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  1. High dimensional feature space generally degrades classification in several applications. In this paper, we propose a strategy called gene masking, in which non-contributing dimensions are heuristically remove...

    Authors: Harsh Saini, Sunil Pranit Lal, Vimal Vikash Naidu, Vincel Wince Pickering, Gurmeet Singh, Tatsuhiko Tsunoda and Alok Sharma
    Citation: BMC Medical Genomics 2016 9(Suppl 3):74
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  2. The hypergeometric enrichment analysis approach typically fares poorly in feature-selection stability due to its upstream reliance on the t-test to generate differential protein lists before testing for enrichmen...

    Authors: Wilson Wen Bin Goh
    Citation: BMC Medical Genomics 2016 9(Suppl 3):67
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  3. Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits...

    Authors: Åsa K. Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind and Erik Ingelsson
    Citation: BMC Medical Genomics 2016 9:72
    Content type: Research article Published on:

  4. Research suggests that multidisciplinary genomic tumor boards (MGTB) can inform cancer patient care, though little is known about factors influencing how MGTBs interpret genomic test results, make recommendati...

    Authors: Michelle L. McGowan, Roselle S. Ponsaran, Paula Silverman, Lyndsay N. Harris and Patricia A. Marshall
    Citation: BMC Medical Genomics 2016 9:71
    Content type: Research article Published on:

  5. Systemic Lupus Erythematosus (SLE) is a complex, multi-systemic, autoimmune disease for which the underlying aetiological mechanisms are poorly understood. The genetic and molecular processes underlying lupus ...

    Authors: Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner and Nicki Tiffin
    Citation: BMC Medical Genomics 2016 9:66
    Content type: Research article Published on:

  6. The KRAS gene is mutated in about 40 % of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistance to anti-EGFR inhibitor (EGFRi) therapy. Since...

    Authors: Bernard Omolo, Mingli Yang, Fang Yin Lo, Michael J. Schell, Sharon Austin, Kellie Howard, Anup Madan and Timothy J. Yeatman
    Citation: BMC Medical Genomics 2016 9:65
    Content type: Technical advance Published on:

  7. The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adeq...

    Authors: Lei Wei, Antonios Papanicolau-Sengos, Song Liu, Jianmin Wang, Jeffrey M. Conroy, Sean T. Glenn, Elizabeth Brese, Qiang Hu, Kiersten Marie Miles, Blake Burgher, Maochun Qin, Karen Head, Angela R. Omilian, Wiam Bshara, John Krolewski, Donald L. Trump…
    Citation: BMC Medical Genomics 2016 9:64
    Content type: Research article Published on:

  8. The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, ...

    Authors: Haixu Tang, Xiaoqian Jiang, Xiaofeng Wang, Shuang Wang, Heidi Sofia, Dov Fox, Kristin Lauter, Bradley Malin, Amalio Telenti, Li Xiong and Lucila Ohno-Machado
    Citation: BMC Medical Genomics 2016 9:63
    Content type: Technical advance Published on:

  9. The increasing use of next generation DNA sequencing in clinical medicine is exposing the need for more genetics education in physician training. We piloted an initiative to determine the feasibility of incorp...

    Authors: Glenn S. Gerhard, Qunyan Jin, Barbara V. Paynton and Steven N. Popoff
    Citation: BMC Medical Genomics 2016 9:62
    Content type: Correspondence Published on:

  10. Noninvasive prenatal testing (NIPT) using massively parallel sequencing of cell-free DNA (cfDNA) is increasingly being used to predict fetal chromosomal abnormalities. However, concerns over erroneous predicti...

    Authors: Sunshin Kim, HeeJung Jung, Sung Hee Han, SeungJae Lee, JeongSub Kwon, Min Gyun Kim, Hyungsik Chu, Kyudong Han, Hwanjong Kwak, Sunghoon Park, Hee Jae Joo, Minae An, Jungsu Ha, Kyusang Lee, Byung Chul Kim, Hailing Zheng…
    Citation: BMC Medical Genomics 2016 9:61
    Content type: Research article Published on:

  11. Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only...

