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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: Technical advance

    The amount of publicly available cancer-related “omics” data is constantly growing and can potentially be used to gain insights into the tumour biology of new cancer patients, their diagnosis and suitable trea...

    Authors: Petr V. Nazarov, Anke K. Wienecke-Baldacchino, Andrei Zinovyev, Urszula Czerwińska, Arnaud Muller, Dorothée Nashan, Gunnar Dittmar, Francisco Azuaje and Stephanie Kreis

    Citation: BMC Medical Genomics 2019 12:132

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  2. Content type: Research article

    The five-year survival rate and therapeutic effect of malignant glioma is low. Identification of key/associated proteins and pathways in glioma is necessary for developing effective diagnosis and targeted ther...

    Authors: Yongqin Yin, Bo Li, Kejie Mou, Muhammad T. Khan, Aman C. Kaushik, Dongqing Wei and Yu-Juan Zhang

    Citation: BMC Medical Genomics 2019 12:125

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  3. Content type: Research article

    Psoriasis and atopic dermatitis are two inflammatory skin diseases with a high prevalence and a significant burden on the patients. Underlying molecular mechanisms include chronic inflammation and abnormal pro...

    Authors: Zandra C. Félix Garza, Michael Lenz, Joerg Liebmann, Gökhan Ertaylan, Matthias Born, Ilja C. W. Arts, Peter A. J. Hilbers and Natal A. W. van Riel

    Citation: BMC Medical Genomics 2019 12:121

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  4. Content type: Research article

    microRNA (miRNA) is a short RNA (~ 22 nt) that regulates gene expression at the posttranscriptional level. Aberration of miRNA expressions could affect their targeting mRNAs involved in cancer-related signalin...

    Authors: Lizhong Ding, Zheyun Feng and Yongsheng Bai

    Citation: BMC Medical Genomics 2019 12:117

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  5. Content type: Technical advance

    Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling...

    Authors: Dimitrios Kleftogiannis, Marco Punta, Anuradha Jayaram, Shahneen Sandhu, Stephen Q. Wong, Delila Gasi Tandefelt, Vincenza Conteduca, Daniel Wetterskog, Gerhardt Attard and Stefano Lise

    Citation: BMC Medical Genomics 2019 12:115

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  6. Content type: Research article

    Familial adenomatous polyposis (FAP) is an autosomal dominant colorectal tumor characterized by numerous adenomatous colonic polyps that often lead to colon cancer. Although most patients with FAP harbored ger...

    Authors: Borahm Kim, Dongju Won, Mi Jang, Hoguen Kim, Jong Rak Choi, Tae Il Kim and Seung-Tae Lee

    Citation: BMC Medical Genomics 2019 12:103

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  7. Content type: Technical advance

    Patient-derived xenograft (PDX) models are in vivo models of human cancer that have been used for translational cancer research and therapy selection for individual patients. The Jackson Laboratory (JAX) PDX r...

    Authors: Xing Yi Woo, Anuj Srivastava, Joel H. Graber, Vinod Yadav, Vishal Kumar Sarsani, Al Simons, Glen Beane, Stephen Grubb, Guruprasad Ananda, Rangjiao Liu, Grace Stafford, Jeffrey H. Chuang, Susan D. Airhart, R. Krishna Murthy Karuturi, Joshy George and Carol J. Bult

    Citation: BMC Medical Genomics 2019 12:92

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  8. Content type: Research article

    The availability and generation of large amounts of genomic data has led to the development of a new paradigm in cancer treatment emphasizing a precision approach at the molecular and genomic level. Statistica...

    Authors: Joshua D. Mannheimer, Dawn L. Duval, Ashok Prasad and Daniel L. Gustafson

    Citation: BMC Medical Genomics 2019 12:87

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  9. Content type: Research article

    RNA-seq is poised to play a major role in the management of kidney transplant patients. Rigorous definition of housekeeping genes (HKG) is essential for further progress in this field. Using single genes or a ...

    Authors: Zijie Wang, Zili Lyu, Ling Pan, Gang Zeng and Parmjeet Randhawa

    Citation: BMC Medical Genomics 2019 12:86

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  10. Content type: Research article

    Germline mutations in the BRCA1 and BRCA2 genes predispose carriers to breast and ovarian cancer, and there remains a need to identify the specific genomic mechanisms by which cancer evolves in these patients....

    Authors: Avantika Lal, Daniele Ramazzotti, Ziming Weng, Keli Liu, James M. Ford and Arend Sidow

    Citation: BMC Medical Genomics 2019 12:84

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  11. Content type: Research article

    The ability to generate recombinant drug target proteins is important for drug discovery research as it facilitates the investigation of drug-target-interactions in vitro. To accomplish this, the target’s exac...

    Authors: Julia F. Söllner, Germán Leparc, Matthias Zwick, Tanja Schönberger, Tobias Hildebrandt, Kay Nieselt and Eric Simon

    Citation: BMC Medical Genomics 2019 12:69

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  12. Content type: Research article

    The accurate screening of tumor genomic landscapes for somatic mutations using high-throughput sequencing involves a crucial step in precise clinical diagnosis and targeted therapy. However, the complex inhere...

    Authors: Irantzu Anzar, Angelina Sverchkova, Richard Stratford and Trevor Clancy

    Citation: BMC Medical Genomics 2019 12:63

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  14. Content type: Research article

    T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy. Aberrant expressed genes contribute to the development and progression of T-ALL. However, the regulation underlying their ...

    Authors: Mengxuan Xia, Qiong Zhang, Mei Luo, Pan Li, Yingxue Wang, Qian Lei and An-Yuan Guo

    Citation: BMC Medical Genomics 2019 12:8

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  15. Content type: Technical advance

    The integration of high-quality, genome-wide analyses offers a robust approach to elucidating genetic factors involved in complex human diseases. Even though several methods exist to integrate heterogeneous om...

    Authors: Haley R. Eidem, Jacob L. Steenwyk, Jennifer H. Wisecaver, John A. Capra, Patrick Abbot and Antonis Rokas

    Citation: BMC Medical Genomics 2018 11:107

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  16. Content type: Research article

    Recent large-scale cancer sequencing studies have discovered many novel cancer driver genes (CDGs) in human cancers. Some studies also suggest that CDG mutations contribute to cancer-associated epigenomic and ...

    Authors: Ahrim Youn, Kyung In Kim, Raul Rabadan, Benjamin Tycko, Yufeng Shen and Shuang Wang

    Citation: BMC Medical Genomics 2018 11:98

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  17. Content type: Technical advance

    Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe...

    Authors: Velina Kozareva, Clayton Stroff, Maxwell Silver, Jonathan F. Freidin and Nigel F. Delaney

    Citation: BMC Medical Genomics 2018 11:91

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  18. Content type: Research article

    Noninvasive prenatal screening (NIPS) of common aneuploidies using cell-free DNA from maternal plasma is part of routine prenatal care and is widely used in both high-risk and low-risk patient populations. Hig...

    Authors: Kristjan Eerik Kaseniit, Gregory J Hogan, Kevin M D’Auria, Carrie Haverty and Dale Muzzey

    Citation: BMC Medical Genomics 2018 11:90

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  20. 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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  21. 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

  22. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  30. 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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  31. 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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  32. 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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  33. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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