Articles

WISARD: workbench for integrated superfast association studies for related datasets

A Mendelian transmission produces phenotypic and genetic relatedness between family members, giving family-based analytical methods an important role in genetic epidemiological studies—from heritability estima...

Authors: Sungyoung Lee, Sungkyoung Choi, Dandi Qiao, Michael Cho, Edwin K. Silverman, Taesung Park and Sungho Won

An integrated clinical and genomic information system for cancer precision medicine

Increasing affordability of next-generation sequencing (NGS) has created an opportunity for realizing genomically-informed personalized cancer therapy as a path to precision oncology. However, the complex natu...

Authors: Yeongjun Jang, Taekjin Choi, Jongho Kim, Jisub Park, Jihae Seo, Sangok Kim, Yeajee Kwon, Seungjae Lee and Sanghyuk Lee

Mut2Vec: distributed representation of cancerous mutations

Embedding techniques for converting high-dimensional sparse data into low-dimensional distributed representations have been gaining popularity in various fields of research. In deep learning models, embedding ...

Authors: Sunkyu Kim, Heewon Lee, Keonwoo Kim and Jaewoo Kang

Fuzzy set-based generalized multifactor dimensionality reduction analysis of gene-gene interactions

Gene-gene interactions (GGIs) are a known cause of missing heritability. Multifactor dimensionality reduction (MDR) is one of most commonly used methods for GGI detection. The generalized multifactor dimension...

Authors: Hye-Young Jung, Sangseob Leem and Taesung Park

Identifying statistically significant combinatorial markers for survival analysis

Survival analysis methods have been widely applied in different areas of health and medicine, spanning over varying events of interest and target diseases. They can be utilized to provide relationships between...

Authors: Raissa T. Relator, Aika Terada and Jun Sese

Exact association test for small size sequencing data

Recent statistical methods for next generation sequencing (NGS) data have been successfully applied to identifying rare genetic variants associated with certain diseases. However, most commonly used methods (e...

Authors: Joowon Lee, Seungyeoun Lee, Jin-Young Jang and Taesung Park

Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes

It is well recognized that accumulation of somatic mutations in cancer genomes plays a role in carcinogenesis; however, the temporal sequence and evolutionary relationship of somatic mutations remain largely u...

Authors: Je-Keun Rhee and Tae-Min Kim

EAGLE: Explicit Alternative Genome Likelihood Evaluator

Reliable detection of genome variations, especially insertions and deletions (indels), from single sample DNA sequencing data remains challenging, partially due to the inherent uncertainty involved in aligning...

Authors: Tony Kuo, Martin C. Frith, Jun Sese and Paul Horton

LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data

Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to ...

Authors: Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M. Przytycka, Chee Keong Kwoh and Jie Zheng

IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics

With the advancement of next generation sequencing technology, researchers are now able to identify important variants and structural changes in DNA and RNA in cancer patient samples. With this information, we...

Authors: Jennifer D. Hintzsche, Minjae Yoo, Jihye Kim, Carol M. Amato, William A. Robinson and Aik Choon Tan

CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data

The Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types. Transforming the large size and high complexity of TC...

Authors: Seonggyun Han, Dongwook Kim, Youngjun Kim, Kanghoon Choi, Jason E. Miller, Dokyoon Kim and Younghee Lee

A meta-analysis of public microarray data identifies biological regulatory networks in Parkinson’s disease

Parkinson’s disease (PD) is a long-term degenerative disease that is caused by environmental and genetic factors. The networks of genes and their regulators that control the progression and development of PD r...

Authors: Lining Su, Chunjie Wang, Chenqing Zheng, Huiping Wei and Xiaoqing Song

Genetic analysis of Wnt/PCP genes in neural tube defects

Mouse homozygous mutants in Wnt/planar cell polarity (PCP) pathway genes have been shown to cause neural tube defects (NTDs) through the disruption of normal morphogenetic processes critical to neural tube clo...

Authors: Zhongzhong Chen, Yunping Lei, Xuanye Cao, Yufang Zheng, Fang Wang, Yihua Bao, Rui Peng, Richard H. Finnell, Ting Zhang and Hongyan Wang

Patient with multiple acyl-CoA dehydrogenase deficiency disease and ETFDH mutations benefits from riboflavin therapy: a case report

Lipid storage myopathy (LSM) is a diverse group of lipid metabolic disorders with great variations in the clinical phenotype and age of onset. Classical multiple acyl-CoA dehydrogenase deficiency (MADD) is kno...