    Authors: Subhojit Sen, Kirsten F. Block, Alice Pasini, Stephen B. Baylin and Hariharan Easwaran
    Citation: BMC Medical Genomics 2016 9:60
    Content type: Research article Published on:

  12. The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene ex...

    Authors: Andréanne Morin, Tony Kwan, Bing Ge, Louis Letourneau, Maria Ban, Karolina Tandre, Maxime Caron, Johanna K. Sandling, Jonas Carlsson, Guillaume Bourque, Catherine Laprise, Alexandre Montpetit, Ann-Christine Syvanen, Lars Ronnblom, Stephen J. Sawcer, Mark G. Lathrop…
    Citation: BMC Medical Genomics 2016 9:59
    Content type: Research article Published on:

  13. Histopathological assessment has a low potential to predict clinical outcome in patients with the same stage of colorectal cancer. More specific and sensitive biomarkers to determine patients’ survival are nee...

    Authors: Nurul Ainin Abdul Aziz, Norfilza M. Mokhtar, Roslan Harun, Md Manir Hossain Mollah, Isa Mohamed Rose, Ismail Sagap, Azmi Mohd Tamil, Wan Zurinah Wan Ngah and Rahman Jamal
    Citation: BMC Medical Genomics 2016 9:58
    Content type: Research article Published on:

  15. Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a defin...

    Authors: Chen Du, Barbara N. Pusey, Christopher J. Adams, C. Christopher Lau, William P. Bone, William A. Gahl, Thomas C. Markello and David R. Adams
    Citation: BMC Medical Genomics 2016 9:56
    Content type: Debate Published on:

  16. DNA methylation levels will be important for detection of epigenetic effects. However, there are few reports showing sex-related differences in the sensitivity to DNA methylation. To evaluate their sex-related...

    Authors: Mikio Watanabe, Chika Honda, Yoshinori Iwatani, Shiro Yorifuji, Hiroyasu Iso, Kei Kamide, Jun Hatazawa, Shinji Kihara, Norio Sakai, Hiroko Watanabe, Kiyoko Makimoto, Mikio Watanabe, Chika Honda and Yoshinori Iwatani
    Citation: BMC Medical Genomics 2016 9:55
    Content type: Research article Published on:

  17. The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, select...

    Authors: Mahesh Iddawela, Oscar M. Rueda, Marcus Klarqvist, Stefan Graf, Helena M. Earl and Carlos Caldas
    Citation: BMC Medical Genomics 2016 9:54
    Content type: Research article Published on:

  19. CpG islands (CGIs) are interspersed DNA sequences that have unusually high CpG ratios and GC contents. CGIs are typically located in the promoter of protein-coding genes. They normally lack DNA methylation but...

    Authors: Min Gyun Bae, Jeong Yeon Kim and Jung Kyoon Choi
    Citation: BMC Medical Genomics 2016 9(Suppl 1):38
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  20. Kawasaki disease (KD) is an autoimmune disease preferentially attacking children younger than five years worldwide. So far, the principal treatment to KD is the administration of Intravenous immunoglobulin (IV...

    Authors: Sung-Chou Li, Wen-Ching Chan, Ying-Hsien Huang, Mindy Ming-Huey Guo, Hong-Ren Yu, Fu-Chen Huang, Hsing-Chun Kuo and Ho-Chang Kuo
    Citation: BMC Medical Genomics 2016 9(Suppl 1):37
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  21. Sequencing technologies are generating enormous amounts of read data, however assembly of genomes and metagenomes remain among the most challenging tasks. In this paper we study the comparison of genomes and m...

    Authors: Matteo Comin and Michele Schimd
    Citation: BMC Medical Genomics 2016 9(Suppl 1):36
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  22. Exome sequencing has been emerged as a primary method to identify detailed sequence variants associated with complex diseases including Crohn’s disease in the protein-coding regions of human genome. However, c...

