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  1. Although feeding behavior and food habit are ecologically and economically important properties, little is known about formation and evolution of herbivory. Grass carp (Ctenopharyngodon idella) is an ecologically...

    Authors: Shan He, Xu-Fang Liang, Ling Li, Jian Sun, Zheng-Yong Wen, Xiao-Yan Cheng, Ai-Xuan Li, Wen-Jing Cai, Yu-Hui He, Ya-Ping Wang, Ya-Xiong Tao and Xiao-Chen Yuan
    Citation: BMC Genomics 2015 16:15
    Content type: Research article Published on:

  2. Garlic is cultivated and consumed worldwide as a popular condiment and green vegetable with medicinal and neutraceutical properties. Garlic cultivars do not produce seeds, and therefore, this plant has not bee...

    Authors: Rina Kamenetsky, Adi Faigenboim, Einat Shemesh Mayer, Tomer Ben Michael, Chen Gershberg, Sagie Kimhi, Itzhak Esquira, Sarit Rohkin Shalom, Dani Eshel, Haim D Rabinowitch and Amir Sherman
    Citation: BMC Genomics 2015 16:12
    Content type: Research article Published on:

  3. Expression quantitative trait loci (eQTL) play an important role in the regulation of gene expression. Gene expression levels and eQTLs are expected to vary from tissue to tissue, and therefore multi-tissue an...

    Authors: Eric F Lock, Karen L Soldano, Melanie E Garrett, Heidi Cope, Christina A Markunas, Herbert Fuchs, Gerald Grant, David B Dunson, Simon G Gregory and Allison E Ashley-Koch
    Citation: BMC Genomics 2015 16:11
    Content type: Research article Published on:

  5. RNA-Seq based transcriptome assembly has become a fundamental technique for studying expressed mRNAs (i.e., transcripts or isoforms) in a cell using high-throughput sequencing technologies, and is serving as a ba...

    Authors: Masruba Tasnim, Shining Ma, Ei-Wen Yang, Tao Jiang and Wei Li
    Citation: BMC Genomics 2015 16(Suppl 2):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  7. Next generation sequencing (NGS) technologies have made it possible to exhaustively detect structural variations (SVs) in genomes. Although various methods for detecting SVs have been developed, the global str...

    Authors: Tomohiro Yasuda and Satoru Miyano
    Citation: BMC Genomics 2015 16(Suppl 2):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

    The Erratum to this article has been published in BMC Genomics 2015 16:276

  8. MicroRNAs (miRNAs) simultaneously target many transcripts through partial complementarity binding, and have emerged as a key type of post-transcriptional regulator for gene expression. How miRNA accomplishes i...

    Authors: Sheng-Da Hsu, Hsi-Yuan Huang, Chih-Hung Chou, Yi-Ming Sun, Ming-Ta Hsu and Ann-Ping Tsou
    Citation: BMC Genomics 2015 16(Suppl 2):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  9. Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chro...

    Authors: Renhua Song, Qian Liu, Tao Liu and Jinyan Li
    Citation: BMC Genomics 2015 16(Suppl 2):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  10. Protein-protein interactions (PPIs) are key to understanding diverse cellular processes and disease mechanisms. However, current PPI databases only provide low-resolution knowledge of PPIs, in the sense that "...

    Authors: Yu-Ting Tseng, Wenyuan Li, Ching-Hsien Chen, Shihua Zhang, Jeremy JW Chen, Xianghong Jasmine Zhou and Chun-Chi Liu
    Citation: BMC Genomics 2015 16(Suppl 2):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  11. The emergence of next-generation RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate detection of intron retenti...

    Authors: Yang Bai, Shufan Ji and Yadong Wang
    Citation: BMC Genomics 2015 16(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  12. Epigenetic modifications are essential for controlling gene expression. Recent studies have shown that not only single epigenetic modifications but also combinations of multiple epigenetic modifications play v...

    Authors: Kazuki Ichikawa and Shinichi Morishita
    Citation: BMC Genomics 2015 16(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  13. Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA...

