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  1. The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are fou...

    Authors: Kai K. Lie, Ole K. Tørresen, Monica Hongrø Solbakken, Ivar Rønnestad, Ave Tooming-Klunderud, Alexander J. Nederbragt, Sissel Jentoft and Øystein Sæle
    Citation: BMC Genomics 2018 19:186
    Content type: Research article Published on:

  2. Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover...

    Authors: Yuanting Jin, Yubin Wo, Haojie Tong, Sen Song, Lixun Zhang and Richard P. Brown
    Citation: BMC Genomics 2018 19:185
    Content type: Research article Published on:

  3. Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) are globally distributed in tropical and subtropical freshwater eco...

    Authors: Jack C. H. Ip, Huawei Mu, Qian Chen, Jin Sun, Santiago Ituarte, Horacio Heras, Bert Van Bocxlaer, Monthon Ganmanee, Xin Huang and Jian-Wen Qiu
    Citation: BMC Genomics 2018 19:179
    Content type: Database Published on:

  4. The mitogen-activated protein kinase (MAPK) family is involved in signal transduction networks that underpin many different biological processes in plants, ranging from development to biotic and abiotic stress...

    Authors: Ravinder K. Goyal, Dan Tulpan, Nora Chomistek, Dianevys González-Peña Fundora, Connor West, Brian E. Ellis, Michele Frick, André Laroche and Nora A. Foroud
    Citation: BMC Genomics 2018 19:178
    Content type: Research article Published on:

  5. A strain of Leghorn chickens (rd/rd), unable to produce a functional riboflavin-binding protein, lays riboflavin-deficient eggs, in which all embryos suddenly die at mid-incubation (days 13-15). This malady, caus...

    Authors: Larry A. Cogburn, Danielle N. Smarsh, Xiaofei Wang, Nares Trakooljul, Wilfrid Carré and Harold B. White III
    Citation: BMC Genomics 2018 19:177
    Content type: Research article Published on:

  6. Increased reports of Neisseria meningitidis urethritis in multiple U.S. cities during 2015 have been attributed to the emergence of a novel clade of nongroupable N. meningitidis within the ST-11 clonal complex, t...

    Authors: Adam C. Retchless, Cécilia B. Kretz, How-Yi Chang, Jose A. Bazan, A. Jeanine Abrams, Abigail Norris Turner, Laurel T. Jenkins, David L. Trees, Yih-Ling Tzeng, David S. Stephens, Jessica R. MacNeil and Xin Wang
    Citation: BMC Genomics 2018 19:176
    Content type: Research article Published on:

  7. Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene region...

    Authors: Bai-Han Zhu, Jun Xiao, Wei Xue, Gui-Cai Xu, Ming-Yuan Sun and Jiong-Tang Li
    Citation: BMC Genomics 2018 19:175
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:524

  8. Members of the MtN3/saliva/SWEET gene family are present in various organisms and are highly conserved. Their precise biochemical functions remain unclear, especially in Chinese cabbage. Based on the whole gen...

    Authors: Liming Miao, Yanxia Lv, Lijun Kong, Qizhen Chen, Chaoquan Chen, Jia Li, Fanhuan Zeng, Shenyun Wang, Jianbin Li, Li Huang, Jiashu Cao and Xiaolin Yu
    Citation: BMC Genomics 2018 19:174
    Content type: Research article Published on:

  9. Gestational disorders such as intrauterine growth restriction (IUGR) and pre-eclampsia (PE) are main causes of poor perinatal outcomes worldwide. Both diseases are related with impaired materno-fetal nutrient ...

    Authors: Xiao Huang, Pascale Anderle, Lu Hostettler, Marc U. Baumann, Daniel V. Surbek, Edgar C. Ontsouka and Christiane Albrecht
    Citation: BMC Genomics 2018 19:173
    Content type: Research article Published on:

  10. The advantages of Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology include long reads, low systematic bias, and high consensus read accuracy. Here we use these attributes to improve on ...

