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  1. The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to addres...

    Authors: I-Min A. Chen, Victor M. Markowitz, Krishna Palaniappan, Ernest Szeto, Ken Chu, Jinghua Huang, Anna Ratner, Manoj Pillay, Michalis Hadjithomas, Marcel Huntemann, Natalia Mikhailova, Galina Ovchinnikova, Natalia N. Ivanova and Nikos C. Kyrpides
    Citation: BMC Genomics 2016 17:307
    Content type: Software Published on:

  2. Trypanosoma brucei is a unicellular parasite which multiplies in mammals (bloodstream form) and Tsetse flies (procyclic form). Trypanosome RNA polymerase II transcription is polycistro...

    Authors: Enoch B. Antwi, Jurgen R. Haanstra, Gowthaman Ramasamy, Bryan Jensen, Dorothea Droll, Federico Rojas, Igor Minia, Monica Terrao, Clémentine Mercé, Keith Matthews, Peter J. Myler, Marilyn Parsons and Christine Clayton
    Citation: BMC Genomics 2016 17:306
    Content type: Research article Published on:

  3. Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell o...

    Authors: Jessica M. Vera and Robin D. Dowell
    Citation: BMC Genomics 2016 17:305
    Content type: Research article Published on:

  4. cAMP signaling produces dramatic changes in astrocyte morphology and physiology. However, its involvement in phenotype acquisition and the transcriptionally mediated mechanisms of action are largely unknown.

    Authors: Sonia Paco, Manuela Hummel, Virginia Plá, Lauro Sumoy and Fernando Aguado
    Citation: BMC Genomics 2016 17:304
    Content type: Research article Published on:

  5. Valeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots ...

    Authors: Yun Ji Park, Xiaohua Li, Seung Jae Noh, Jae Kwang Kim, Soon Sung Lim, Nam Il Park, Soonok Kim, Yeon Bok Kim, Young Ock Kim, Sang Won Lee, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi and Sang Un Park
    Citation: BMC Genomics 2016 17:303
    Content type: Research article Published on:

  6. Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinf...

    Authors: Jelena Čuklina, Julia Hahn, Maxim Imakaev, Ulrich Omasits, Konrad U. Förstner, Nikolay Ljubimov, Melanie Goebel, Gabriella Pessi, Hans-Martin Fischer, Christian H. Ahrens, Mikhail S. Gelfand and Elena Evguenieva-Hackenberg
    Citation: BMC Genomics 2016 17:302
    Content type: Research article Published on:

  7. Pine wilt disease (PWD) is a worldwide threat to pine forests, and is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus. Bacteria are known to be associated with PWN and may have an important role...

    Authors: Claudia S. L. Vicente, Francisco X. Nascimento, Yoriko Ikuyo, Peter J. A. Cock, Manuel Mota and Koichi Hasegawa
    Citation: BMC Genomics 2016 17:301
    Content type: Research article Published on:

  8. Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatib...

    Authors: P. Gramazio, J. Blanca, P. Ziarsolo, F. J. Herraiz, M. Plazas, J. Prohens and S. Vilanova
    Citation: BMC Genomics 2016 17:300
    Content type: Research article Published on:

  9. Dissecting the role copy number variants (CNVs) play in disease pathogenesis is directly reliant on accurate methods for quantification. The Shar-Pei dog breed is predisposed to a complex autoinflammatory dise...

    Authors: M. Olsson, M. Kierczak, Å. Karlsson, J. Jabłońska, P. Leegwater, M. Koltookian, J. Abadie, C. Dufaure De Citres, A. Thomas, Å. Hedhammar, L. Tintle, K. Lindblad-Toh and J. R. S. Meadows
    Citation: BMC Genomics 2016 17:299
    Content type: Research article Published on:

  10. Nonalcoholic fatty liver disease (NAFLD) is a major health problem and a leading cause of chronic liver disease in the United States and Western countries. In humans, genetic factors greatly influence individu...

    Authors: Volodymyr P. Tryndyak, Tao Han, James C. Fuscoe, Sharon A. Ross, Frederick A. Beland and Igor P. Pogribny
    Citation: BMC Genomics 2016 17:298
    Content type: Research article Published on:

  11. Non-heading Chinese cabbage (NHCC, Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, little is known about the molecular mechanisms underlying tolerance for extreme temperatur...

