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  2. Kawasaki Disease (KD) can cause potentially life-threatening coronary arteritis in young children, and has a likely infectious etiology. Transcriptome profiling is a powerful approach to investigate gene expre...

    Authors: Anne H. Rowley, Kristine M. Wylie, Kwang-Youn A. Kim, Adam J. Pink, Amy Yang, Rebecca Reindel, Susan C. Baker, Stanford T. Shulman, Jan M. Orenstein, Mark W. Lingen, George M. Weinstock and Todd N. Wylie
    Citation: BMC Genomics 2015 16:1076
    Content type: Research article Published on:

  3. Rickettsia species are obligate intracellular Gram-negative pathogenic bacteria and the etiologic agents of diseases such as Rocky Mountain spotted fever (RMSF), Mediterranean spotted ...

    Authors: Casey L. C. Schroeder, Hema P. Narra, Mark Rojas, Abha Sahni, Jignesh Patel, Kamil Khanipov, Thomas G. Wood, Yuriy Fofanov and Sanjeev K. Sahni
    Citation: BMC Genomics 2015 16:1075
    Content type: Research article Published on:

  4. Homeostasis of ions and water is important for the maintenance of cellular functions. The regulation of the homeostasis is particularly important in euryhaline fish that migrate between freshwater (FW) and sea...

    Authors: Keng Po Lai, Jing-Woei Li, Je Gu, Ting-Fung Chan, William Ka Fai Tse and Chris Kong Chu Wong
    Citation: BMC Genomics 2015 16:1072
    Content type: Research article Published on:

  5. Comparison between multiple protein datasets requires the choice of an appropriate reference system and a number of variables to describe their differences. Here we introduce an innovative approach to discrimi...

    Authors: Petr Klus, Riccardo Delli Ponti, Carmen Maria Livi and Gian Gaetano Tartaglia
    Citation: BMC Genomics 2015 16:1071
    Content type: Software Published on:

  6. Zygosaccharomyces bailii is considered the most problematic acidic food spoilage yeast species due to its exceptional capacity to tolerate high concentrations of weak acids used as fun...

    Authors: Margarida Palma, Filipa de Canaveira Roque, Joana Fernandes Guerreiro, Nuno Pereira Mira, Lise Queiroz and Isabel Sá-Correia
    Citation: BMC Genomics 2015 16:1070
    Content type: Research article Published on:

  7. Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amou...

    Authors: Wenli Li, Amy Turner, Praful Aggarwal, Andrea Matter, Erin Storvick, Donna K. Arnett and Ulrich Broeckel
    Citation: BMC Genomics 2015 16:1069
    Content type: Research article Published on:

  8. While transcriptomics have become a valuable tool for linking physiology and ecology in aquatic microbes, the temporal dynamics of global transcriptomic patterns in Microcystis have rarely been assessed. Furtherm...

    Authors: Matthew J. Harke and Christopher J. Gobler
    Citation: BMC Genomics 2015 16:1068
    Content type: Research article Published on:

  9. Increasing rice (Oryza sativa L.) yield is a crucial challenge for modern agriculture. The ideal plant architecture is considered to be critical to enhance rice yield. Elite plant morphological traits should incl...

    Authors: Qing Lu, Mengchen Zhang, Xiaojun Niu, Shan Wang, Qun Xu, Yue Feng, Caihong Wang, Hongzhong Deng, Xiaoping Yuan, Hanyong Yu, Yiping Wang and Xinghua Wei
    Citation: BMC Genomics 2015 16:1067
    Content type: Research article Published on:

  10. Several Gram-negative species undergo development leading to the formation of metabolically dormant desiccation resistant cysts. Recent analysis of cyst development has revealed that ~20 % of the Rhodospirillum c...

    Authors: Qian Dong, Mingxu Fang, Sugata Roychowdhury and Carl E. Bauer
    Citation: BMC Genomics 2015 16:1066
    Content type: Research article Published on:

  11. The molecular mechanisms that determine the organism's response to a variety of doses and modalities of stress factors are not well understood.

    Authors: Alexey Moskalev, Svetlana Zhikrivetskaya, George Krasnov, Mikhail Shaposhnikov, Ekaterina Proshkina, Dmitry Borisoglebsky, Anton Danilov, Darya Peregudova, Irina Sharapova, Eugenia Dobrovolskaya, Ilya Solovev, Nadezhda Zemskaya, Lyubov Shilova, Anastasia Snezhkina and Anna Kudryavtseva
    Citation: BMC Genomics 2015 16(Suppl 13):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  12. The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DN...

