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Bioinformatic and algorithmical studies

Section edited by Youping Deng

This section considers studies on the development and application of novel computational and statistical methods to the analysis of genomic data for the study of health and disease.

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  1. Content type: Research article

    CRISPR/CAS9 (epi)genome editing revolutionized the field of gene and cell therapy. Our previous study demonstrated that a rapid and robust reactivation of the HIV latent reservoir by a catalytically-deficient ...

    Authors: Yonggang Zhang, Gustavo Arango, Fang Li, Xiao Xiao, Raj Putatunda, Jun Yu, Xiao-Feng Yang, Hong Wang, Layne T. Watson, Liqing Zhang and Wenhui Hu

    Citation: BMC Medical Genomics 2018 11:78

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  2. Content type: Database

    The Cancer Genome Atlas (TCGA) is an important data resource for cancer biologists and oncologists. However, a lack of bioinformatics expertise often hinders experimental cancer biologists and oncologists from...

    Authors: Qingrong Sun, Mengyuan Li and Xiaosheng Wang

    Citation: BMC Medical Genomics 2018 11:63

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    The Correction to this article has been published in BMC Medical Genomics 2018 11:74

  3. Content type: Research article

    Common metabolic diseases, including type 2 diabetes, coronary artery disease, and hypertension, arise from disruptions of the body’s metabolic homeostasis, with relatively strong contributions from genetic ri...

    Authors: Hyung Jun Woo and Jaques Reifman

    Citation: BMC Medical Genomics 2018 11:54

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  4. Content type: Research article

    Plasma neurofilament light (NFL) is a promising biomarker for Alzheimer disease (AD), which increases in the early stage of AD and is associated with the progression of AD. We performed a genome-wide associati...

    Authors: Jie-Qiong Li, Xiang-Zhen Yuan, Hai-Yan Li, Xi-Peng Cao, Jin-Tai Yu, Lan Tan and Wei-An Chen

    Citation: BMC Medical Genomics 2018 11:47

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  5. Content type: Research article

    The use of next-generation sequencing approaches in clinical diagnostics has led to a tremendous increase in data and a vast number of variants of uncertain significance that require interpretation. Therefore,...

    Authors: Corinna Ernst, Eric Hahnen, Christoph Engel, Michael Nothnagel, Jonas Weber, Rita K. Schmutzler and Jan Hauke

    Citation: BMC Medical Genomics 2018 11:35

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  6. Content type: Research article

    The presentation of HLA peptide complexes to T cells is a highly regulated and tissue specific process involving multiple transcriptionally controlled cellular components. The extensive polymorphism of HLA gen...

    Authors: Sebastian Boegel, Martin Löwer, Thomas Bukur, Patrick Sorn, John C. Castle and Ugur Sahin

    Citation: BMC Medical Genomics 2018 11:36

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  7. Content type: Research article

    Using high-dimensional penalized regression we studied genome-wide DNA-methylation in bone biopsies of 80 postmenopausal women in relation to their bone mineral density (BMD). The women showed BMD varying from...

    Authors: Tonje G. Lien, Ørnulf Borgan, Sjur Reppe, Kaare Gautvik and Ingrid Kristine Glad

    Citation: BMC Medical Genomics 2018 11:24

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  8. Content type: Research article

    The usage of Artificial Neural Networks (ANNs) for genome-enabled classifications and establishing genome-phenotype correlations have been investigated more extensively over the past few years. The reason for ...

    Authors: Aida Catic, Lejla Gurbeta, Amina Kurtovic-Kozaric, Senad Mehmedbasic and Almir Badnjevic

    Citation: BMC Medical Genomics 2018 11:19

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  9. Content type: Research article

    Genome-wide association studies (GWASs) have revealed relationships between over 57,000 genetic variants and diseases. However, unlike Mendelian diseases, complex diseases arise from the interplay of multiple ...

    Authors: Takashi Kido, Weronika Sikora-Wohlfeld, Minae Kawashima, Shinichi Kikuchi, Naoyuki Kamatani, Anil Patwardhan, Richard Chen, Marina Sirota, Keiichi Kodama, Dexter Hadley and Atul J. Butte

    Citation: BMC Medical Genomics 2018 11:3

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  10. Content type: Research article

    MiRNAs are frequently abnormally expressed in the progression of human osteosarcoma. Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is one of the tumor suppressors in various types of human c...