    Authors: Xiaoming Song, Gaofeng Liu, Zhinan Huang, Weike Duan, Huawei Tan, Ying Li and Xilin Hou
    Citation: BMC Genomics 2016 17:297
    Content type: Research article Published on:

  13. Improving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci (Q...

    Authors: Dexin Liu, Jian Zhang, Xueying Liu, Wenwen Wang, Dajun Liu, Zhonghua Teng, Xiaomei Fang, Zhaoyun Tan, Shiyi Tang, Jinghong Yang, Jianwei Zhong and Zhengsheng Zhang
    Citation: BMC Genomics 2016 17:295
    Content type: Research article Published on:

  14. Spermatogenesis is a complex differentiation process that involves the successive and simultaneous execution of three different gene expression programs: mitotic proliferation of spermatogonia, meiosis, and sp...

    Authors: Irene da Cruz, Rosana Rodríguez-Casuriaga, Federico F. Santiñaque, Joaquina Farías, Gianni Curti, Carlos A. Capoano, Gustavo A. Folle, Ricardo Benavente, José Roberto Sotelo-Silveira and Adriana Geisinger
    Citation: BMC Genomics 2016 17:294
    Content type: Research article Published on:

  15. Campylobacter is the leading cause of foodborne diarrhoeal illness in humans and is mostly acquired from consumption or handling of contaminated poultry meat. In the absence of effecti...

    Authors: A. Psifidi, M. Fife, J. Howell, O. Matika, P. M. van Diemen, R. Kuo, J. Smith, P. M. Hocking, N. Salmon, M. A. Jones, D. A. Hume, G. Banos, M. P. Stevens and P. Kaiser
    Citation: BMC Genomics 2016 17:293
    Content type: Research article Published on:

  17. De-etiolation is the switch from skoto- to photomorphogenesis, enabling the heterotrophic etiolated seedling to develop into an autotrophic plant. Upon exposure to blue light (BL), reduction of hypocotyl growt...

    Authors: Petra Hloušková and Véronique Bergougnoux
    Citation: BMC Genomics 2016 17:291
    Content type: Research article Published on:

  19. The commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called ‘palm oil’) with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturat...

    Authors: Ngoot-Chin Ting, Zulkifli Yaakub, Katialisa Kamaruddin, Sean Mayes, Festo Massawe, Ravigadevi Sambanthamurthi, Johannes Jansen, Leslie Eng Ti Low, Maizura Ithnin, Ahmad Kushairi, Xaviar Arulandoo, Rozana Rosli, Kuang-Lim Chan, Nadzirah Amiruddin, Kandha Sritharan, Chin Ching Lim…
    Citation: BMC Genomics 2016 17:289
    Content type: Research article Published on:

  20. Stallion fertility is an economically important trait due to the increase of artificial insemination in horses. The availability of whole genome sequence data facilitates identification of rare high-impact var...

    Authors: Rahel Schrimpf, Maren Gottschalk, Julia Metzger, Gunilla Martinsson, Harald Sieme and Ottmar Distl
    Citation: BMC Genomics 2016 17:288
    Content type: Research article Published on:

  21. Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemist...

    Authors: Angelica Van Goor, Christopher M. Ashwell, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt and Susan J. Lamont
    Citation: BMC Genomics 2016 17:287
    Content type: Research article Published on:

  22. Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus ...

    Authors: C. Drury, K. E. Dale, J. M. Panlilio, S. V. Miller, D. Lirman, E. A. Larson, E. Bartels, D. L. Crawford and M. F. Oleksiak
    Citation: BMC Genomics 2016 17:286
    Content type: Research article Published on:

  23. To date, studies investigating the association between ACTN3 R577X and ACE I/D gene variants and elite sprint/power performance have been limited by small cohorts from mixed sport disciplines, without quantitativ...

