Cemalettin Bekpen, Sven Künzel, Chen Xie, Muthukrishnan Eaaswarkhanth, Yen-Lung Lin, Omer Gokcumen, Cezmi A. Akdis and Diethard Tautz

    BMC Genomics 2017 18:222

    Published on: 6 March 2017

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