    Authors: Biao Zhong, Shang Guo, Wei Zhang, Chi Zhang, Yukai Wang and Changqing Zhang

    Citation: BMC Medical Genomics 2017 10:64

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  11. Content type: Research article

    Significant clinical and research applications are driving large scale adoption of individualized tumor sequencing in cancer in order to identify tumors-specific mutations. When a matched germline sample is av...

    Authors: Rebecca F. Halperin, John D. Carpten, Zarko Manojlovic, Jessica Aldrich, Jonathan Keats, Sara Byron, Winnie S. Liang, Megan Russell, Daniel Enriquez, Ana Claasen, Irene Cherni, Baffour Awuah, Joseph Oppong, Max S. Wicha, Lisa A. Newman, Evelyn Jaigge…

    Citation: BMC Medical Genomics 2017 10:61

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  12. Content type: Research article

    Preimplantation genetic diagnosis (PGD) is now widely used to select embryos free of chromosomal copy number variations (CNV) from chromosome balanced translocation carriers. However, it remains a difficulty t...

    Authors: Shuo Zhang, Caixia Lei, Junping Wu, Jing Zhou, Haiyan Sun, Jing Fu, Yijuan Sun, Xiaoxi Sun, Daru Lu and Yueping Zhang

    Citation: BMC Medical Genomics 2017 10:60

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  13. Content type: Research article

    With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmaco...

    Authors: Petr Ponomarenko, Alex Ryutov, Dennis T. Maglinte, Ancha Baranova, Tatiana V. Tatarinova and Xiaowu Gai

    Citation: BMC Medical Genomics 2017 10:57

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  14. Content type: Research article

    Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of the cellular transcriptome is a promising approach ...

    Authors: Vinay K. Mittal and John F. McDonald

    Citation: BMC Medical Genomics 2017 10:53

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  15. Content type: Research article

    Preeclampsia is a multifactorial disease with unknown pathogenesis. Even when recent studies explored this disease using several bioinformatics tools, the main objective was not directed to pathogenesis. Addit...

    Authors: Eduardo Tejera, Maykel Cruz-Monteagudo, Germán Burgos, María-Eugenia Sánchez, Aminael Sánchez-Rodríguez, Yunierkis Pérez-Castillo, Fernanda Borges, Maria Natália Dias Soeiro Cordeiro, César Paz-y-Miño and Irene Rebelo

    Citation: BMC Medical Genomics 2017 10:50

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  16. Content type: Research article

    Lung cancer is a leading cause of cancer-related death worldwide and is the most commonly diagnosed cancer. Like other cancers, it is a complex and highly heterogeneous disease involving multiple signaling pat...

    Authors: Salem A. El-aarag, Amal Mahmoud, Medhat H. Hashem, Hatem Abd Elkader, Alaa E. Hemeida and Mahmoud ElHefnawi

    Citation: BMC Medical Genomics 2017 10:40

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  17. Content type: Software

    An increasing number of precision oncology programmes are being launched world-wide. To support this development, we present the Cancer Variant Explorer (CVE), an R package with an interactive Shiny web browse...

    Authors: Andreas Mock, Suzanne Murphy, James Morris, Francesco Marass, Nitzan Rosenfeld and Charlie Massie

    Citation: BMC Medical Genomics 2017 10:37

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  18. Content type: Research article

    To realize potential public health benefits from genetic and genomic innovations, understanding how best to implement the innovations into clinical care is important. The objective of this study was to synthes...

    Authors: Nina R. Sperber, Janet S. Carpenter, Larisa H. Cavallari, Laura J. Damschroder, Rhonda M. Cooper-DeHoff, Joshua C. Denny, Geoffrey S. Ginsburg, Yue Guan, Carol R. Horowitz, Kenneth D. Levy, Mia A. Levy, Ebony B. Madden, Michael E. Matheny, Toni I. Pollin, Victoria M. Pratt, Marc Rosenman…

    Citation: BMC Medical Genomics 2017 10:35

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  19. Content type: Research article

    Colon cancer, one of the most common causes of cancer-related deaths, arises from adenomatous polyps. In these years, circulating microRNAs (miRNAs) have attracted increasing attention as novel biomarkers for ...