    Authors: Ioannis D. Papadimitriou, Alejandro Lucia, Yannis P. Pitsiladis, Vladimir P. Pushkarev, Dmitry A. Dyatlov, Evgeniy F. Orekhov, Guilherme G. Artioli, João Paulo L. F. Guilherme, Antonio H. Lancha Jr, Valentina Ginevičienė, Pawel Cieszczyk, Agnieszka Maciejewska-Karlowska, Marek Sawczuk, Carlos A. Muniesa, Anastasia Kouvatsi, Myosotis Massidda…
    Citation: BMC Genomics 2016 17:285
    Content type: Research article Published on:

  24. The inherent potential of filamentous fungi, especially of Ascomycota, for producing diverse bioactive metabolites remains largely silent under standard laboratory culture conditions. Innumerable strategies ha...

    Authors: Paula C. Alves, Diego O. Hartmann, Oscar Núñez, Isabel Martins, Teresa L. Gomes, Helga Garcia, Maria Teresa Galceran, Richard Hampson, Jörg D. Becker and Cristina Silva Pereira
    Citation: BMC Genomics 2016 17:284
    Content type: Research article Published on:

  25. MicroRNAs (miRNAs), which comprise a large family of endogenous small non-coding RNA molecules, play important roles in the regulation of gene expression in various biological processes. The Chinese rare minnow (

    Authors: Xiangsheng Hong, Jianhui Qin, Rui Chen, Lilai Yuan, Jinmiao Zha and Zijian Wang
    Citation: BMC Genomics 2016 17:283
    Content type: Research article Published on:

  26. Studying transcription factors, which are some of the key players in gene expression, is of outstanding interest for the investigation of the evolutionary history of organisms through lineage-specific features...

    Authors: Stanislas Thiriet-Rupert, Grégory Carrier, Benoît Chénais, Camille Trottier, Gaël Bougaran, Jean-Paul Cadoret, Benoît Schoefs and Bruno Saint-Jean
    Citation: BMC Genomics 2016 17:282
    Content type: Research article Published on:

  27. Despite the broad diet range of many predatory ladybirds, the mechanisms involved in their adaptation to diet shifts are not completely understood. Here, we explored how a primarily coccidophagous ladybird Crypto...

    Authors: Hao-Sen Li, Chang Pan, Patrick De Clercq, Adam Ślipiński and Hong Pang
    Citation: BMC Genomics 2016 17:281
    Content type: Research article Published on:

  28. The invertebrate immune system comprises physiological mechanisms, physical barriers and also behavioral responses. It is generally related to the vertebrate innate immune system and widely believed to provide...

    Authors: Rania Nakad, L. Basten Snoek, Wentao Yang, Sunna Ellendt, Franziska Schneider, Timm G. Mohr, Lone Rösingh, Anna C. Masche, Philip C. Rosenstiel, Katja Dierking, Jan E. Kammenga and Hinrich Schulenburg
    Citation: BMC Genomics 2016 17:280
    Content type: Research article Published on:

  29. Infectious Pancreatic Necrosis (IPN) is a highly contagious birnavirus disease of farmed salmonid fish, which often causes high levels of morbidity and mortality. A large host genetic component to resistance h...

    Authors: Diego Robledo, John B. Taggart, Jacqueline H. Ireland, Brendan J. McAndrew, William G. Starkey, Chris S. Haley, Alastair Hamilton, Derrick R. Guy, Jose C. Mota-Velasco, Almas A. Gheyas, Alan E. Tinch, David W. Verner-Jeffreys, Richard K. Paley, Georgina S. E. Rimmer, Ian J. Tew, Stephen C. Bishop…
    Citation: BMC Genomics 2016 17:279
    Content type: Research article Published on:

  30. Expression QTLs and epigenetic marks are often employed to provide an insight into the possible biological mechanisms behind GWAS hits. A substantial proportion of the variation in gene expression and DNA meth...

    Authors: Konstantin Shakhbazov, Joseph E. Powell, Gibran Hemani, Anjali K. Henders, Nicholas G. Martin, Peter M. Visscher, Grant W. Montgomery and Allan F. McRae
    Citation: BMC Genomics 2016 17:278
    Content type: Research article Published on:

  31. Cytomegaloviruses belong to a large, ancient, genus of DNA viruses comprised of a wide array of species-specific strains that occur in diverse array of hosts.