Authors: Liuh Ling Goh, Yingshan Lee, Ee Shien Tan, James Soon Chuan Lim, Chia Wei Lim and Rinkoo Dalan

HLA and proteasome expression body map

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

Performance of in silico prediction tools for the classification of rare BRCA1/2 missense variants in clinical diagnostics

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

Integrated analysis of DNA-methylation and gene expression using high-dimensional penalized regression: a cohort study on bone mineral density in postmenopausal women

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

Whole exome sequencing in three families segregating a pediatric case of sarcoidosis

Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To fi...

Authors: Alain Calender, Pierre Antoine Rollat Farnier, Adrien Buisson, Stéphane Pinson, Abderrazzaq Bentaher, Serge Lebecque, Harriet Corvol, Rola Abou Taam, Véronique Houdouin, Claire Bardel, Pascal Roy, Gilles Devouassoux, Vincent Cottin, Pascal Seve, Jean-François Bernaudin, Clarice X. Lim…

A combined linkage, microarray and exome analysis suggests MAP3K11 as a candidate gene for left ventricular hypertrophy

Electrocardiographic measures of left ventricular hypertrophy (LVH) are used as predictors of cardiovascular risk. We combined linkage and association analyses to discover novel rare genetic variants involved ...

Authors: Claudia Tamar Silva, Irina V. Zorkoltseva, Maartje N. Niemeijer, Marten E. van den Berg, Najaf Amin, Ayşe Demirkan, Elisa van Leeuwen, Adriana I. Iglesias, Laura B. Piñeros-Hernández, Carlos M. Restrepo, Jan A. Kors, Anatoly V. Kirichenko, Rob Willemsen, Ben A. Oostra, Bruno H. Stricker, André G. Uitterlinden…

Impaired type I interferon regulation in the blood transcriptome of recurrent asthma exacerbations

Asthma exacerbations are an important cause of morbidity in asthma. Respiratory infections are often involved in asthma exacerbations in both children and adults. Some individuals with asthma have increased su...

Authors: Jose L. Gomez, Maria P. Diaz, Gustavo Nino and Clemente J. Britto

Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection

Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that vi...

Authors: Na Zhang, Yun-Juan Bao, Amy Hin-Yan Tong, Scott Zuyderduyn, Gary D. Bader, J. S. Malik Peiris, Si Lok and Suki Man-Yan Lee

Application of Neural Networks for classification of Patau, Edwards, Down, Turner and Klinefelter Syndrome based on first trimester maternal serum screening data, ultrasonographic findings and patient demographics

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

Adopting clinical genomics: a systematic review of genomic literacy among physicians in cancer care

This article investigates the genomic knowledge of oncology care physicians in the adoption of clinical genomics. We apply Rogers’ knowledge framework from his diffusion of innovation theory to identify three ...

Authors: Vu T. Dung Ha, Julie Frizzo-Barker and Peter Chow-White

Exome analysis of carotid body tumor

Carotid body tumor (CBT) is a form of head and neck paragangliomas (HNPGLs) arising at the bifurcation of carotid arteries. Paragangliomas are commonly associated with germline and somatic mutations involving ...

Authors: Anastasiya V. Snezhkina, Elena N. Lukyanova, Dmitry V. Kalinin, Anatoly V. Pokrovsky, Alexey A. Dmitriev, Nadezhda V. Koroban, Elena A. Pudova, Maria S. Fedorova, Nadezhda N. Volchenko, Oleg A. Stepanov, Ekaterina A. Zhevelyuk, Sergey L. Kharitonov, Anastasiya V. Lipatova, Ivan S. Abramov, Alexander V. Golovyuk, Yegor E. Yegorov…

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females

Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We...

Authors: Yu-Feng Huang, Yen-Ju Chen, Tan-Chi Fan, Nai-Chuan Chang, Yi-Jie Chen, Mohit K. Midha, Tzu-Han Chen, Hsiao-Hsiang Yang, Yu-Tai Wang, Alice L. Yu and Kuo-Ping Chiu

Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks

Hypertension and bronchial asthma are a major issue for people’s health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235–330 million peopl...

Authors: Olga V. Saik, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena Yu Bragina, Maxim B. Freidin, Irina A. Goncharova, Victor E. Dosenko, Olga I. Zolotareva, Ralf Hofestaedt, Inna N. Lavrik, Evgeny I. Rogaev and Vladimir A. Ivanisenko

Circadian succession of molecular processes in living tissues

Oscillations of different origin, period and amplitude play an important role in the regulation of cellular processes. Most widely studied is the circadian or approximately daily variation in gene expression a...