    Authors: Konstantin Kozlov, Vitaly V Gursky, Ivan V Kulakovskiy, Arina Dymova and Maria Samsonova
    Citation: BMC Genomics 2015 16(Suppl 13):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  13. Recently fibroblasts of many mammalian species have been reprogrammed to pluripotent state using overexpression of several transcription factors. This technology allows production of induced pluripotent stem (...

    Authors: Aleksei G Menzorov, Natalia M Matveeva, Marios N Markakis, Venyamin S Fishman, Knud Christensen, Anna A Khabarova, Inna E Pristyazhnyuk, Elena A Kizilova, Susanna Cirera, Razvan Anistoroaei and Oleg L Serov
    Citation: BMC Genomics 2015 16(Suppl 13):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  14. Obesity affects quality of life and life expectancy and is associated with cardiovascular disorders, cancer, diabetes, reproductive disorders in women, prostate diseases in men, and congenital anomalies in chi...

    Authors: Olga V Arkova, Mikhail P Ponomarenko, Dmitry A Rasskazov, Irina A Drachkova, Tatjana V Arshinova, Petr M Ponomarenko, Ludmila K Savinkova and Nikolay A Kolchanov
    Citation: BMC Genomics 2015 16(Suppl 13):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  15. As the evolution of miRNA genes has been found to be one of the important factors in formation of the modern type of man, we performed a comparative analysis of the evolution of miRNA genes in two archaic homi...

    Authors: Konstantin V Gunbin, Dmitry A Afonnikov, Nikolay A Kolchanov, Anatoly P Derevianko and Eugeny I Rogaev
    Citation: BMC Genomics 2015 16(Suppl 13):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  16. An important issue in the target identification for the drug design is the tissue-specific effect of inhibition of target genes. The task of assessing the tissue-specific effect in suppressing gene activity is...

    Authors: Evgeny D Petrovskiy, Olga V Saik, Evgeny S Tiys, Inna N Lavrik, Nikolay A Kolchanov and Vladimir A Ivanisenko
    Citation: BMC Genomics 2015 16(Suppl 13):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  17. Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowl...

    Authors: Irina V Medvedeva, Pavel S Demenkov and Vladimir A Ivanisenko
    Citation: BMC Genomics 2015 16(Suppl 13):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  18. The assessment of cell-free circulating DNA fragments, also known as a "liquid biopsy" of the patient's plasma, is an important source for the discovery and subsequent non-invasive monitoring of cancer and oth...

    Authors: Maxim Ivanov, Ancha Baranova, Timothy Butler, Paul Spellman and Vladislav Mileyko
    Citation: BMC Genomics 2015 16(Suppl 13):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  19. Large collections of paraffin-embedded tissue represent a rich resource to test hypotheses based on gene expression patterns; however, measurement of genome-wide expression is cost-prohibitive on a large scale...

    Authors: James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene and Jennifer A. Doherty
    Citation: BMC Genomics 2015 16:1065
    Content type: Methodology article Published on:

  20. Revealing genetic mechanisms behind specific physiological characteristics of Saccharomyces cerevisiae from specific environments is important for industrial applications and requires precise understanding.

    Authors: Xiaowei Lu, Qun Wu, Yan Zhang and Yan Xu
    Citation: BMC Genomics 2015 16:1064
    Content type: Research article Published on:

  21. The barnacle Balanus amphitrite is widely distributed in marine shallow and tidal waters, and has significant economic and ecological importance. Nauplii, the first larval stage of most crustaceans, are extremely...

    Authors: Kondethimmanahalli H. Chandramouli, Sarah Al-Aqeel, Taewoo Ryu, Huoming Zhang, Loqmane Seridi, Yanal Ghosheh, Pei-Yuan Qian and Timothy Ravasi
    Citation: BMC Genomics 2015 16:1063
    Content type: Research article Published on:

  22. Jute fiber, extracted from stem bast, is called golden fiber. It is essential for fiber improvement to discover the genes associated with jute development at the vegetative growth stage. However, only 858 EST ...

    Authors: Liwu Zhang, Ray Ming, Jisen Zhang, Aifen Tao, Pingping Fang and Jianmin Qi
    Citation: BMC Genomics 2015 16:1062
    Content type: Research article Published on:

  23. The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of spe...

    Authors: Jonathan Filée, Jacques-Deric Rouault, Myriam Harry and Aurélie Hua-Van
    Citation: BMC Genomics 2015 16:1061
    Content type: Research article Published on:

  25. The initiation of translation via cellular internal ribosome entry sites plays an important role in the stress response and certain physiological conditions in which canonical cap-dependent translation initiat...

