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  1. Mitogen-activated protein kinase kinase kinases (MAPKKKs) are the important components of MAPK cascades, which play the crucial role in plant growth and development as well as in response to diverse stresses. ...

    Authors: Meng Wang, Hong Yue, Kewei Feng, Pingchuan Deng, Weining Song and Xiaojun Nie
    Citation: BMC Genomics 2016 17:668
    Content type: Research article Published on:

  2. Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding ...

    Authors: Claire Anderson, Muhammad Adil Khan, Ann-Maree Catanzariti, Cameron A. Jack, Adnane Nemri, Gregory J. Lawrence, Narayana M. Upadhyaya, Adrienne R. Hardham, Jeffrey G. Ellis, Peter N. Dodds and David A. Jones
    Citation: BMC Genomics 2016 17:667
    Content type: Research article Published on:

  3. Duchenne muscular dystrophy (DMD) causes progressive muscle degeneration, cardiomyopathy and respiratory failure in approximately 1/5,000 boys. Golden Retriever muscular dystrophy (GRMD) resembles DMD both cli...

    Authors: Candice Brinkmeyer-Langford, Cynthia Balog-Alvarez, James J. Cai, Brian W. Davis and Joe N. Kornegay
    Citation: BMC Genomics 2016 17:665
    Content type: Research article Published on:

  5. Tumor suppressor genes (TSGs) encode the guardian molecules to control cell growth. The genomic alteration of TSGs may cause tumorigenesis and promote cancer progression. So far, investigators have mainly stud...

    Authors: Min Zhao and Zhongming Zhao
    Citation: BMC Genomics 2016 17(Suppl 7):532
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  6. Proper cell models for breast cancer primary tumors have long been the focal point in the cancer’s research. The genomic comparison between cell lines and tumors can investigate the similarity and dissimilarit...

    Authors: Guanglong Jiang, Shijun Zhang, Aida Yazdanparast, Meng Li, Aniruddha Vikram Pawar, Yunlong Liu, Sai Mounika Inavolu and Lijun Cheng
    Citation: BMC Genomics 2016 17(Suppl 7):525
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  7. We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected...

    Authors: Kun Huang, Yunlong Liu, Yufei Huang, Lang Li, Lee Cooper, Jianhua Ruan and Zhongming Zhao
    Citation: BMC Genomics 2016 17(Suppl 7):524
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  8. Clinical proteomics application aims at solving a specific clinical problem within the context of a clinical study. It has been growing rapidly in the field of biomarker discovery, especially in the area of ca...

    Authors: Fan Zhang and Jake Y. Chen
    Citation: BMC Genomics 2016 17(Suppl 7):522
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  9. The recent advent of the state-of-art high throughput sequencing technology, known as Methylated RNA Immunoprecipitation combined with RNA sequencing (MeRIP-seq) revolutionizes the area of mRNA epigenetics and...

    Authors: Xiaodong Cui, Jia Meng, Shaowu Zhang, Manjeet K. Rao, Yidong Chen and Yufei Huang
    Citation: BMC Genomics 2016 17(Suppl 7):520
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  10.  Gene co-expression network analysis (GCNA) is widely adopted in bioinformatics and biomedical research with applications such as gene function prediction, protein-protein interaction inference, disease marker...

    Authors: Zhi Han, Jie Zhang, Guoyuan Sun, Gang Liu and Kun Huang
    Citation: BMC Genomics 2016 17(Suppl 7):519
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  11. Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer. Recent large-scale next-generation sequencing analyses reveal that PBRM1 is the second most frequently mutated gene harboring many...

    Authors: Yuanyuan Wang, Xingyi Guo, Michael J. Bray, Zhiyong Ding and Zhongming Zhao
    Citation: BMC Genomics 2016 17(Suppl 7):515
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

    The Erratum to this article has been published in BMC Genomics 2016 17:821

  12. Sensitive detection of low-frequency single nucleotide variants carries great significance in many applications. In cancer genetics research, tumor biopsies are a mixture of normal and tumor cells from various...

    Authors: Yangyang Hao, Pengyue Zhang, Xiaoling Xuei, Harikrishna Nakshatri, Howard J. Edenberg, Lang Li and Yunlong Liu
    Citation: BMC Genomics 2016 17(Suppl 7):514
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  13. We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated...