    Authors: Naoki Nariai, Kaname Kojima, Sakae Saito, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Jun Yasuda and Masao Nagasaki
    Citation: BMC Genomics 2015 16(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  14. In general, the expression of gene alters conditionally to catalyze a specific metabolic pathway. Microarray-based datasets have been massively produced to monitor gene expression levels in parallel with numer...

    Authors: Chia-Hung Chien, Chi-Nga Chow, Nai-Yun Wu, Yi-Fan Chiang-Hsieh, Ping-Fu Hou and Wen-Chi Chang
    Citation: BMC Genomics 2015 16(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  15. Single-nucleotide polymorphisms (SNPs) selection and identification are the most important tasks in Genome-wide association data analysis. The problem is difficult because genome-wide association data is very ...

    Authors: Thanh-Tung Nguyen, Joshua Zhexue Huang, Qingyao Wu, Thuy Thi Nguyen and Mark Junjie Li
    Citation: BMC Genomics 2015 16(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  16. Accurate determination of protein complexes is crucial for understanding cellular organization and function. High-throughput experimental techniques have generated a large amount of protein-protein interaction...

    Authors: Yijia Zhang, Hongfei Lin, Zhihao Yang and Jian Wang
    Citation: BMC Genomics 2015 16(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  17. Pinpointing genes involved in inherited human diseases remains a great challenge in the post-genomics era. Although approaches have been proposed either based on the guilt-by-association principle or making us...

    Authors: Rui Jiang, Mengmeng Wu and Lianshuo Li
    Citation: BMC Genomics 2015 16(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  18. Identification of genes with ascending or descending monotonic expression patterns over time or stages of stem cells is an important issue in time-series microarray data analysis. We propose a method named Mon...

    Authors: Hsei-Wei Wang, Hsing-Jen Sun, Ting-Yu Chang, Hung-Hao Lo, Wei-Chung Cheng, George C Tseng, Chin-Teng Lin, Shing-Jyh Chang, Nikhil Ranjan Pal and I-Fang Chung
    Citation: BMC Genomics 2015 16(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  20. A central problem of computational metagenomics is determining the correct placement into an existing phylogenetic tree of individual reads (nucleotide sequences of varying lengths, ranging from hundreds to th...

    Authors: Alan Filipski, Koichiro Tamura, Paul Billing-Ross, Oscar Murillo and Sudhir Kumar
    Citation: BMC Genomics 2015 16(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  21. We report a consanguineous couple that has experienced three consecutive pregnancy losses following the foetal ultrasound finding of short limbs. Post-termination examination revealed no skeletal dysplasia, bu...

    Authors: Christian R Marshall, Sandra A Farrell, Donna Cushing, Tara Paton, Tracy L Stockley, Dimitri J Stavropoulos, Peter N Ray, Michael Szego, Lynette Lau, Sergio L Pereira, Ronald D Cohn, Richard F Wintle, Adel M Abuzenadah, Muhammad Abu-Elmagd and Stephen W Scherer
    Citation: BMC Genomics 2015 16(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  22. Breast cancer incidence rates are increasing at an alarming rate among Saudi Arabian females. Most molecular genetic discoveries on breast cancer and other cancers have arisen from studies examining European a...

    Authors: Adnan Merdad, Sajjad Karim, Hans-Juergen Schulten, Manikandan Jayapal, Ashraf Dallol, Abdelbaset Buhmeida, Fatima Al-Thubaity, Mamdooh A GariI, Adeel GA Chaudhary, Adel M Abuzenadah and Mohammed H Al-Qahtani
    Citation: BMC Genomics 2015 16(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  23. Epilepsy is genetically complex neurological disorder affecting millions of people of different age groups varying in its type and severity. Copy number variants (CNVs) are key players in the genetic etiology ...

    Authors: Muhammad Imran Naseer, Muhammad Faheem, Adeel G Chaudhary, Taha A Kumosani, Maha Mohsin Al-Quaiti, Mohammed M Jan, Hasan Saleh Jamal and Mohammad H Al-Qahtani
    Citation: BMC Genomics 2015 16(Suppl 1):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  24. Selection of the best oocyte for subsequent steps of fertilization and embryo transfer was shown to be the crucial step in human infertility treatment procedure. Oocyte selection using morphological criteria m...