    Authors: Yajie Zhang, Min Li, Yijiang Ding, Zhimin Fan, Jinchun Zhang, Hongying Zhang, Bin Jiang and Yong Zhu

    Citation: BMC Medical Genomics 2017 10:23

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  20. Content type: Research article

    Patient stratification to identify subtypes with different disease manifestations, severity, and expected survival time is a critical task in cancer diagnosis and treatment. While stratification approaches usi...

    Authors: Kiley Graim, Tiffany Ting Liu, Achal S. Achrol, Evan O. Paull, Yulia Newton, Steven D. Chang, Griffith R. Harsh IV, Sergio P. Cordero, Daniel L. Rubin and Joshua M. Stuart

    Citation: BMC Medical Genomics 2017 10:20

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  21. Content type: Research Article

    The distinct types of hematological malignancies have different biological mechanisms and prognoses. For instance, myelodysplastic syndrome (MDS) is generally indolent and low risk; however, it may transform i...

    Authors: Amir Foroushani, Rupesh Agrahari, Roderick Docking, Linda Chang, Gerben Duns, Monika Hudoba, Aly Karsan and Habil Zare

    Citation: BMC Medical Genomics 2017 10:16

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  22. Content type: Research article

    Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedu...

    Authors: Zhenhua Yu, Ao Li and Minghui Wang

    Citation: BMC Medical Genomics 2017 10:15

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  23. Content type: Research article

    Epithelial to mesenchymal transition, and mimicking processes, contribute to cancer invasion and metastasis, and are known to be responsible for resistance to various therapeutic agents in many cancers. While ...

    Authors: Orieta Celiku, Anita Tandle, Joon-Yong Chung, Stephen M. Hewitt, Kevin Camphausen and Uma Shankavaram

    Citation: BMC Medical Genomics 2017 10:13

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  24. Content type: Research article

    Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, ther...

    Authors: Han Fang, Yiyang Wu, Hui Yang, Margaret Yoon, Laura T. Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang and Gholson J. Lyon

    Citation: BMC Medical Genomics 2017 10:10

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  25. Content type: Research article

    Type 1 diabetes (T1D) is an autoimmune disease and extensive evidence has indicated a critical role of both the innate and the adaptive arms of immune system in disease development. To date most clinical trial...

    Authors: Shouguo Gao, Nathaniel Wolanyk, Ye Chen, Shuang Jia, Martin J. Hessner and Xujing Wang

    Citation: BMC Medical Genomics 2017 10:7

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  26. Content type: Research article

    Clonal expansion of leukemic cells leads to onset of adult T-cell leukemia (ATL), an aggressive lymphoid malignancy with a very poor prognosis. Infection with human T-cell leukemia virus type-1 (HTLV-1) is the...

    Authors: Amir Farmanbar, Sanaz Firouzi, Sung-Joon Park, Kenta Nakai, Kaoru Uchimaru and Toshiki Watanabe

    Citation: BMC Medical Genomics 2017 10:4

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Technical advance

    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

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  30. Content type: Research article

    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

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  31. Content type: Debate

    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

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  32. Content type: Research Article

    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

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  33. Content type: Research article

    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

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  34. Content type: Technical advance

    Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significa...

    Authors: Eliseos J. Mucaki, Natasha G. Caminsky, Ami M. Perri, Ruipeng Lu, Alain Laederach, Matthew Halvorsen, Joan H. M. Knoll and Peter K. Rogan

    Citation: BMC Medical Genomics 2016 9:19

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  35. Content type: Software

    Breast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient...

    Authors: Tobias Meißner, Kathleen M Fisch, Louis Gioia and Andrew I Su

    Citation: BMC Medical Genomics 2015 8:24

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  36. Content type: Research article

    Schizophrenia is a neurodevelopmental disorder with genetic and environmental factors contributing to its pathogenesis, although the mechanism is unknown due to the difficulties in accessing diseased tissue du...

    Authors: Mariana Maschietto, Ana C Tahira, Renato Puga, Leandro Lima, Daniel Mariani, Bruna da Silveira Paulsen, Paulo Belmonte-de-Abreu, Henrique Vieira, Ana CV Krepischi, Dirce M Carraro, Joana A Palha, Stevens Rehen and Helena Brentani

    Citation: BMC Medical Genomics 2015 8:23

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  37. Content type: Research article

    A novel class of transcripts, long non-coding RNAs (lncRNAs), has recently emerged as a key player in several biological processes, and important roles for these molecules have been reported in a number of com...