    Authors: Chan-Seok Jeong and Dongsup Kim
    Citation: BMC Medical Genomics 2016 9(Suppl 1):35
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  23. Multifunctional transcription factor (TF) gene EWS/EWSR1 is involved in various cellular processes such as transcription regulation, noncoding RNA regulation, splicing regulation, genotoxic stress response, and c...

    Authors: Chai-Jin Lee, Hongryul Ahn, Sean Bong Lee, Jong-Yeon Shin, Woong-Yang Park, Jong-Il Kim, Junghee Lee, Hoon Ryu and Sun Kim
    Citation: BMC Medical Genomics 2016 9(Suppl 1):33
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  24. We explored premature stop-gain variants to test the hypothesis that variants, which are likely to have a consequence on protein structure and function, will reveal important insights with respect to the pheno...

    Authors: Anurag Verma, Shefali S. Verma, Sarah A. Pendergrass, Dana C. Crawford, David R. Crosslin, Helena Kuivaniemi, William S. Bush, Yuki Bradford, Iftikhar Kullo, Suzette J. Bielinski, Rongling Li, Joshua C. Denny, Peggy Peissig, Scott Hebbring, Mariza De Andrade, Marylyn D. Ritchie…
    Citation: BMC Medical Genomics 2016 9(Suppl 1):32
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  25. The increasing availability of multiple types of genomic profiles measured from the same cancer patients has provided numerous opportunities for investigating genomic mechanisms underlying cancer. In particula...

    Authors: Reddy Rani Vangimalla, Hyun-hwan Jeong and Kyung-Ah Sohn
    Citation: BMC Medical Genomics 2016 9(Suppl 1):31
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  26. Pathogenic mutations in PSEN1 are known to cause familial early-onset Alzheimer’s disease (EOAD) but common variants in PSEN1 have not been found to strongly influence late-onset AD (LOAD). The association of rar...

    Authors: Kwangsik Nho, Emrin Horgusluoglu, Sungeun Kim, Shannon L. Risacher, Dokyoon Kim, Tatiana Foroud, Paul S. Aisen, Ronald C. Petersen, Clifford R. Jack Jr., Leslie M. Shaw, John Q. Trojanowski, Michael W. Weiner, Robert C. Green, Arthur W. Toga and Andrew J. Saykin
    Citation: BMC Medical Genomics 2016 9(Suppl 1):30
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  27. Tyrosine kinase inhibitor (TKI)-based therapy is a recommended treatment for patients with chronic myeloid leukemia (CML). However, a considerable group of CML patients do not respond well to the TKI therapy. ...

    Authors: Kihoon Cha, Yi Li and Gwan-Su Yi
    Citation: BMC Medical Genomics 2016 9(Suppl 1):29
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  28. Non-small cell lung cancer (NSCLC) remains a lethal disease despite many proposed treatments. Recent studies have indicated that epigenetic therapy, which targets epigenetic effects, might be a new therapeutic...

    Authors: Y-h. Taguchi, Mitsuo Iwadate and Hideaki Umeyama
    Citation: BMC Medical Genomics 2016 9(Suppl 1):28
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  29. Whole-exome sequencing (WES) consists in the capture, sequencing and analysis of all exons in the human genome. Originally developed in the research context, this technology is now increasingly used clinically...

    Authors: Gabrielle Bertier, Martin Hétu and Yann Joly
    Citation: BMC Medical Genomics 2016 9:52
    Content type: Research article Published on:

  30. Inferring gene regulatory networks is one of the most interesting research areas in the systems biology. Many inference methods have been developed by using a variety of computational models and approaches. Ho...

    Authors: Dongchul Kim, Mingon Kang, Ashis Biswas, Chunyu Liu and Jean Gao
    Citation: BMC Medical Genomics 2016 9(Suppl 2):50
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  31. Cell segmentation is a critical step for quantification and monitoring of cell cycle progression, cell migration, and growth control to investigate cellular immune response, embryonic development, tumorigenesi...