    Authors: Mourad ASSIDI, Markus MONTAG and Marc-André SIRARD
    Citation: BMC Genomics 2015 16(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  25. We have generated a series of isogenically derived immortalized human colonic epithelial cell (HCEC 1CT and HCEC 2CT) lines, including parental un-immortalized normal cell strains. The CDK4 and hTERT immortali...

    Authors: Lu Zhang, Sang Bum Kim, Gaoxiang Jia, Abdelbaset Buhmeida, Ashraf Dallol, Woodring E Wright, Albert J Fornace, Mohammed Al-Qahtani and Jerry W Shay
    Citation: BMC Genomics 2015 16(Suppl 1):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  26. Follicular variant of papillary thyroid carcinoma (FVPTC) and follicular adenoma (FA) are histologically closely related tumors and differential diagnosis remains challenging. RNA expression profiling is an es...

    Authors: Hans-Juergen Schulten, Zuhoor Al-Mansouri, Ibtisam Baghallab, Nadia Bagatian, Ohoud Subhi, Sajjad Karim, Hosam Al-Aradati, Abdulmonem Al-Mutawa, Adel Johary, Abdulrahman A Meccawy, Khalid Al-Ghamdi, Osman Abdel Al-Hamour, Mohammad Hussain Al-Qahtani and Jaudah Al-Maghrabi
    Citation: BMC Genomics 2015 16(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  27. Whereas 40 % to 70 % of papillary thyroid carcinomas (PTCs) are characterized by a BRAF mutation (BRAFmut), unified biomarkers for the genetically heterogeneous group of BRAF wild type (BRAFwt) PTCs are not estab...

    Authors: Hans-Juergen Schulten, Reem Alotibi, Alaa Al-Ahmadi, Manar Ata, Sajjad Karim, Etimad Huwait, Mamdooh Gari, Khalid Al-Ghamdi, Faisal Al-Mashat, Osman Abdel Al-Hamour, Mohammad Hussain Al-Qahtani and Jaudah Al-Maghrabi
    Citation: BMC Genomics 2015 16(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  28. Acute myeloid leukemia (AML) is a clonal disorder of the blood forming cells characterized by accumulation of immature blast cells in the bone marrow and peripheral blood. Being a heterogeneous disease, AML ha...

    Authors: Asad Muhammad Ilyas, Sultan Ahmad, Muhammad Faheem, Muhammad Imran Naseer, Taha A Kumosani, Muhammad Hussain Al-Qahtani, Mamdooh Gari and Farid Ahmed
    Citation: BMC Genomics 2015 16(Suppl 1):S5
    Content type: Review Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  29. Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simu...

    Authors: Seung Bum Seo, Xiangpei Zeng, Jonathan L King, Bobby L Larue, Mourad Assidi, Mohamed H Al-Qahtani, Antti Sajantila and Bruce Budowle
    Citation: BMC Genomics 2015 16(Suppl 1):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  30. The contribution of genetic factors to the development of breast cancer in the admixed and consanguineous population of the western region of Saudi Arabia is thought to be significant as the disease is early o...

    Authors: Adnan Merdad, Mamdooh A Gari, Shireen Hussein, Shadi Al-Khayat, Hana Tashkandi, Jaudah Al-Maghrabi, Fatma Al-Thubaiti, Ibtessam R Hussein, Taha Koumosani, Nehad Shaer, Adeel G Chaudhary, Adel M Abuzenadah, Mohammed H Al-Qahtani and Ashraf Dallol
    Citation: BMC Genomics 2015 16(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  31. Investigations into novel biomarkers using omics techniques generate large amounts of data. Due to their size and numbers of attributes, these data are suitable for analysis with machine learning methods. A ke...

    Authors: Anna L Swan, Dov J Stekel, Charlie Hodgman, David Allaway, Mohammed H Alqahtani, Ali Mobasheri and Jaume Bacardit
    Citation: BMC Genomics 2015 16(Suppl 1):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  32. Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer deaths worldwide with less than a 6% 5-year survival rate. PDAC is associated with poor prognosis based on the late stage diagnosis...