    Authors: Vincent Magrini, Xin Gao, Bruce A. Rosa, Sean McGrath, Xu Zhang, Kymberlie Hallsworth-Pepin, John Martin, John Hawdon, Richard K. Wilson and Makedonka Mitreva
    Citation: BMC Genomics 2018 19:172
    Content type: Methodology article Published on:

  11. ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin...

    Authors: Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson and Lihua Julie Zhu
    Citation: BMC Genomics 2018 19:169
    Content type: Software Published on:

  12. Metamorphosis takes place within the life cycle of most marine invertebrates. The marine ascidian is a classical model to study complex cellular processes and underlying molecular mechanisms involved in its la...

    Authors: Xiaoming Zhang, Xiaozhuo Liu, Chengzhang Liu, Jiankai Wei, Haiyan Yu and Bo Dong
    Citation: BMC Genomics 2018 19:168
    Content type: Research article Published on:

  13. To continue to meet the increasing demands of soybean worldwide, it is crucial to identify key genes regulating flowering and maturity to expand the cultivated regions into short season areas. Although four so...

    Authors: Tanya R. Copley, Marc-Olivier Duceppe and Louise S. O’Donoughue
    Citation: BMC Genomics 2018 19:167
    Content type: Research article Published on:

  14. The volatile metabolites produced by Saccharomyces cerevisiae during alcoholic fermentation, which are mainly esters, higher alcohols and organic acids, play a vital role in the quality and perception of fermente...

    Authors: Matthias Eder, Isabelle Sanchez, Claire Brice, Carole Camarasa, Jean-Luc Legras and Sylvie Dequin
    Citation: BMC Genomics 2018 19:166
    Content type: Research article Published on:

  15. Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Wester...

    Authors: Barakat A. Al Suwayyid, Geoffrey W. Coombs, David J. Speers, Julie Pearson, Michael J. Wise and Charlene M. Kahler
    Citation: BMC Genomics 2018 19:165
    Content type: Research article Published on:

  16. Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selectio...

    Authors: Gemma B. Danks, Pavla Navratilova, Boris Lenhard and Eric M. Thompson
    Citation: BMC Genomics 2018 19:164
    Content type: Research article Published on:

  17. Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the we...

    Authors: Shannon J. O’Leary, Christopher M. Hollenbeck, Robert R. Vega, John R. Gold and David S. Portnoy
    Citation: BMC Genomics 2018 19:163
    Content type: Research article Published on:

  18. Polyploidy is considered a major driving force in genome expansion, yielding duplicated genes whose expression may be conserved or divergence as a consequence of polyploidization.

    Authors: Bingliang Liu, Xueying Guan, Wenhua Liang, Jiedan Chen, Lei Fang, Yan Hu, Wangzhen Guo, Junkang Rong, Guohua Xu and Tianzhen Zhang
    Citation: BMC Genomics 2018 19:162
    Content type: Research article Published on:

  19. The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics an...

    Authors: Oluwatosin Oluwadare, Yuxiang Zhang and Jianlin Cheng
    Citation: BMC Genomics 2018 19:161
    Content type: Methodology article Published on:

  20. Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas...

    Authors: Pierre De Wit, Evan Durland, Alexander Ventura and Chris J. Langdon
    Citation: BMC Genomics 2018 19:160
    Content type: Research article Published on:

  21. Soybean, a major legume crop native to East Asia, presents a wealth of resources for utilization. The basic leucine zipper (bZIP) transcription factors play important roles in various biological processes incl...

    Authors: Man Zhang, Yanhui Liu, Hang Shi, Mingliang Guo, Mengnan Chai, Qing He, Maokai Yan, Du Cao, Lihua Zhao, Hanyang Cai and Yuan Qin
    Citation: BMC Genomics 2018 19:159
    Content type: Research article Published on:

  22. Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have th...

