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  1. Plant n on-s pecific l ipid t ransfer p roteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, partici...

    Authors: Nai-Jyuan Wang, Chi-Ching Lee, Chao-Sheng Cheng, Wei-Cheng Lo, Ya-Fen Yang, Ming-Nan Chen and Ping-Chiang Lyu
    Citation: BMC Genomics 2012 13(Suppl 1):S9

    This article is part of a Supplement: Volume 13 Supplement 1

  2. Small interfering and non-coding RNAs regulate gene expression across all kingdoms of life. MicroRNAs constitute an important group of metazoan small RNAs regulating development but also disease. Accordingly, ...

    Authors: Soroush Sharbati, Jutta Sharbati, Lena Hoeke, Marc Bohmer and Ralf Einspanier
    Citation: BMC Genomics 2012 13:23
  3. Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole). The steroid andros...

    Authors: Vivi R Gregersen, Lene N Conley, Kirsten K Sørensen, Bernt Guldbrandtsen, Ingela H Velander and Christian Bendixen
    Citation: BMC Genomics 2012 13:22
  4. Eimeria tenella is an apicomplexan parasite that causes coccidiosis in the domestic fowl. Infection with this parasite is diagnosed frequently in intensively reared poultry and its control is usually accorded a h...

    Authors: Nadzirah Amiruddin, Xin-Wei Lee, Damer P Blake, Yutaka Suzuki, Yea-Ling Tay, Lik-Sin Lim, Fiona M Tomley, Junichi Watanabe, Chihiro Sugimoto and Kiew-Lian Wan
    Citation: BMC Genomics 2012 13:21
  5. Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have ma...

    Authors: Binod B Sahu, Rishi Sumit, Subodh K Srivastava and Madan K Bhattacharyya
    Citation: BMC Genomics 2012 13:20
  6. Chinese bayberry (Myrica rubra Sieb. and Zucc.) is an important subtropical fruit crop and an ideal species for fruit quality research due to the rapid and substantial changes that occur during development and ri...

    Authors: Chao Feng, Ming Chen, Chang-jie Xu, Lin Bai, Xue-ren Yin, Xian Li, Andrew C Allan, Ian B Ferguson and Kun-song Chen
    Citation: BMC Genomics 2012 13:19
  7. Sweet cherry (Prunus avium L.), a non-model crop with narrow genetic diversity, is an important member of sub-family Amygdoloideae within Rosaceae. Compared to other important members like peach and apple, sweet ...

    Authors: Tyson Koepke, Scott Schaeffer, Vandhana Krishnan, Derick Jiwan, Artemus Harper, Matthew Whiting, Nnadozie Oraguzie and Amit Dhingra
    Citation: BMC Genomics 2012 13:18
  8. Udder infections with environmental pathogens like Escherichia coli are a serious problem for the dairy industry. Reduction of incidence and severity of mastitis is desirable and mild priming of the immune system...

    Authors: Juliane Günther, Wolfram Petzl, Holm Zerbe, Hans-Joachim Schuberth, Dirk Koczan, Leopold Goetze and Hans-Martin Seyfert
    Citation: BMC Genomics 2012 13:17
  9. The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within thi...

    Authors: Michael P Mullen, Christopher J Creevey, Donagh P Berry, Matt S McCabe, David A Magee, Dawn J Howard, Aideen P Killeen, Stephen D Park, Paul A McGettigan, Matt C Lucy, David E MacHugh and Sinead M Waters
    Citation: BMC Genomics 2012 13:16
  10. Digitalis purpurea is an important ornamental and medicinal plant. There is considerable interest in exploring its transcriptome.

    Authors: Bin Wu, Ying Li, Haixia Yan, Yimian Ma, Hongmei Luo, Lichai Yuan, Shilin Chen and Shanfa Lu
    Citation: BMC Genomics 2012 13:15
  11. With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment bi...

    Authors: Patrick Ollitrault, Javier Terol, Andres Garcia-Lor, Aurélie Bérard, Aurélie Chauveau, Yann Froelicher, Caroline Belzile, Raphaël Morillon, Luis Navarro, Dominique Brunel and Manuel Talon
    Citation: BMC Genomics 2012 13:13
  12. MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Deve...

    Authors: Teshome T Bizuayehu, Carlos FC Lanes, Tomasz Furmanek, BÃ¥rd O Karlsen, Jorge MO Fernandes, Steinar D Johansen and Igor Babiak
    Citation: BMC Genomics 2012 13:11
  13. The transcriptome of the fruit pulp of the sweet orange variety Anliu (WT) and that of its red fleshed mutant Hong Anliu (MT) were compared to understand the dynamics and differential expression of genes expre...