    Authors: Chandirasegaran Massilamany, Akram Mohammed, John Dustin Loy, Tanya Purvis, Bharathi Krishnan, Rakesh H. Basavalingappa, Christy M. Kelley, Chittibabu Guda, Raúl G. Barletta, Etsuko N. Moriyama, Timothy P. L. Smith and Jay Reddy
    Citation: BMC Genomics 2016 17(Suppl 7):511
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  14. Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular responses. LPS pre-conditioning was previously shown to improve the therapeutic efficacy of bone marrow stromal ...

    Authors: Ao Zhou, Meng Li, Bo He, Weixing Feng, Fei Huang, Bing Xu, A. Keith Dunker, Curt Balch, Baiyan Li, Yunlong Liu and Yue Wang
    Citation: BMC Genomics 2016 17(Suppl 7):509
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  15. The advancement of the next-generation sequencing technology enables mapping gene expression at the single-cell level, capable of tracking cell heterogeneity and determination of cell subpopulations using sing...

    Authors: Hung-I Harry Chen, Yufang Jin, Yufei Huang and Yidong Chen
    Citation: BMC Genomics 2016 17(Suppl 7):508
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  16. Improved DNA sequencing methods have transformed the field of genomics over the last decade. This has become possible due to the development of inexpensive short read sequencing technologies which have now res...

    Authors: Yesesri Cherukuri and Sarath Chandra Janga
    Citation: BMC Genomics 2016 17(Suppl 7):507
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  17. Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-qual...

    Authors: Feifei Xu, Jinsong Bao, Qiang He and Yong-Jin Park
    Citation: BMC Genomics 2016 17:663
    Content type: Research article Published on:

  18. Exposure of the budding Saccharomyces cerevisiae to an alkaline environment produces a robust transcriptional response involving hundreds of genes. Part of this response is triggered by an almost immediate burst ...

    Authors: Alicia Roque, Silvia Petrezsélyová, Albert Serra-Cardona and Joaquín Ariño
    Citation: BMC Genomics 2016 17:662
    Content type: Research article Published on:

  19. Agrobacterium tumefaciens strain P4 is atypical, as the strain is not pathogenic and produces a for this species unusual quorum sensing signal, identified as N-(3-hydroxy-octanoyl)-hom...

    Authors: Nadia Mhedbi-Hajri, Noura Yahiaoui, Samuel Mondy, Nathalie Hue, Franck Pélissier, Denis Faure and Yves Dessaux
    Citation: BMC Genomics 2016 17:661
    Content type: Research article Published on:

  20. Cichlid fishes have evolved remarkably diverse reproductive, social, and feeding behaviors. Cell-to-cell signaling molecules, notably neuropeptides and peptide hormones, are known to regulate these behaviors a...

    Authors: Caroline K. Hu, Bruce R. Southey, Elena V. Romanova, Karen P. Maruska, Jonathan V. Sweedler and Russell D. Fernald
    Citation: BMC Genomics 2016 17:660
    Content type: Research article Published on:

  21. The program RepeatMasker and the database Repbase-ISB are part of the most widely used strategy for annotating repeats in animal genomes. They have been used to show that avian genomes have a lower repeat cont...

    Authors: Sébastien Guizard, Benoît Piégu, Peter Arensburger, Florian Guillou and Yves Bigot
    Citation: BMC Genomics 2016 17:659
    Content type: Research article Published on:

  22. Medicago sativa (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Transgenic a...

    Authors: Ruimin Gao, Ryan S. Austin, Lisa Amyot and Abdelali Hannoufa
    Citation: BMC Genomics 2016 17:658
    Content type: Research article Published on:

  23. Soil salinity affects growth and yield of crop plants. Plants respond to salinity by physiological and biochemical adjustments through a coordinated regulation and expression of a cascade of genes. Recently, h...

    Authors: Renesh Bedre, Venkata Ramanarao Mangu, Subodh Srivastava, Luis Eduardo Sanchez and Niranjan Baisakh
    Citation: BMC Genomics 2016 17:657
    Content type: Research article Published on:

  24. Restriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species. RAD-seq is capable of discovering thou...

    Authors: Mohaddeseh Mousavi, Chunfa Tong, Fenxiang Liu, Shentong Tao, Jiyan Wu, Huogen Li and Jisen Shi
    Citation: BMC Genomics 2016 17:656
    Content type: Research article Published on:

  25. Previously, several long non-coding RNAs (lncRNAs) were characterized as regulators in phosphate (Pi) starvation responses. However, systematic studies of novel lncRNAs involved in the Pi starvation signaling ...