    Authors: Joseph J LaConti, Evagelia C Laiakis, Anne Deslattes Mays, Ivana Peran, Sung Eun Kim, Jerry W Shay, Anna T Riegel, Albert J Fornace Jr and Anton Wellstein
    Citation: BMC Genomics 2015 16(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  33. Horizontal gene transfer (HGT) is the stable transmission of genetic material between organisms by means other than vertical inheritance. HGT has an important role in the evolution of prokaryotes but is relati...

    Authors: Vinicio D Armijos Jaramillo, Serenella A Sukno and Michael R Thon
    Citation: BMC Genomics 2015 16:2
    Content type: Research article Published on:

  34. The honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey...

    Authors: Doori Park, Je Won Jung, Beom-Soon Choi, Murukarthick Jayakodi, Jeongsoo Lee, Jongsung Lim, Yeisoo Yu, Yong-Soo Choi, Myeong-Lyeol Lee, Yoonseong Park, Ik-Young Choi, Tae-Jin Yang, Owain R Edwards, Gyoungju Nah and Hyung Wook Kwon
    Citation: BMC Genomics 2015 16:1
    Content type: Research article Published on:

  35. Chromatin remodeling is crucial for proper programing of developmental gene expression. Recent work provides a dynamic view of post-translational histone modifications during differentiation; however there is ...

    Authors: Akshay Shah, Anja Oldenburg and Philippe Collas
    Citation: BMC Genomics 2014 15:1186
    Content type: Research article Published on:

  36. Cyanothece sp. PCC 7822 is an excellent cyanobacterial model organism with great potential to be applied as a biocatalyst for the production of high value compounds. Like other unicellular diazotrophic cyanobacte...

    Authors: David Welkie, Xiaohui Zhang, Meng Lye Markillie, Ronald Taylor, Galya Orr, Jon Jacobs, Ketaki Bhide, Jyothi Thimmapuram, Marina Gritsenko, Hugh Mitchell, Richard D Smith and Louis A Sherman
    Citation: BMC Genomics 2014 15:1185
    Content type: Research article Published on:

  37. The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious bein...

    Authors: Julianne H Grose, Garrett L Jensen, Sandra H Burnett and Donald P Breakwell
    Citation: BMC Genomics 2014 15:1184
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2014 15:855

  38. Gonad differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. The colonial ascidian, Botryllus schl...

    Authors: Delany Rodriguez, Erin N Sanders, Kelsea Farell, Adam D Langenbacher, Daryl A Taketa, Michelle Rae Hopper, Morgan Kennedy, Andrew Gracey and Anthony W De Tomaso
    Citation: BMC Genomics 2014 15:1183
    Content type: Research article Published on:

  39. Earlier studies were focused on the genetics of temperate and tropical maize under drought. We identified genetic loci and their association with functional mechanisms in 240 accessions of subtropical maize us...

    Authors: Nepolean Thirunavukkarasu, Firoz Hossain, Kanika Arora, Rinku Sharma, Kaliyugam Shiriga, Swati Mittal, Sweta Mohan, Pottekatt Mohanlal Namratha, Sreelatha Dogga, Tikka Shobha Rani, Sumalini Katragadda, Abhishek Rathore, Trushar Shah, Trilochan Mohapatra and Hari Shankar Gupta
    Citation: BMC Genomics 2014 15:1182
    Content type: Research article Published on:

  40. Transcriptogram profiling is a method to present and analyze transcription data in a genome-wide scale that reduces noise and facilitates biological interpretation. An ordered gene list is produced, such that ...

    Authors: Samoel RM da Silva, Gabriel C Perrone, João M Dinis and Rita MC de Almeida
    Citation: BMC Genomics 2014 15:1181
    Content type: Research article Published on:

  41. With the development of several new technologies using synthetic biology, it is possible to engineer genetically intractable organisms including Mycoplasma mycoides subspecies capri (Mmc), by cloning the intact b...

