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 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

  2. 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

  3. 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

  4. 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

  5. Research Article

    Conserved expression of transposon-derived non-coding transcripts in primate stem cells

    A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human...

    LeeAnn Ramsay, Maria C. Marchetto, Maxime Caron, Shu-Huang Chen, Stephan Busche, Tony Kwan, Tomi Pastinen, Fred H. Gage and Guillaume Bourque

    BMC Genomics 2017 18:214

    Published on: 28 February 2017

  6. Research article

    Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors

    The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annot...

    Sara J. Oppenheim, Jeffrey A. Rosenfeld and Rob DeSalle

    BMC Genomics 2017 18:205

    Published on: 27 February 2017

  7. Research article

    Chronic nicotine differentially affects murine transcriptome profiling in isolated cortical interneurons and pyramidal neurons

    Nicotine is known to differentially regulate cortical interneuron and pyramidal neuron activities in the neocortex, while the underlying molecular mechanisms have not been well studied. In this study, RNA-sequ...

    Jie Yang, Ai-Yi Liu, Bo Tang, Dong Luo, Yu-Jie Lai, Bing-Lin Zhu, Xue-Feng Wang, Zhen Yan and Guo-Jun Chen

    BMC Genomics 2017 18:194

    Published on: 20 February 2017

  8. Research article

    House spider genome uncovers evolutionary shifts in the diversity and expression of black widow venom proteins associated with extreme toxicity

    Black widow spiders are infamous for their neurotoxic venom, which can cause extreme and long-lasting pain. This unusual venom is dominated by latrotoxins and latrodectins, two protein families virtually unkno...

    Kerry L. Gendreau, Robert A. Haney, Evelyn E. Schwager, Torsten Wierschin, Mario Stanke, Stephen Richards and Jessica E. Garb

    BMC Genomics 2017 18:178

    Published on: 16 February 2017

  9. Research article

    The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish

    Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic s...

    Irene Adrian-Kalchhauser, Ola Svensson, Verena E. Kutschera, Magnus Alm Rosenblad, Martin Pippel, Sylke Winkler, Siegfried Schloissnig, Anders Blomberg and Patricia Burkhardt-Holm

    BMC Genomics 2017 18:177

    Published on: 16 February 2017

  10. Research article

    A vast genomic deletion in the C56BL/6 genome affects different genes within the Ifi200 cluster on chromosome 1 and mediates obesity and insulin resistance

    Obesity, the excessive accumulation of body fat, is a highly heritable and genetically heterogeneous disorder. The complex, polygenic basis for the disease consisting of a network of different gene variants is...

    Heike Vogel, Markus Jähnert, Mandy Stadion, Daniela Matzke, Stephan Scherneck and Annette Schürmann

    BMC Genomics 2017 18:172

    Published on: 15 February 2017

  11. Research article

    The abundance of homoeologue transcripts is disrupted by hybridization and is partially restored by genome doubling in synthetic hexaploid wheat

    The formation of an allopolyploid is a two step process, comprising an initial wide hybridization event, which is later followed by a whole genome doubling. Both processes can affect the transcription of homoe...

    Ming Hao, Aili Li, Tongwei Shi, Jiangtao Luo, Lianquan Zhang, Xuechuan Zhang, Shunzong Ning, Zhongwei Yuan, Deying Zeng, Xingchen Kong, Xiaolong Li, Hongkun Zheng, Xiujin Lan, Huaigang Zhang, Youliang Zheng, Long Mao…

    BMC Genomics 2017 18:149

    Published on: 10 February 2017

  12. Research article

    Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores

    The main function of hemoglobin (Hb) is to transport oxygen in the circulation. It is among the most highly studied proteins due to its roles in physiology and disease, and most of our understanding derives fr...

    Sara Zaldívar-López, Jennie L. Rowell, Elise M. Fiala, Isain Zapata, C. Guillermo Couto and Carlos E. Alvarez

    BMC Genomics 2017 18:141

    Published on: 8 February 2017

  13. Research article

    Melanoma genome evolution across species

    Cancer genomes evolve in both space and time, which contributes to the genetic heterogeneity that underlies tumor progression and drug resistance. In human melanoma, identifying mechanistically important event...

    Emily R. Kansler, Akanksha Verma, Erin M. Langdon, Theresa Simon-Vermot, Alexandra Yin, William Lee, Marc Attiyeh, Olivier Elemento and Richard M. White

    BMC Genomics 2017 18:136

    Published on: 7 February 2017

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