    Authors: Keqin Yu, Qiang Xu, Xinlei Da, Fei Guo, Yuduan Ding and Xiuxin Deng
    Citation: BMC Genomics 2012 13:10
  14. Desirable apple varieties are clonally propagated by grafting vegetative scions onto rootstocks. Rootstocks influence many phenotypic traits of the scion, including resistance to pathogens such as Erwinia amylovo...

    Authors: Philip J Jensen, Noemi Halbrendt, Gennaro Fazio, Izabela Makalowska, Naomi Altman, Craig Praul, Siela N Maximova, Henry K Ngugi, Robert M Crassweller, James W Travis and Timothy W McNellis
    Citation: BMC Genomics 2012 13:9
  15. Identification of protein-protein interactions is a fundamental aspect of understanding protein function. A commonly used method for identifying protein interactions is the yeast two-hybrid system.

    Authors: Jennifer D Lewis, Janet Wan, Rachel Ford, Yunchen Gong, Pauline Fung, Hardeep Nahal, Pauline W Wang, Darrell Desveaux and David S Guttman
    Citation: BMC Genomics 2012 13:8
  16. MicroRNAs (miRNAs), a ubiquitous class of short RNAs, play vital roles in physiological and biochemical processes in plants by mediating gene silencing at post-transcriptional (PTGS) level. Tomato is a model s...

    Authors: Jinhua Zuo, Benzhong Zhu, Daqi Fu, Yi Zhu, Yuanzheng Ma, Lihong Chi, Zheng Ju, Yunxiang Wang, Baiqiang Zhai and Yunbo Luo
    Citation: BMC Genomics 2012 13:7
  17. Bed bugs (Cimex lectularius) are hematophagous nocturnal parasites of humans that have attained high impact status due to their worldwide resurgence. The sudden and rampant resurgence of C. lectularius has been a...

    Authors: Praveen Mamidala, Asela J Wijeratne, Saranga Wijeratne, Karl Kornacker, Babu Sudhamalla, Loren J Rivera-Vega, Andrew Hoelmer, Tea Meulia, Susan C Jones and Omprakash Mittapalli
    Citation: BMC Genomics 2012 13:6
  18. The data from high throughput genomics technologies provide unique opportunities for studies of complex biological systems, but also pose many new challenges. The shift to the genome scale in evolutionary biol...

    Authors: Francisco Prosdocimi, Benjamin Linard, Pierre Pontarotti, Olivier Poch and Julie D Thompson
    Citation: BMC Genomics 2012 13:5
  19. MicroRNAs (miRNAs) play key roles in regulating post-transcriptional gene expression and are essential for development in the free-living nematode Caenorhabditis elegans and in higher organisms. Whether microRNAs...

    Authors: Alan D Winter, William Weir, Martin Hunt, Matthew Berriman, John S Gilleard, Eileen Devaney and Collette Britton
    Citation: BMC Genomics 2012 13:4
  20. The globe artichoke (Cynara cardunculus L. var. scolymus) genome is relatively poorly explored, especially compared to those of the other major Asteraceae crops sunflower and lettuce. No SNP markers are in the pu...

    Authors: Davide Scaglione, Alberto Acquadro, Ezio Portis, Matteo Tirone, Steven J Knapp and Sergio Lanteri
    Citation: BMC Genomics 2012 13:3
  21. The increasing number of developmental events and molecular mechanisms associated with the Hedgehog (Hh) pathway from Drosophila to vertebrates, suggest that gene regulation is crucial for diverse cellular respon...

    Authors: Luis A Milla, Claudio R Cortés, Christian Hodar Q, Maritza G Oñate, Veronica Cambiazo, Shawn M Burgess and Verónica Palma
    Citation: BMC Genomics 2012 13:2
  22. Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In s...

    Authors: Samuel O Oyola, Thomas D Otto, Yong Gu, Gareth Maslen, Magnus Manske, Susana Campino, Daniel J Turner, Bronwyn MacInnis, Dominic P Kwiatkowski, Harold P Swerdlow and Michael A Quail
    Citation: BMC Genomics 2012 13:1
  23. The sequencing of the cow genome was recently published (Btau_4.0 assembly). A second, alternate cow genome assembly (UMD2), based on the same raw sequence data, was also published. The two assemblies have bee...

    Authors: Giulia Partipilo, Pietro D'Addabbo, Giovanni M Lacalandra, George E Liu and Mariano Rocchi
    Citation: BMC Genomics 2011 12:639
  24. Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny ...