    Authors: Fatima Boukari and Sokratis Makrogiannis
    Citation: BMC Medical Genomics 2016 9(Suppl 2):49
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  32. Genomic variations are associated with the metabolism and the occurrence of adverse reactions of many therapeutic agents. The polymorphisms on over 2000 locations of cytochrome P450 enzymes (CYP) due to many f...

    Authors: Zhaohui Liang, Jimmy Xiangji Huang, Xing Zeng and Gang Zhang
    Citation: BMC Medical Genomics 2016 9(Suppl 2):48
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  33. Development of biologically relevant models from gene expression data notably, microarray data has become a topic of great interest in the field of bioinformatics and clinical genetics and oncology. Only a sma...

    Authors: Johra Muhammad Moosa, Rameen Shakur, Mohammad Kaykobad and Mohammad Sohel Rahman
    Citation: BMC Medical Genomics 2016 9(Suppl 2):47
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  34. Fragment-based approaches have now become an important component of the drug discovery process. At the same time, pharmaceutical chemists are more often turning to the natural world and its extremely large and...

    Authors: Sunandini Sharma, Kritika Karri, Ishwor Thapa, Dhundy Bastola and Dario Ghersi
    Citation: BMC Medical Genomics 2016 9(Suppl 2):46
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  35. In biomedical research, events revealing complex relations between entities play an important role. Biomedical event trigger identification has become a research hotspot since its important role in biomedical ...

    Authors: Jian Wang, Jianhai Zhang, Yuan An, Hongfei Lin, Zhihao Yang, Yijia Zhang and Yuanyuan Sun
    Citation: BMC Medical Genomics 2016 9(Suppl 2):45
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  36. Measurement of various markers of single cells using flow cytometry has several biological applications. These applications include improving our understanding of behavior of cellular systems, identifying rare...

    Authors: Maziyar Baran Pouyan, Vasu Jindal, Javad Birjandtalab and Mehrdad Nourani
    Citation: BMC Medical Genomics 2016 9(Suppl 2):41
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  37. The high cost and the long time required to bring drugs into commerce is driving efforts to repurpose FDA approved drugs—to find new uses for which they weren’t intended, and to thereby reduce the overall cost...

    Authors: Hsiao-Rong Chen, David H. Sherr, Zhenjun Hu and Charles DeLisi
    Citation: BMC Medical Genomics 2016 9:51
    Content type: Research article Published on:

  38. Based on age of presentation, celiac disease (CD) is categorised as pediatric CD and adult CD. It however remains unclear if these are genetically and/or phenotypically distinct disorders or just different spe...

    Authors: Sabyasachi Senapati, Ajit Sood, Vandana Midha, Neena Sood, Suresh Sharma, Lalit Kumar and B. K. Thelma
    Citation: BMC Medical Genomics 2016 9:44
    Content type: Research article Published on:

  39. Identification of prognostic gene expression markers from clinical cohorts might help to better understand disease etiology. A set of potentially important markers can be automatically selected when linking ge...

    Authors: Harald Binder, Thorsten Kurz, Sven Teschner, Clemens Kreutz, Marcel Geyer, Johannes Donauer, Annette Kraemer-Guth, Jens Timmer, Martin Schumacher and Gerd Walz
    Citation: BMC Medical Genomics 2016 9:43
    Content type: Research Article Published on:

  40. Neurodevelopment is orchestrated by a wide range of genes, and the genetic causes of neurodevelopmental disorders are thus heterogeneous. We applied whole exome sequencing (WES) for molecular diagnosis and in sil...

    Authors: Wu-Lin Charng, Ender Karaca, Zeynep Coban Akdemir, Tomasz Gambin, Mehmed M. Atik, Shen Gu, Jennifer E. Posey, Shalini N. Jhangiani, Donna M. Muzny, Harsha Doddapaneni, Jianhong Hu, Eric Boerwinkle, Richard A. Gibbs, Jill A. Rosenfeld, Hong Cui, Fan Xia…
    Citation: BMC Medical Genomics 2016 9:42
    Content type: Research article Published on:

  41. The diagnosis of acute appendicitis can be surprisingly difficult without computed tomography, which carries significant radiation exposure. Circulating blood cells may carry informative changes in their RNA e...

