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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. Cancer neoantigens have attracted great interest in immunotherapy due to their capacity to elicit antitumoral responses. These molecules arise from somatic mutations in cancer cells, resulting in alterations o...

    Authors: Ana Carolina M. F. Coelho, André L. Fonseca, Danilo L. Martins, Paulo B. R. Lins, Lucas M. da Cunha and Sandro J. de Souza

    Citation: BMC Medical Genomics 2020 13:30

    Content type: Software

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  2. Single cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simult...

    Authors: Jerome Samir, Simone Rizzetto, Money Gupta and Fabio Luciani

    Citation: BMC Medical Genomics 2020 13:29

    Content type: Software

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  3. Next-Generation Sequencing (NGS) enables large-scale and cost-effective sequencing of genetic samples in order to detect genetic variants. After successful use in research-oriented projects, NGS is now enterin...

    Authors: Christian Wünsch, Henrik Banck, Carsten Müller-Tidow and Martin Dugas

    Citation: BMC Medical Genomics 2020 13:17

    Content type: Software

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  4. The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant gene...

    Authors: Dvir Dahary, Yaron Golan, Yaron Mazor, Ofer Zelig, Ruth Barshir, Michal Twik, Tsippi Iny Stein, Guy Rosner, Revital Kariv, Fei Chen, Qiang Zhang, Yiping Shen, Marilyn Safran, Doron Lancet and Simon Fishilevich

    Citation: BMC Medical Genomics 2019 12:200

    Content type: Software

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  5. When ordering genetic testing or triaging candidate variants in exome and genome sequencing studies, it is critical to generate and test a comprehensive list of candidate genes that succinctly describe the com...

    Authors: Aditya Ekawade, Matt Velinder, Alistair Ward, Tonya DiSera, Chase Miller, Yi Qiao and Gabor Marth

    Citation: BMC Medical Genomics 2019 12:190

    Content type: Software

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  6. Immune escape is one of the hallmarks of cancer and several new treatment approaches attempt to modulate and restore the immune system’s capability to target cancer cells. At the heart of the immune recognitio...

    Authors: Eric Blanc, Manuel Holtgrewe, Arunraj Dhamodaran, Clemens Messerschmidt, Gerald Willimsky, Thomas Blankenstein and Dieter Beule

    Citation: BMC Medical Genomics 2019 12:171

    Content type: Research Article

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  7. In 2012, Venet et al. proposed that at least in the case of breast cancer, most published signatures are not significantly more associated with outcome than randomly generated signatures. They suggested that n...

    Authors: Elnaz Saberi Ansar, Changiz Eslahchii, Mahsa Rahimi, Lobat Geranpayeh, Marzieh Ebrahimi, Rosa Aghdam and Gwenneg Kerdivel

    Citation: BMC Medical Genomics 2019 12:160

    Content type: Research Article

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  8. Dementia with Lewy bodies (DLB) is the second most common subtype of neurodegenerative dementia in humans following Alzheimer’s disease (AD). Present clinical diagnosis of DLB has high specificity and low sens...

    Authors: Daichi Shigemizu, Shintaro Akiyama, Yuya Asanomi, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda, Takashi Sakurai, Kouichi Ozaki, Takahiro Ochiya and Shumpei Niida

    Citation: BMC Medical Genomics 2019 12:150

    Content type: Research article

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  9. 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

    Content type: Technical advance

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  10. 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

    Content type: Research article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Technical advance

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Technical advance

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  16. 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

    Content type: Research article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Research article

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  20. Somatic mutations in cancer genomes occur through a variety of molecular mechanisms, which contribute to different mutational patterns. To summarize these, mutational signatures have been defined using a large...

    Authors: Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils and Carl Herrmann

    Citation: BMC Medical Genomics 2019 12:64

    Content type: Research article

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  21. 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

    Content type: Research article

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  22. 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

    Content type: Research article

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  23. 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

    Content type: Technical advance

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Technical advance

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Database

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

  29. One of the major goals of genomic medicine is the identification of causal genomic variants in a patient and their relation to the observed clinical phenotypes. Prioritizing the genomic variants by considering...

    Authors: Aditya Rao, Saipradeep VG, Thomas Joseph, Sujatha Kotte, Naveen Sivadasan and Rajgopal Srinivasan

    Citation: BMC Medical Genomics 2018 11:57

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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  42. 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

    Content type: Research article

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  43. 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

    Content type: Research article

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  44. 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

    Content type: Software

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