    Authors: Gergely Ivády, László Madar, Erika Dzsudzsák, Katalin Koczok, János Kappelmayer, Veronika Krulisova, Milan Macek Jr, Attila Horváth and István Balogh
    Citation: BMC Genomics 2018 19:158
    Content type: Research article Published on:

  23. High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS pro...

    Authors: Michael P. Meers, Karen Adelman, Robert J. Duronio, Brian D. Strahl, Daniel J. McKay and A. Gregory Matera
    Citation: BMC Genomics 2018 19:157
    Content type: Research article Published on:

  25. The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos ...

    Authors: Josiah T. Wagner, Param Priya Singh, Amie L. Romney, Claire L. Riggs, Patrick Minx, Steven C. Woll, Jake Roush, Wesley C. Warren, Anne Brunet and Jason E. Podrabsky
    Citation: BMC Genomics 2018 19:155
    Content type: Research article Published on:

  26. RNA-binding proteins (RBPs) play vital roles in many processes in the cell. Different RBPs bind RNA with different sequence and structure specificities. While sequence specificities for a large set of 205 RBPs...

    Authors: Yaron Orenstein, Uwe Ohler and Bonnie Berger
    Citation: BMC Genomics 2018 19:154
    Content type: Research article Published on:

  27. The rise and fall of the Y chromosome was demonstrated in animals but plants often possess the large evolutionarily young Y chromosome that is thought has expanded recently. Break-even points dividing expansio...

    Authors: Janka Puterova, Zdenek Kubat, Eduard Kejnovsky, Wojciech Jesionek, Jana Cizkova, Boris Vyskot and Roman Hobza
    Citation: BMC Genomics 2018 19:153
    Content type: Research article Published on:

  28. Peptidases (EC 3.4) consist of a large group of hydrolytic enzymes that catalyze the hydrolysis of proteins accounting for approximately 65% of the total worldwide enzyme production. Peptidases from thermophil...

    Authors: Tássio Brito de Oliveira, Cene Gostinčar, Nina Gunde-Cimerman and Andre Rodrigues
    Citation: BMC Genomics 2018 19:152
    Content type: Research article Published on:

  29. Chromocenters are defined as a punctate condensed blocks of chromatin in the interphase cell nuclei of certain cell types with unknown biological significance. In recent years a progress in revealing of chromo...

    Authors: Dmitrii I. Ostromyshenskii, Ekaterina N. Chernyaeva, Inna S. Kuznetsova and Olga I. Podgornaya
    Citation: BMC Genomics 2018 19:151
    Content type: Research article Published on:

  30. Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy.

    Authors: Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi…
    Citation: BMC Genomics 2018 19:150
    Content type: Research article Published on:

  31. The size of the phenotypic effect of a gene has been thoroughly investigated in terms of fitness and specific morphological traits in the budding yeast Saccharomyces cerevisiae, but little is known about gross mo...

    Authors: Godai Suzuki, Yang Wang, Karen Kubo, Eri Hirata, Shinsuke Ohnuki and Yoshikazu Ohya
    Citation: BMC Genomics 2018 19:149
    Content type: Research article Published on:

  32. Improving the efficiency of animal production is a relentless pursuit of ruminant producers. Energy utilization and partition can be affected by dietary composition and nutrient availability. Furthermore, the ...

    Authors: Haitao Shi, Jun Zhang, Shengli Li, Shoukun Ji, Zhijun Cao, Hongtao Zhang and Yajing Wang
    Citation: BMC Genomics 2018 19:148
    Content type: Research article Published on:

  33. RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure.

    Authors: Kriti Kaushik, Ambily Sivadas, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Rijith Jayarajan, Satyaprakash Pandey, Tavprithesh Sethi, Souvik Maiti, Vinod Scaria and Sridhar Sivasubbu
    Citation: BMC Genomics 2018 19:147
    Content type: Research article Published on:

  34. Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The down...

    Authors: Tian Gao, Jiang Shu and Juan Cui
    Citation: BMC Genomics 2018 19:146
    Content type: Research article Published on:

  35. The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypi...

    Authors: Tainã Figueiredo Cardoso, Raquel Quintanilla, Anna Castelló, Rayner González-Prendes, Marcel Amills and Ángela Cánovas
    Citation: BMC Genomics 2018 19:145
    Content type: Research article Published on:

  37. Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have ...

    Authors: Jian Wu, Wei Dai, Lin Wu and Jinke Wang
    Citation: BMC Genomics 2018 19:143
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:327

  38. Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling ...