    Authors: Esteban Peguero-Sanchez, Liliana Pardo-Lopez and Enrique Merino
    Citation: BMC Genomics 2015 16:1059
    Content type: Research article Published on:

  26. Powdery mildew (PM) is the most common fungal disease of cucumber and other cucurbit crops, while breeding the PM-resistant materials is the effective way to defense this disease, and the recent development of...

    Authors: Peng Zhang, Yuqiang Zhu, Lili Wang, Liping Chen and Shengjun Zhou
    Citation: BMC Genomics 2015 16:1058
    Content type: Research article Published on:

  27. Pines are the most important tree species to the international forestry industry, covering 42 % of the global industrial forest plantation area. One of the most pressing threats to cultivation of some pine spe...

    Authors: Erik A. Visser, Jill L. Wegrzyn, Emma T. Steenkmap, Alexander A. Myburg and Sanushka Naidoo
    Citation: BMC Genomics 2015 16:1057
    Content type: Research article Published on:

  28. Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data ...

    Authors: Jarmo Ritari, Jarkko Salojärvi, Leo Lahti and Willem M. de Vos
    Citation: BMC Genomics 2015 16:1056
    Content type: Research article Published on:

  29. Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. A particular situation is the...

    Authors: Magali SanCristobal, Florian Rohart, Christine Lascor, Marcel Bouffaud, Lidwine Trouilh, Pascal G.P. Martin, Yannick Lippi, Thierry Tribout, Thomas Faraut, Marie-José Mercat, Denis Milan and Laurence Liaubet
    Citation: BMC Genomics 2015 16:1055
    Content type: Research article Published on:

  30. Serine proteases (SPs) are crucial proteolytic enzymes responsible for digestion and other processes including signal transduction and immune responses in insects. Serine protease homologs (SPHs) lack catalyti...

    Authors: Hailan Lin, Xiaofeng Xia, Liying Yu, Liette Vasseur, Geoff M. Gurr, Fengluan Yao, Guang Yang and Minsheng You
    Citation: BMC Genomics 2015 16:1054
    Content type: Research article Published on:

  31. Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be ...

    Authors: Zhihui Wang, Ke Cheng, Liyun Wan, Liying Yan, Huifang Jiang, Shengyi Liu, Yong Lei and Boshou Liao
    Citation: BMC Genomics 2015 16:1053
    Content type: Research article Published on:

  32. Genomic information is increasingly used in medical practice giving rise to the need for efficient analysis methodology able to cope with thousands of individuals and millions of variants. The widely used Hado...

    Authors: Aidan R. O’Brien, Neil F. W. Saunders, Yi Guo, Fabian A. Buske, Rodney J. Scott and Denis C. Bauer
    Citation: BMC Genomics 2015 16:1052
    Content type: Software Published on:

  33. Bacterial small RNAs (sRNAs) are recognized as posttranscriptional regulators involved in the control of bacterial lifestyle and adaptation to stressful conditions. Although chemical stress due to the toxicity...

    Authors: Martin Holm Rau, Klara Bojanovič, Alex Toftgaard Nielsen and Katherine S. Long
    Citation: BMC Genomics 2015 16:1051
    Content type: Research article Published on:

  35. DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation...

    Authors: Apichart Intarapanich, Saowaluck Kaewkamnerd, Philip J Shaw, Kittipat Ukosakit, Somvong Tragoonrung and Sissades Tongsima
    Citation: BMC Genomics 2015 16(Suppl 12):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  36. Whole genome bisulfite sequencing (WGBS) is a high-throughput technique for profiling genome-wide DNA methylation at single nucleotide resolution. However, the applications of WGBS are limited by low accuracy ...

    Authors: Jong-Hun Lee, Sung-Joon Park and Nakai Kenta
    Citation: BMC Genomics 2015 16(Suppl 12):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  37. Toll-like receptors, which stimulated by pathogen-associated molecular patterns such as lipopolysaccharides (LPS), induces the releasing of many kinds of proinflammatory cytokines to activate subsequent immune...

    Authors: Chia-Chun Chiu and Wei-Sheng Wu
    Citation: BMC Genomics 2015 16(Suppl 12):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  38. Mass Spectrometry (MS) is a ubiquitous analytical tool in biological research and is used to measure the mass-to-charge ratio of bio-molecules. Peak detection is the essential first step in MS data analysis. P...