Authors: Abeer Fadda, Mohammed El Anbari and Andrey Ptitsyn

Targeted sequencing reveals complex, phenotype-correlated genotypes in cystic fibrosis

Cystic fibrosis (CF) is one of the most common life-threatening genetic disorders. Around 2000 variants in the CFTR gene have been identified, with some proportion known to be pathogenic and 300 disease-causin...

Authors: Maxim Ivanov, Alina Matsvay, Olga Glazova, Stanislav Krasovskiy, Mariya Usacheva, Elena Amelina, Aleksandr Chernyak, Mikhail Ivanov, Sergey Musienko, Timofey Prodanov, Sergey Kovalenko, Ancha Baranova and Kamil Khafizov

Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3

Small molecule Nutlin-3 reactivates p53 in cancer cells by interacting with the complex between p53 and its repressor Mdm-2 and causing an increase in cancer cell apoptosis. Therefore, Nutlin-3 has potent anti...

Authors: Ulyana Boyarskikh, Sergey Pintus, Nikita Mandrik, Daria Stelmashenko, Ilya Kiselev, Ivan Evshin, Ruslan Sharipov, Philip Stegmaier, Fedor Kolpakov, Maxim Filipenko and Alexander Kel

Medical genomics at Belyaev Conference – 2017

Authors: Yuriy L. Orlov, Julio R. Fernandez-Masso, Ming Chen and Ancha V. Baranova

Cumulative prognostic power of laminin genes in colorectal cancer

Laminins are a major family of extracellular matrix proteins and the main component of basement membranes. Laminins are involved in many if not all stages of cancer progression, and expression of laminin genes...

Authors: Vladimir V. Galatenko, Diana V. Maltseva, Alexey V. Galatenko, Sergey Rodin and Alexander G. Tonevitsky

Primary microcephaly case from the Karachay-Cherkess Republic poses an additional support for microcephaly and Seckel syndrome spectrum disorders

Primary microcephaly represents an example of clinically and genetically heterogeneous condition. Here we describe a case of primary microcephaly from the Karachay-Cherkess Republic, which was initially diagno...

Authors: Andrey V. Marakhonov, Fedor A. Konovalov, Amin Kh. Makaov, Tatyana A. Vasilyeva, Vitaly V. Kadyshev, Varvara A. Galkina, Elena L. Dadali, Sergey I. Kutsev and Rena A. Zinchenko

Unearthing new genomic markers of drug response by improved measurement of discriminative power

Oncology drugs are only effective in a small proportion of cancer patients. Our current ability to identify these responsive patients before treatment is still poor in most cases. Thus, there is a pressing nee...

Authors: Cuong C. Dang, Antonio Peón and Pedro J. Ballester

Methylation of the genes ROD1, NLRC5, and HKR1 is associated with aging in Hainan centenarians

Human aging is a hot topic in biology, and it has been associated with DNA methylation changes at specific genomic sites. We aimed to study the changes of DNA methylation at a single-CpG-site resolution using ...

Authors: Qian Zeng, Xiaoping Chen, Chaoxue Ning, Qiao Zhu, Yao Yao, Yali Zhao and Fuxin Luan

Efficient strategy for the molecular diagnosis of intractable early-onset epilepsy using targeted gene sequencing

We intended to evaluate diagnostic utility of a targeted gene sequencing by using next generation sequencing (NGS) panel in patients with intractable early-onset epilepsy (EOE) and find the efficient analytica...

Authors: John Hoon Rim, Se Hee Kim, In Sik Hwang, Soon Sung Kwon, Jieun Kim, Hyun Woo Kim, Min Jung Cho, Ara Ko, Song Ee Youn, Jihun Kim, Young Mock Lee, Hee Jung Chung, Joon Soo Lee, Heung Dong Kim, Jong Rak Choi, Seung-Tae Lee…

Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years

To address the need for more effective genomics training, beginning in 2012 the Icahn School of Medicine at Mount Sinai has offered a unique laboratory-style graduate genomics course, “Practical Analysis of Yo...

Authors: Michael D. Linderman, Saskia C. Sanderson, Ali Bashir, George A. Diaz, Andrew Kasarskis, Randi Zinberg, Milind Mahajan, Sabrina A. Suckiel, Micol Zweig and Eric E. Schadt

Deleterious genetic variants in ciliopathy genes increase risk of ritodrine-induced cardiac and pulmonary side effects

Ritodrine is a commonly used tocolytic to prevent preterm labour. However, it can cause unexpected serious adverse reactions, such as pulmonary oedema, pulmonary congestion, and tachycardia. It is unknown whet...