    Authors: Justen N. Hoffman Russell, Angie K. Marsh, David O. Willer, Aruna P. N. Ambagala, Misko Dzamba, Jacqueline K. Chan, Richard Pilon, Jocelyn Fournier, Michael Brudno, Joseph M. Antony, Paul Sandstrom, Ben J. Evans and Kelly S. MacDonald
    Citation: BMC Genomics 2016 17:277
    Content type: Research article Published on:

  32. The variation in serum uric acid concentrations is under significant genetic influence. Elevated SUA concentrations have been linked to increased risk for gout, kidney stones, chronic kidney disease, and cardi...

    Authors: Geetha Chittoor, Jack W. Kent Jr, Marcio Almeida, Sobha Puppala, Vidya S. Farook, Shelley A. Cole, Karin Haack, Harald H. H. Göring, Jean W. MacCluer, Joanne E. Curran, Melanie A. Carless, Matthew P. Johnson, Eric K. Moses, Laura Almasy, Michael C. Mahaney, Donna M. Lehman…
    Citation: BMC Genomics 2016 17:276
    Content type: Research article Published on:

  33. We performed an analysis of the transcriptome during the blastogenesis of the chordate Botryllus schlosseri, focusing in particular on genes involved in cell death by apoptosis. The tunicate B. schlosseri is an a...

    Authors: Davide Campagna, Fabio Gasparini, Nicola Franchi, Nicola Vitulo, Francesca Ballin, Lucia Manni, Giorgio Valle and Loriano Ballarin
    Citation: BMC Genomics 2016 17:275
    Content type: Research article Published on:

  34. Identification of locus-locus contacts at the chromatin level provides a valuable foundation for understanding of nuclear architecture and function and a valuable tool for inferring long-range linkage relation...

    Authors: Idan Gabdank, Sreejith Ramakrishnan, Anne M. Villeneuve and Andrew Z. Fire
    Citation: BMC Genomics 2016 17:274
    Content type: Methodology article Published on:

  35. Proton irradiation poses a potential hazard to astronauts during and following a mission, with post-mitotic cells at most risk because they cannot dilute resultant epigenetic changes via cell division. Persist...

    Authors: Soren Impey, Carl Pelz, Amanuel Tafessu, Tessa Marzulla, Mitchell S. Turker and Jacob Raber
    Citation: BMC Genomics 2016 17:273
    Content type: Research article Published on:

  36. The protist Plasmodiophora brassicae is a soil-borne pathogen of cruciferous species and the causal agent of clubroot disease of Brassicas including agriculturally important crops such as canola/rapeseed (Brassic...

    Authors: Stephen A. Rolfe, Stephen E. Strelkov, Matthew G. Links, Wayne E. Clarke, Stephen J. Robinson, Mohammad Djavaheri, Robert Malinowski, Parham Haddadi, Sateesh Kagale, Isobel A. P. Parkin, Ali Taheri and M. Hossein Borhan
    Citation: BMC Genomics 2016 17:272
    Content type: Research article Published on:

  37. Sheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to de...

    Authors: Shailaja Hittalmani, H. B. Mahesh, Channappa Mahadevaiah and Mothukapalli Krishnareddy Prasannakumar
    Citation: BMC Genomics 2016 17:271
    Content type: Research article Published on:

  39. Optimization of shade avoidance response (SAR) is crucial for enhancing crop yield in high-density planting conditions in modern agriculture, but a comprehensive study of the regulatory network of SAR is still...

    Authors: Hai Wang, Guangxia Wu, Binbin Zhao, Baobao Wang, Zhihong Lang, Chunyi Zhang and Haiyang Wang
    Citation: BMC Genomics 2016 17:269
    Content type: Research article Published on:

  40. Membrane proteins are key components in a large spectrum of diverse functions and thus account for the major proportion of the drug-targeted portion of the genome. From a structural perspective, the α-helical ...

    Authors: Misty M. Attwood, Arunkumar Krishnan, Valentina Pivotti, Samira Yazdi, Markus Sällman Almén and Helgi B. Schiöth
    Citation: BMC Genomics 2016 17:268
    Content type: Research article Published on:

  41. Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies o...