    Authors: Hugo J Parker, Paul Piccinelli, Tatjana Sauka-Spengler, Marianne Bronner and Greg Elgar
    Citation: BMC Genomics 2011 12:637
  25. The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial.

    Authors: Michele A Busby, Jesse M Gray, Allen M Costa, Chip Stewart, Michael P Stromberg, Derek Barnett, Jeffrey H Chuang, Michael Springer and Gabor T Marth
    Citation: BMC Genomics 2011 12:635
  26. Disruption of thyroid hormone signalling can alter growth, development and energy metabolism. Thyroid hormones exert their effects through interactions with thyroid receptors that directly bind thyroid respons...

    Authors: Martin A Paquette, Hongyan Dong, Rémi Gagné, Andrew Williams, Morie Malowany, Mike G Wade and Carole L Yauk
    Citation: BMC Genomics 2011 12:634
  27. The characterization of DNA replication origins in yeast has shed much light on the mechanisms of initiation of DNA replication. However, very little is known about the evolution of origins or the evolution of...

    Authors: Ivan Liachko, Emi Tanaka, Katherine Cox, Shau Chee Claire Chung, Lu Yang, Arael Seher, Lindsay Hallas, Eugene Cha, Gina Kang, Heather Pace, Jasmine Barrow, Maki Inada, Bik-Kwoon Tye and Uri Keich
    Citation: BMC Genomics 2011 12:633
  28. Cluster thinning is an agronomic practice in which a proportion of berry clusters are removed from the vine to increase the source/sink ratio and improve the quality of the remaining berries. Until now no tran...

    Authors: Chiara Pastore, Sara Zenoni, Giovanni Battista Tornielli, Gianluca Allegro, Silvia Dal Santo, Gabriele Valentini, Cesare Intrieri, Mario Pezzotti and Ilaria Filippetti
    Citation: BMC Genomics 2011 12:631
  29. DNA methylation in the 5' promoter regions of genes and microRNA (miRNA) regulation at the 3' untranslated regions (UTRs) are two major epigenetic regulation mechanisms in most eukaryotes. Both DNA methylation...

    Authors: Zhixi Su, Junfeng Xia and Zhongming Zhao
    Citation: BMC Genomics 2011 12(Suppl 5):S15

    This article is part of a Supplement: Volume 12 Supplement 5

  30. Speckles in ultrasound imaging affect image quality and can make the post-processing difficult. Speckle reduction technologies have been employed for removing speckles for some time. One of the effective speck...

    Authors: Xiaoming Liu, Jun Liu, Xin Xu, Lei Chun, Jinshan Tang and Youping Deng
    Citation: BMC Genomics 2011 12(Suppl 5):S14

    This article is part of a Supplement: Volume 12 Supplement 5

  31. Dynamic Bayesian Network (DBN) is an approach widely used for reconstruction of gene regulatory networks from time-series microarray data. Its performance in network reconstruction depends on a structure learn...

    Authors: Haoni Li, Nan Wang, Ping Gong, Edward J Perkins and Chaoyang Zhang
    Citation: BMC Genomics 2011 12(Suppl 5):S13

    This article is part of a Supplement: Volume 12 Supplement 5

  32. Along with obesity, physical inactivity, and family history of metabolic disorders, African American ethnicity is a risk factor for type 2 diabetes (T2D) in the United States. However, little is known about th...

    Authors: Jinghe Mao, Junmei Ai, Xinchun Zhou, Ming Shenwu, Manuel Ong Jr, Marketta Blue, Jasmine T Washington, Xiaonan Wang and Youping Deng
    Citation: BMC Genomics 2011 12(Suppl 5):S12

    This article is part of a Supplement: Volume 12 Supplement 5

  33. Studies of toxicity and unintended side effects can lead to improved drug safety and efficacy. One promising form of study comes from molecular systems biology in the form of "systems pharmacology". Systems ph...

    Authors: Liang-Chin Huang, Xiaogang Wu and Jake Y Chen
    Citation: BMC Genomics 2011 12(Suppl 5):S11

    This article is part of a Supplement: Volume 12 Supplement 5

  34. The recent advancement in array CGH (aCGH) research has significantly improved tumor identification using DNA copy number data. A number of unsupervised learning methods have been proposed for clustering aCGH ...

    Authors: Ke Zhang, Yi Yang, Viswanath Devanarayan, Linglin Xie, Youping Deng and Sens Donald
    Citation: BMC Genomics 2011 12(Suppl 5):S10

    This article is part of a Supplement: Volume 12 Supplement 5

  35. Malaria continues to be one of the most severe global infectious diseases, responsible for 1-2 million deaths yearly. The rapid evolution and spread of drug resistance in parasites has led to an urgent need fo...