    Authors: Jiapei Yuan, Ye Zhang, Jinsong Dong, Yuzhe Sun, Boon L. Lim, Dong Liu and Zhi John Lu
    Citation: BMC Genomics 2016 17:655
    Content type: Research article Published on:

  27. Marine and freshwater zooplankton exhibit daily rhythmic patterns of behavior and physiology which may be regulated directly by the light:dark (LD) cycle and/or a molecular circadian clock. One of the best-stu...

    Authors: Samuel S. C. Rund, Boyoung Yoo, Camille Alam, Taryn Green, Melissa T. Stephens, Erliang Zeng, Gary F. George, Aaron D. Sheppard, Giles E. Duffield, Tijana Milenković and Michael E. Pfrender
    Citation: BMC Genomics 2016 17:653
    Content type: Research article Published on:

  28. Understanding the regulation mechanism of var gene expression is crucial for explaining antigenic variation in Plasmodium falciparum. Recent work observed that while all var genes produce transcripts, only a few

    Authors: Chengqi Wang, Swamy R. Adapa, Justin Gibbons, Stephen Sutton and Rays H. Y. Jiang
    Citation: BMC Genomics 2016 17:652
    Content type: Research article Published on:

  29. Eogystia hippophaecolus (Hua et al.) (Lepidoptera: Cossidae) is the major threat to seabuckthorn plantations in China. Specific and highly efficient artificial sex pheromone traps was ...

    Authors: Ping Hu, Jing Tao, Mingming Cui, Chenglong Gao, Pengfei Lu and Youqing Luo
    Citation: BMC Genomics 2016 17:651
    Content type: Research article Published on:

  30. Structural excursions of a protein at equilibrium are key to biomolecular recognition and function modulation. Protein modeling research is driven by the need to aid wet laboratories in characterizing equilibr...

    Authors: Emmanuel Sapin, Daniel B. Carr, Kenneth A. De Jong and Amarda Shehu
    Citation: BMC Genomics 2016 17(Suppl 4):546
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  31. A fundamental challenge in quantitation of biomolecules for cancer biomarker discovery is owing to the heterogeneous nature of human biospecimens. Although this issue has been a subject of discussion in cancer...

    Authors: Minkun Wang, Tsung-Heng Tsai, Cristina Di Poto, Alessia Ferrarini, Guoqiang Yu and Habtom W. Ressom
    Citation: BMC Genomics 2016 17(Suppl 4):545
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  32. The longest common subsequence (LCS) problem is a classical problem in computer science, and forms the basis of the current best-performing reference-based compression schemes for genome resequencing data.

    Authors: Richard Beal, Tazin Afrin, Aliya Farheen and Donald Adjeroh
    Citation: BMC Genomics 2016 17(Suppl 4):544
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  33. In biological systems, diseases are caused by small perturbations in a complex network of interactions between proteins. Perturbations typically affect only a small number of proteins, which go on to disturb a...

    Authors: Narmada Sambaturu, Madhulika Mishra and Nagasuma Chandra
    Citation: BMC Genomics 2016 17(Suppl 4):543
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  34. Motif search is an important step in extracting meaningful patterns from biological data. The general problem of motif search is intractable and there is a pressing need to develop efficient, exact and approxi...

    Authors: Soumitra Pal, Peng Xiao and Sanguthevar Rajasekaran
    Citation: BMC Genomics 2016 17(Suppl 4):465
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  35. High throughput molecular sequencing and increased biospecimen variety have introduced significant informatics challenges for research biorepository infrastructures. We applied a modular system integration app...

    Authors: Alex S. Felmeister, Aaron J. Masino, Tyler J. Rivera, Adam C. Resnick and Jeffrey W. Pennington
    Citation: BMC Genomics 2016 17(Suppl 4):434
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  36. Diabetes mellitus characterized by hyperglycemia as a result of insufficient production of or reduced sensitivity to insulin poses a growing threat to the health of people. It is a heterogeneous disorder with ...

    Authors: Xiwei Tang, Xiaohua Hu, Xuejun Yang, Yetian Fan, Yongfan Li, Wei Hu, Yongzhong Liao, Ming cai Zheng, Wei Peng and Li Gao
    Citation: BMC Genomics 2016 17(Suppl 4):433
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  37. Since its initial discovery in 1975, DNA methylation has been intensively studied and shown to be involved in various biological processes, such as development, aging and tumor progression. Many experimental t...