    Authors: ZhaoHui Luo, Ye Li, XiaoFang Liu, MengChuan Luo, LiQun Xu, YueBei Luo, Bo Xiao and Huan Yang

    Citation: BMC Medical Genomics 2015 8:13

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  38. Content type: Software

    Single base level information from next-generation sequencing (NGS) allows for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells. S...

    Authors: Alessandro Romanel, Sara Lago, Davide Prandi, Andrea Sboner and Francesca Demichelis

    Citation: BMC Medical Genomics 2015 8:9

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  39. Content type: Research article

    African Americans (AA) have more pronounced insulin resistance and higher insulin secretion than European Americans (Caucasians or CA) when matched for age, gender, and body mass index (BMI). We hypothesize th...

    Authors: Swapan Kumar Das, Neeraj Kumar Sharma and Bin Zhang

    Citation: BMC Medical Genomics 2015 8:4

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  40. Content type: Research article

    Personalized medicine has become a priority in breast cancer patient management. In addition to the routinely used clinicopathological characteristics, clinicians will have to face an increasing amount of data...

    Authors: Tatiana Kempowsky-Hamon, Carine Valle, Magali Lacroix-Triki, Lyamine Hedjazi, Lidwine Trouilh, Sophie Lamarre, Delphine Labourdette, Laurence Roger, Loubna Mhamdi, Florence Dalenc, Thomas Filleron, Gilles Favre, Jean-Marie François, Marie-Véronique Le Lann and Véronique Anton-Leberre

    Citation: BMC Medical Genomics 2015 8:3

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  41. Content type: Research article

    Tumorigenesis is characterised by changes in transcriptional control. Extensive transcript expression data have been acquired over the last decade and used to classify prostate cancers. Prostate cancer is, how...

    Authors: Stefan J Barfeld, Phil East, Verena Zuber and Ian G Mills

    Citation: BMC Medical Genomics 2014 7:513

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  42. Content type: Research article

    Clinical and histological parameters are valid prognostic markers in renal disease, although they may show considerable interindividual variability and sometimes limited prognostic value. Novel molecular marke...

    Authors: Hannes Neuwirt, Paul Perco, Alexander Kainz, Irmgard Mühlberger, Johannes Leierer, Suzie-Jane Braniff, Bernd Mayer, Gert Mayer and Michael Rudnicki

    Citation: BMC Medical Genomics 2014 7:75

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  43. Content type: Research article

    The incidence of Acute Megakaryoblastic Leukemia (AMKL) is 500-fold higher in children with Down Syndrome (DS) compared with non-DS children, but the relevance of trisomy 21 as a specific background of AMKL in...

    Authors: Maria Chiara Pelleri, Allison Piovesan, Maria Caracausi, Anna Concetta Berardi, Lorenza Vitale and Pierluigi Strippoli

    Citation: BMC Medical Genomics 2014 7:63

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  44. Content type: Research article

    Improvements in both performance and cost for next-generation sequencing (NGS) have spurred its rapid adoption for clinical applications. We designed and optimized a pan-cancer target-enrichment panel for 51 w...

    Authors: Ashish Choudhary, Elizabeth Mambo, Tiffany Sanford, Michael Boedigheimer, Brian Twomey, Joseph Califano, Andrew Hadd, Kelly S Oliner, Sylvie Beaudenon, Gary J Latham and Alex T Adai

    Citation: BMC Medical Genomics 2014 7:62

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  45. Content type: Research article

    Cytokine-induced killer (CIK) cells are an emerging approach of cancer treatment. Our previous study have shown that CIK cells stimulated with combination of IL-2 and IL-15 displayed improved proliferation cap...

    Authors: Wenju Wang, Mingyao Meng, Yayong Zhang, Chuanyu Wei, Yanhua Xie, Lihong Jiang, Chunhui Wang, Fang Yang, Weiwei Tang, Xingfang Jin, Dai Chen, Jie Zong, Zongliu Hou and Ruhong Li

    Citation: BMC Medical Genomics 2014 7:49

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