    Authors: Lakhmir S. Chawla, Ian Toma, Danielle Davison, Khashayar Vaziri, Juliet Lee, Raymond Lucas, Michael G. Seneff, Aoibhinn Nyhan and Timothy A. McCaffrey
    Citation: BMC Medical Genomics 2016 9:40
    Content type: Research article Published on:

  43. Authors: Scott M. Riester, Diren Arsoy, Emily T. Camilleri, Amel Dudakovic, Christopher R. Paradise, Jared M. Evans, Jorge Torres-Mora, Marco Rizzo, Peter Kloen, Marianna Kruithof-de Julio, Andre J. van Wijnen and Sanjeev Kakar
    Citation: BMC Medical Genomics 2016 9:34
    Content type: Erratum Published on:

    The original article was published in BMC Medical Genomics 2015 8:59

  44. Accurate discovery of molecular biomarkers that are prognostic of a clinical outcome is an important yet challenging task, partly due to the combination of the typically weak genomic signal for a clinical outc...

    Authors: Li-Xuan Qin and Douglas A. Levine
    Citation: BMC Medical Genomics 2016 9:27
    Content type: Research article Published on:

  45. At the molecular level breast cancer comprises a heterogeneous set of subtypes associated with clear differences in gene expression and clinical outcomes. Single sample predictors (SSPs) are built via a two-st...

    Authors: Herman MJ. Sontrop, Marcel JT. Reinders and Perry D. Moerland
    Citation: BMC Medical Genomics 2016 9:26
    Content type: Research Article Published on:

    The Erratum to this article has been published in BMC Medical Genomics 2016 9:39

  46. The use of an overall risk assessment based on genomic information is consistent with precision medicine. Despite the enthusiasm, there is a need for public engagement on the appropriate use of such emerging t...

    Authors: Stuart G. Nicholls, Holly Etchegary, June C. Carroll, David Castle, Louise Lemyre, Beth K. Potter, Samantha Craigie and Brenda J. Wilson
    Citation: BMC Medical Genomics 2016 9:25
    Content type: Research article Published on:

  47. Genetic screening to identify carriers of autosomal recessive diseases has become an integral part of routine prenatal care. In spite of the rapid growth of known mutations, most current screening programs inc...

    Authors: Moran Gal, Khen Khermesh, Michal Barak, Min Lin, Hadas Lahat, Haike Reznik Wolf, Michael Lin, Elon Pras and Erez Y. Levanon
    Citation: BMC Medical Genomics 2016 9:24
    Content type: Research article Published on:

  49. Noninvasive prenatal testing (NIPT) to detect fetal aneuploidy using next-generation sequencing on ion semiconductor platforms has become common. There are several sequencers that can generate sufficient DNA r...

    Authors: Sunshin Kim, HeeJung Jung, Sung Hee Han, SeungJae Lee, JeongSub Kwon, Min Gyun Kim, Hyungsik Chu, Hongliang Chen, Kyudong Han, Hwanjong Kwak, Sunghoon Park, Hee Jae Joo, Byung Chul Kim and Jong Bhak
    Citation: BMC Medical Genomics 2016 9:22
    Content type: Research article Published on:

  50. MicroRNAs (miRNAs) have been implicated in the incidence and progression of cancer. It has been proposed that single nucleotide polymorphisms (SNPs) influence cancer risk due to their position within genes inv...

    Authors: Lila E. Mullany, Jennifer S. Herrick, Roger K. Wolff, Matthew F. Buas and Martha L. Slattery
    Citation: BMC Medical Genomics 2016 9:21
    Content type: Research article Published on:
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BMC Medical Genomics

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