    Authors: Yuanhang Liu, Desiree Wilson, Robin J. Leach and Yidong Chen
    Citation: BMC Genomics 2016 17(Suppl 4):432
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  38. The human kinome contains many important drug targets. It is well-known that inhibitors of protein kinases bind with very different selectivity profiles. This is also the case for inhibitors of many other prot...

    Authors: Mark Moll, Paul W. Finn and Lydia E. Kavraki
    Citation: BMC Genomics 2016 17(Suppl 4):431
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  39. Accurately identifying gene regulatory network is an important task in understanding in vivo biological activities. The inference of such networks is often accomplished through the use of gene expression data....

    Authors: Lu Zhang, Xi Kang Feng, Yen Kaow Ng and Shuai Cheng Li
    Citation: BMC Genomics 2016 17(Suppl 4):430
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  40. Cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Many cubozoans have a particularly potent sting, effected by stinging structures called nematocysts; cubozoans ha...

    Authors: Cheryl Lewis Ames, Joseph F. Ryan, Alexandra E. Bely, Paulyn Cartwright and Allen G. Collins
    Citation: BMC Genomics 2016 17:650
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:980

  41. MicroRNAs (miRNA) are varied in length, under 25 nucleotides, single-stranded noncoding RNA that regulate post-transcriptional gene expression via translational repression or mRNA degradation. Elevated levels ...

    Authors: Erik M. Koenig, Craig Fisher, Hugues Bernard, Francis S. Wolenski, Joseph Gerrein, Mary Carsillo, Matt Gallacher, Aimy Tse, Rachel Peters, Aaron Smith, Alexa Meehan, Stephen Tirrell and Patrick Kirby
    Citation: BMC Genomics 2016 17:649
    Content type: Research article Published on:

  42. Drosophila suzukii differs from other melanogaster group members in their proclivity for laying eggs in fresh fruit rather than in fermenting fruits. Olfaction and gustation play a cri...

    Authors: Paul V. Hickner, Chissa L. Rivaldi, Cole M. Johnson, Madhura Siddappaji, Gregory J. Raster and Zainulabeuddin Syed
    Citation: BMC Genomics 2016 17:648
    Content type: Research article Published on:

  44. Zearalenone (ZEA) is a secondary metabolite produced by Fusarium species. ZEA was proved to exert a wide range of unwanted side effects, but its mechanism of action, particularly at duodenum levels, remains un...

    Authors: Cornelia Braicu, Roxana Cojocneanu-Petric, Ancuta Jurj, Diana Gulei, Ionelia Taranu, Alexandru Mihail Gras, Daniela Eliza Marin and Ioana Berindan-Neagoe
    Citation: BMC Genomics 2016 17:646
    Content type: Research article Published on:

  46. Epstein-Barr virus (EBV) establishes lifelong infections in its human host. The virus is associated with a broad range of malignancies of lymphoid and epithelial origin, including Burkitt’s lymphoma, post-tran...

    Authors: Marjolein J. G. Hooykaas, Elisabeth Kruse, Emmanuel J. H. J. Wiertz and Robert Jan Lebbink
    Citation: BMC Genomics 2016 17:644
    Content type: Research article Published on:

  47. Building up of pathway-/disease-relevant signatures provides a persuasive tool for understanding the functional relevance of gene alterations and gene network associations in multifactorial human diseases. Ova...

    Authors: Martin Svoboda, Anastasia Meshcheryakova, Georg Heinze, Markus Jaritz, Dietmar Pils, Dan Cacsire Castillo-Tong, Gudrun Hager, Theresia Thalhammer, Erika Jensen-Jarolim, Peter Birner, Ioana Braicu, Jalid Sehouli, Sandrina Lambrechts, Ignace Vergote, Sven Mahner, Philip Zimmermann…
    Citation: BMC Genomics 2016 17:643
    Content type: Research article Published on:

  48. Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size...

    Authors: Sandip Chatterjee, Gregory S. Stupp, Sung Kyu Robin Park, Jean-Christophe Ducom, John R. Yates III, Andrew I. Su and Dennis W. Wolan
    Citation: BMC Genomics 2016 17:642
    Content type: Methodology article Published on:

  49. A combined supplement of vitamins B9 and B12 was reported to increase milk and milk component yields of dairy cows without effect on feed intake. The present study was undertaken to verify whether this supplem...

    Authors: Bazoumana Ouattara, Nathalie Bissonnette, Melissa Duplessis and Christiane L. Girard
    Citation: BMC Genomics 2016 17:640
    Content type: Research article Published on:

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