    Authors: Suchismita Chandran, Vladimir N Noskov, Thomas H Segall-Shapiro, Li Ma, Caitlin Whiteis, Carole Lartigue, Joerg Jores, Sanjay Vashee and Ray-Yuan Chuang
    Citation: BMC Genomics 2014 15:1180
    Content type: Methodology article Published on:

  42. Haemophilus parasuis is the etiologic agent of Glässer’s disease in pigs and causes devastating losses to the farming industry. Whilst some hyper-virulent isolates have been described, the relationship between ge...

    Authors: Kate J Howell, Lucy A Weinert, Roy R Chaudhuri, Shi-Lu Luan, Sarah E Peters, Jukka Corander, David Harris, Øystein Angen, Virginia Aragon, Albert Bensaid, Susanna M Williamson, Julian Parkhill, Paul R Langford, Andrew N Rycroft, Brendan W Wren, Matthew T G Holden…
    Citation: BMC Genomics 2014 15:1179
    Content type: Research article Published on:

  43. In the competing endogenous RNA (ceRNA) hypothesis, different transcripts communicate through a competition for their common targeting microRNAs (miRNAs). Individual examples have clearly shown the functional ...

    Authors: Danny Kit-Sang Yip, Iris K Pang and Kevin Y Yip
    Citation: BMC Genomics 2014 15:1178
    Content type: Methodology article Published on:

  44. Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been stud...

    Authors: Morana Vitezic, Nicolas Bertin, Robin Andersson, Leonard Lipovich, Hideya Kawaji, Timo Lassmann, Albin Sandelin, Peter Heutink, Dan Goldowitz, Thomas Ha, Peter Zhang, Annarita Patrizi, Michela Fagiolini, Alistair RR Forrest, Piero Carninci and Alka Saxena
    Citation: BMC Genomics 2014 15:1177
    Content type: Research article Published on:

  45. Atherosclerosis is a progressive disease characterized by inflammation and accumulation of lipids in vascular tissue. Porphyromonas gingivalis (Pg) and Chlamydia pneumoniae (Cp) are associated with inflammatory a...

    Authors: Carolyn D Kramer, Ellen O Weinberg, Adam C Gower, Xianbao He, Samrawit Mekasha, Connie Slocum, Lea M Beaulieu, Lee Wetzler, Yuriy Alekseyev, Frank C Gibson III, Jane E Freedman, Robin R Ingalls and Caroline A Genco
    Citation: BMC Genomics 2014 15:1176
    Content type: Research article Published on:

  48. Cell proliferation is a hallmark of cancer and depends on complex signaling networks that are chiefly supported by protein kinase activities. Therapeutic strategies have been used to target specific kinases bu...

    Authors: Philippe Nizard, Frédéric Ezan, Dominique Bonnier, Nolwenn Le Meur, Sophie Langouët, Georges Baffet, Yannick Arlot-Bonnemains and Nathalie Théret
    Citation: BMC Genomics 2014 15:1169
    Content type: Research article Published on:

  49. Supplementation of broiler chicken diets with probiotics may improve carcass characteristics and meat quality. However, the underlying molecular mechanism remains unclear. In the present study, 2D-DIGE-based p...

    Authors: Aijuan Zheng, Jianjie Luo, Kun Meng, Jianke Li, Shu Zhang, Ke Li, Guohua Liu, Huiyi Cai, Wayne L Bryden and Bin Yao
    Citation: BMC Genomics 2014 15:1167
    Content type: Research article Published on:

  50. Muscle ageing contributes to both loss of functional autonomy and increased morbidity. Muscle atrophy accelerates after 50 years of age, but the mechanisms involved are complex and likely result from the alter...

    Authors: Marine Gueugneau, Cécile Coudy-Gandilhon, Ophélie Gourbeyre, Christophe Chambon, Lydie Combaret, Cécile Polge, Daniel Taillandier, Didier Attaix, Bertrand Friguet, Andrea B Maier, Gillian Butler-Browne and Daniel Béchet
    Citation: BMC Genomics 2014 15:1165
    Content type: Research article Published on:

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BMC Genomics

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