    Authors: Timothy G Lilburn, Hong Cai, Zhan Zhou and Yufeng Wang
    Citation: BMC Genomics 2011 12(Suppl 5):S9

    This article is part of a Supplement: Volume 12 Supplement 5

  36. RNA-binding proteins (RBPs) play diverse roles in eukaryotic RNA processing. Despite their pervasive functions in coding and noncoding RNA biogenesis and regulation, elucidating the sequence specificities that...

    Authors: Xin Wang, Liran Juan, Junjie Lv, Kejun Wang, Jeremy R Sanford and Yunlong Liu
    Citation: BMC Genomics 2011 12(Suppl 5):S8

    This article is part of a Supplement: Volume 12 Supplement 5

  37. In microarray experiments with small sample sizes, it is a challenge to estimate p-values accurately and decide cutoff p-values for gene selection appropriately. Although permutation-based methods have proved ...

    Authors: Zhongxue Chen, Qingzhong Liu, Monnie McGee, Megan Kong, Xudong Huang, Youping Deng and Richard H Scheuermann
    Citation: BMC Genomics 2011 12(Suppl 5):S7

    This article is part of a Supplement: Volume 12 Supplement 5

  38. The use of gene signatures can potentially be of considerable value in the field of clinical diagnosis. However, gene signatures defined with different methods can be quite various even when applied the same d...

    Authors: Chang Chang, Junwei Wang, Chen Zhao, Jennifer Fostel, Weida Tong, Pierre R Bushel, Youping Deng, Lajos Pusztai, W Fraser Symmans and Tieliu Shi
    Citation: BMC Genomics 2011 12(Suppl 5):S6

    This article is part of a Supplement: Volume 12 Supplement 5

  39. Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding th...

    Authors: Hongmei Luo, Chao Sun, Yongzhen Sun, Qiong Wu, Ying Li, Jingyuan Song, Yunyun Niu, Xianglin Cheng, Hongxi Xu, Chuyuan Li, Juyan Liu, André Steinmetz and Shilin Chen
    Citation: BMC Genomics 2011 12(Suppl 5):S5

    This article is part of a Supplement: Volume 12 Supplement 5

  40. One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish th...

    Authors: Ken D Nguyen, Yi Pan and Ge Nong
    Citation: BMC Genomics 2011 12(Suppl 5):S4

    This article is part of a Supplement: Volume 12 Supplement 5

  41. Microarray data have been used for gene signature selection to predict clinical outcomes. Many studies have attempted to identify factors that affect models' performance with only little success. Fine-tuning o...

    Authors: Chen Zhao, Leming Shi, Weida Tong, John D Shaughnessy Jr, André Oberthuer, Lajos Pusztai, Youping Deng, W Fraser Symmans and Tieliu Shi
    Citation: BMC Genomics 2011 12(Suppl 5):S3

    This article is part of a Supplement: Volume 12 Supplement 5

  42. Recent studies suggest that many proteins or regions of proteins lack 3D structure. Defined as intrinsically disordered proteins, these proteins/peptides are functionally important. Recent advances in next gen...

    Authors: Yang Hu, Yunlong Liu, Jeesun Jung, A Keith Dunker and Yadong Wang
    Citation: BMC Genomics 2011 12(Suppl 5):S2

    This article is part of a Supplement: Volume 12 Supplement 5

  43. Microarray data have a high dimension of variables and a small sample size. In microarray data analyses, two important issues are how to choose genes, which provide reliable and good prediction for disease sta...

    Authors: Qingzhong Liu, Andrew H Sung, Zhongxue Chen, Jianzhong Liu, Lei Chen, Mengyu Qiao, Zhaohui Wang, Xudong Huang and Youping Deng
    Citation: BMC Genomics 2011 12(Suppl 5):S1

    This article is part of a Supplement: Volume 12 Supplement 5

  44. This is an editorial report of the supplement to BMC Genomics that includes 15 papers selected from the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology as well as other...

    Authors: Ke Zhang, Mehdi Pirooznia, Hamid R Arabnia, Jack Y Yang, Liangjiang Wang, Zuojie Luo and Youping Deng
    Citation: BMC Genomics 2011 12(Suppl 5):I1

    This article is part of a Supplement: Volume 12 Supplement 5

  45. We introduce a method to analyze the states of regulatory Boolean models that identifies important network states and their biological influence on the global network dynamics. It consists in (1) finding the s...

    Authors: Cristhian A Bugs, Giovani R Librelotto and José CM Mombach
    Citation: BMC Genomics 2011 12(Suppl 4):S10

    This article is part of a Supplement: Volume 12 Supplement 4

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