    Authors: Chalini D Wijetunge, Isaam Saeed, Berin A Boughton, Ute Roessner and Saman K Halgamuge
    Citation: BMC Genomics 2015 16(Suppl 12):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  39. DNA methylation is a major epigenetic modification regulating several biological processes. A standard approach to measure DNA methylation is bisulfite sequencing (BS-Seq). BS-Seq couples bisulfite conversion ...

    Authors: Wen-Wei Liao, Ming-Ren Yen, Evaline Ju, Fei-Man Hsu, Larry Lam and Pao-Yang Chen
    Citation: BMC Genomics 2015 16(Suppl 12):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  40. Transcriptional regulation of gene expression in eukaryotes is usually accomplished by cooperative transcription factors (TFs). Computational identification of cooperative TF pairs has become a hot research to...

    Authors: Wei-Sheng Wu and Fu-Jou Lai
    Citation: BMC Genomics 2015 16(Suppl 12):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  41. Recent progress in next-generation sequencing technology has afforded several improvements such as ultra-high throughput at low cost, very high read quality, and substantially increased sequencing depth. State...

    Authors: Chih-Hao Fang, Yu-Jung Chang, Wei-Chun Chung, Ping-Heng Hsieh, Chung-Yen Lin and Jan-Ming Ho
    Citation: BMC Genomics 2015 16(Suppl 12):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  42. Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emer...

    Authors: Chieh-Hua Lin, Yu-Bin Wang, Shu-Hwa Chen, Chao Agnes Hsiung and Chung-Yen Lin
    Citation: BMC Genomics 2015 16(Suppl 12):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  43. Recently, a wide range of diseases have been associated with changes in DNA methylation levels, which play a vital role in gene expression regulation. With ongoing developments in technology, attempts to under...

    Authors: Bugra Ozer and Osman Uğur Sezerman
    Citation: BMC Genomics 2015 16(Suppl 12):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  44. Identifying putative membrane transport proteins (MTPs) and understanding the transport mechanisms involved remain important challenges for the advancement of structural and functional genomics. However, the t...

    Authors: Yi-Fan Liou, Tamara Vasylenko, Chia-Lun Yeh, Wei-Chun Lin, Shih-Hsiang Chiu, Phasit Charoenkwan, Li-Sun Shu, Shinn-Ying Ho and Hui-Ling Huang
    Citation: BMC Genomics 2015 16(Suppl 12):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  45. Transcription factors, regulating the expression inventory of a cell, interact with its respective DNA subjugated by a specific recognition pattern, which if well exploited may ensure targeted genome engineeri...

    Authors: Shayoni Dutta, Yoshita Agrawal, Aditi Mishra, Jaspreet Kaur Dhanjal and Durai Sundar
    Citation: BMC Genomics 2015 16(Suppl 12):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  46. Deciphering gene interaction networks (GINs) from time-course gene expression (TCGx) data is highly valuable to understand gene behaviors (e.g., activation, inhibition, time-lagged causality) at the system lev...

    Authors: Qian Liu, Renhua Song and Jinyan Li
    Citation: BMC Genomics 2015 16(Suppl 12):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  47. Detection of differential methylation between biological samples is an important task in bisulfite-seq data analysis. Several studies have attempted de novo finding of differentially methylated regions (DMRs) ...

    Authors: Yutaka Saito and Toutai Mituyama
    Citation: BMC Genomics 2015 16(Suppl 12):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  48. Triple-Negative Breast Cancer (TNBC) is an aggressive disease with a poor prognosis. Clinically, TNBC patients have limited treatment options besides chemotherapy. The goal of this study was to determine the k...

    Authors: Karen A Ryall, Jihye Kim, Peter J Klauck, Jimin Shin, Minjae Yoo, Anastasia Ionkina, Todd M Pitts, John J Tentler, Jennifer R Diamond, S Gail Eckhardt, Lynn E Heasley, Jaewoo Kang and Aik Choon Tan
    Citation: BMC Genomics 2015 16(Suppl 12):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  49. Meiotic recombination hotspots play important roles in various aspects of genomics, but the underlying mechanisms for regulating the locations and strengths of recombination hotspots are not yet fully revealed...

    Authors: Hao Chen, Peng Yang, Jing Guo, Chee Keong Kwoh, Teresa M Przytycka and Jie Zheng
    Citation: BMC Genomics 2015 16(Suppl 12):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  50. Knowledge discovery in bioinformatics thrives on joint and inclusive efforts of stakeholders. Similarly, knowledge dissemination is expected to be more effective and scalable through joint efforts. Therefore, ...

    Authors: Christian Schönbach, Paul Horton, Siu-Ming Yiu, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Genomics 2015 16(Suppl 12):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

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BMC Genomics

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