    Authors: Marijke J. van Baren, Charles Bachy, Emily Nahas Reistetter, Samuel O. Purvine, Jane Grimwood, Sebastian Sudek, Hang Yu, Camille Poirier, Thomas J. Deerinck, Alan Kuo, Igor V. Grigoriev, Chee-Hong Wong, Richard D. Smith, Stephen J. Callister, Chia-Lin Wei, Jeremy Schmutz…
    Citation: BMC Genomics 2016 17:267
    Content type: Research article Published on:

  42. Affymetrix Axiom single nucleotide polymorphism (SNP) arrays provide a cost-effective, high-density, and high-throughput genotyping solution for population-optimized analyses. However, no public software is av...

    Authors: Mei-Chu Huang, Tzu-Po Chuang, Chien-Hsiun Chen, Jer-Yuarn Wu, Yuan-Tsong Chen, Ling-Hui Li and Hsin-Chou Yang
    Citation: BMC Genomics 2016 17:266
    Content type: Research article Published on:

  43. The reduced cost and improved efficiency of whole genome sequencing (WGS) is drastically improving the development of cats as biomedical models. Persian cats are models for Leber’s congenital amaurosis (LCA), ...

    Authors: Leslie A. Lyons, Erica K. Creighton, Hasan Alhaddad, Holly C. Beale, Robert A. Grahn, HyungChul Rah, David J. Maggs, Christopher R. Helps and Barbara Gandolfi
    Citation: BMC Genomics 2016 17:265
    Content type: Research article Published on:

  44. The microtubule associated protein Tau (MAPT) promotes assembly and interaction of microtubules with the cytoskeleton, impinging on axonal transport and synaptic plasticity. Its neuronal expression and intrins...

    Authors: Frederik Sündermann, Maria-Pilar Fernandez and Reginald O. Morgan
    Citation: BMC Genomics 2016 17:264
    Content type: Research article Published on:

  45. It has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive mod...

    Authors: Matt R. Paul, Nicholas P. Levitt, David E. Moore, Patricia M. Watson, Robert C. Wilson, Chadrick E. Denlinger, Dennis K. Watson and Paul E. Anderson
    Citation: BMC Genomics 2016 17:263
    Content type: Research Article Published on:

  46. Ridge regression models can be used for predicting heterosis and hybrid performance. Their application to mRNA transcription profiles has not yet been investigated. Our objective was to compare the prediction ...

    Authors: Carola Zenke-Philippi, Alexander Thiemann, Felix Seifert, Tobias Schrag, Albrecht E. Melchinger, Stefan Scholten and Matthias Frisch
    Citation: BMC Genomics 2016 17:262
    Content type: Research Article Published on:

  47. Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important tra...

    Authors: Zetao Bai, Jinfeng Chen, Yi Liao, Meijiao Wang, Rong Liu, Song Ge, Rod A. Wing and Mingsheng Chen
    Citation: BMC Genomics 2016 17:261
    Content type: Research article Published on:

  48. Liver regeneration is inhibited by chronic ethanol consumption and this impaired repair response may contribute to the risk for alcoholic liver disease. We developed and applied a novel data analysis approach ...

    Authors: Lakshmi Kuttippurathu, Egle Juskeviciute, Rachael P Dippold, Jan B. Hoek and Rajanikanth Vadigepalli
    Citation: BMC Genomics 2016 17:260
    Content type: Research article Published on:

  49. We have previously found substantial animal-to-animal and age-dependent variation in the response of Holstein fibroblast cultures challenged with LPS. To expand on this finding, fibroblast cultures were establ...

    Authors: Aimee L. Benjamin, Benjamin B. Green, Brian A. Crooker, Stephanie D. McKay and David E. Kerr
    Citation: BMC Genomics 2016 17:258
    Content type: Research article Published on:

  50. Rubber tree (Hevea brasiliensis) is an important industrial crop cultivated in tropical areas for natural rubber production. Treatment of the bark of rubber trees with ehephon (an ethylene releaser) has been a ro...

    Authors: Jin-Ping Liu, Yu-Fen Zhuang, Xiu-Li Guo and Yi-Jian Li
    Citation: BMC Genomics 2016 17:257
    Content type: Research article Published on:

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BMC Genomics

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