Authors: Heewon Seo, Eun Jin Kwon, Young-Ah You, Yoomi Park, Byung Joo Min, Kyunghun Yoo, Han-Sung Hwang, Ju Han Kim and Young Ju Kim

Are minor alleles more likely to be risk alleles?

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

Insights into the genetics of blood pressure in black South African individuals: the Birth to Twenty cohort

Cardiovascular diseases (CVDs) are the leading cause of non-communicable disease deaths globally, with hypertension being a major risk factor contributing to CVDs. Blood pressure is a heritable trait, with rel...

Authors: Liesl M. Hendry, Venesa Sahibdeen, Ananyo Choudhury, Shane A. Norris, Michèle Ramsay and Zané Lombard

Peripheral blood gene expression signatures which reflect smoking and aspirin exposure are associated with cardiovascular events

Cardiovascular disease and its sequelae are major causes of global mortality, and better methods are needed to identify patients at risk for future cardiovascular events. Gene expression analysis can inform on...

Authors: James A. Wingrove, Karen Fitch, Brian Rhees, Steven Rosenberg and Deepak Voora

Platform-independent gene expression signature differentiates sessile serrated adenomas/polyps and hyperplastic polyps of the colon

Sessile serrated adenomas/polyps are distinguished from hyperplastic colonic polyps subjectively by their endoscopic appearance and histological morphology. However, hyperplastic and sessile serrated polyps ca...

Authors: Yasir Rahmatallah, Magomed Khaidakov, Keith K. Lai, Hannah E. Goyne, Laura W. Lamps, Curt H. Hagedorn and Galina Glazko

iOPTICS-GSO for identifying protein complexes from dynamic PPI networks

Identifying protein complexes plays an important role for understanding cellular organization and functional mechanisms. As plenty of evidences have indicated that dense sub-networks in dynamic protein-protein...

Authors: Xiujuan Lei, Huan Li, Aidong Zhang and Fang-Xiang Wu

Predicting drug-disease interactions by semi-supervised graph cut algorithm and three-layer data integration

Prediction of drug-disease interactions is promising for either drug repositioning or disease treatment fields. The discovery of novel drug-disease interactions, on one hand can help to find novel indictions f...

Authors: Guangsheng Wu, Juan Liu and Caihua Wang

Stable solution to l _2,1-based robust inductive matrix completion and its application in linking long noncoding RNAs to human diseases

A large number of long intergenic non-coding RNAs (lincRNAs) are linked to a broad spectrum of human diseases. The disease association with many other lincRNAs still remain as puzzle. Validation of such links ...

Authors: Ashis Kumer Biswas, Dongchul Kim, Mingon Kang, Chris Ding and Jean X. Gao

Probability-based collaborative filtering model for predicting gene–disease associations

Accurately predicting pathogenic human genes has been challenging in recent research. Considering extensive gene–disease data verified by biological experiments, we can apply computational methods to perform a...

Authors: Xiangxiang Zeng, Ningxiang Ding, Alfonso Rodríguez-Patón and Quan Zou

Disease named entity recognition from biomedical literature using a novel convolutional neural network

Automatic disease named entity recognition (DNER) is of utmost importance for development of more sophisticated BioNLP tools. However, most conventional CRF based DNER systems rely on well-designed features wh...

Authors: Zhehuan Zhao, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin and Jian Wang

Reverse-engineering of gene networks for regulating early blood development from single-cell measurements

Recent advances in omics technologies have raised great opportunities to study large-scale regulatory networks inside the cell. In addition, single-cell experiments have measured the gene and protein activitie...

Authors: Jiangyong Wei, Xiaohua Hu, Xiufen Zou and Tianhai Tian

Measuring disease similarity and predicting disease-related ncRNAs by a novel method

Similar diseases are always caused by similar molecular origins, such as diasease-related protein-coding genes (PCGs). And the molecular associations reflect their similarity. Therefore, current methods for ca...

Authors: Yang Hu, Meng Zhou, Hongbo Shi, Hong Ju, Qinghua Jiang and Liang Cheng

Classifying cancer genome aberrations by their mutually exclusive effects on transcription

Malignant tumors are typically caused by a conglomeration of genomic aberrations—including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemothe...

Authors: Jonathan B. Dayton and Stephen R. Piccolo

Predicting binary, discrete and continued lncRNA-disease associations via a unified framework based on graph regression

In human genomes, long non-coding RNAs (lncRNAs) have attracted more and more attention because their dysfunctions are involved in many diseases. However, the associations between lncRNAs and diseases (LDA) st...

Authors: Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Yu-Xi Long and Siu-Ming Yiu