    Authors: Hugo A. Carignano, Dana L. Roldan, María J. Beribe, María A. Raschia, Ariel Amadio, Juan P. Nani, Gerónimo Gutierrez, Irene Alvarez, Karina Trono, Mario A. Poli and Marcos M. Miretti
    Citation: BMC Genomics 2018 19:142
    Content type: Research article Published on:

  39. Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted...

    Authors: Zihao Yuan, Shikai Liu, Tao Zhou, Changxu Tian, Lisui Bao, Rex Dunham and Zhanjiang Liu
    Citation: BMC Genomics 2018 19:141
    Content type: Research article Published on:

  40. High-fidelity preservation strategies for primary tissues are in great demand in the single cell RNAseq community. A reliable method would greatly expand the scope of feasible multi-site collaborations and max...

    Authors: Wanxin Wang, Lolita Penland, Ozgun Gokce, Derek Croote and Stephen R. Quake
    Citation: BMC Genomics 2018 19:140
    Content type: Methodology article Published on:

  41. Gene fusions often occur in cancer cells and in some cases are the main driver of oncogenesis. Correct identification of oncogenic gene fusions thus has implications for targeted cancer therapy. Recognition of...

    Authors: Jackson A. Killian, Taha M. Topiwala, Alex R. Pelletier, David E. Frankhouser, Pearlly S. Yan and Ralf Bundschuh
    Citation: BMC Genomics 2018 19:139
    Content type: Software Published on:

  43. Comprehensive understanding of intratumor heterogeneity requires identification of molecular markers, which are capable of differentiating different subpopulations and which also have clinical significance. On...

    Authors: Fan Wang, Zachariah Dohogne, Jin Yang, Yu Liu and Benjamin Soibam
    Citation: BMC Genomics 2018 19:137
    Content type: Research article Published on:

  44. Our previous comparative genomic analysis of Staphylococcus equorum KS1039 with five S. equorum strains illuminated the genomic basis of its safety and salt tolerance. However, a comprehensive picture of the cell...

    Authors: Jong-Hoon Lee, Sojeong Heo and Do-Won Jeong
    Citation: BMC Genomics 2018 19:136
    Content type: Research article Published on:

  46. Heilongjiang Province located in northeast China is a multi-ethnic region with people who have lived in cold conditions for several generations. Fatty acids are important to people with cold resistance. CPT1A ...

    Authors: Qiuyan Li, Kexian Dong, Lidan Xu, Xueyuan Jia, Jie Wu, Wenjing Sun, Xuelong Zhang and Songbin Fu
    Citation: BMC Genomics 2018 19:134
    Content type: Research article Published on:

  47. Atlantic salmon production in Tasmania (Southern Australia) occurs near the upper limits of the species thermal tolerance. Summer water temperatures can average over 19 °C over several weeks and have negative eff...

    Authors: Waldo G. Nuez-Ortín, Chris G. Carter, Peter D. Nichols, Ira R. Cooke and Richard Wilson
    Citation: BMC Genomics 2018 19:133
    Content type: Research article Published on:

  48. The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene ...

    Authors: Bharati Pandey, Abhinav Grover and Pradeep Sharma
    Citation: BMC Genomics 2018 19:132
    Content type: Research article Published on:

  49. Colorectal cancer (CRC) is a common cancer worldwide. The main cause of death in CRC includes tumor progression and metastasis. At molecular level, these processes may be triggered by epithelial-mesenchymal tr...

    Authors: Elena A. Pudova, Anna V. Kudryavtseva, Maria S. Fedorova, Andrew R. Zaretsky, Dmitry S. Shcherbo, Elena N. Lukyanova, Anatoly Y. Popov, Asiya F. Sadritdinova, Ivan S. Abramov, Sergey L. Kharitonov, George S. Krasnov, Kseniya M. Klimina, Nadezhda V. Koroban, Nadezhda N. Volchenko, Kirill M. Nyushko, Nataliya V. Melnikova…
    Citation: BMC Genomics 2018 19(Suppl 3):113
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 3

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