Articles

TNFPred: identifying tumor necrosis factors using hybrid features based on word embeddings

Cytokines are a class of small proteins that act as chemical messengers and play a significant role in essential cellular processes including immunity regulation, hematopoiesis, and inflammation. As one import...

Authors: Trinh-Trung-Duong Nguyen, Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Dinh-Van Phan and Yu-Yen Ou

Pan-cancer analysis of differential DNA methylation patterns

DNA methylation is a key epigenetic regulator contributing to cancer development. To understand the role of DNA methylation in tumorigenesis, it is important to investigate and compare differential methylation...

Authors: Mai Shi, Stephen Kwok-Wing Tsui, Hao Wu and Yingying Wei

DBCSMOTE: a clustering-based oversampling technique for data-imbalanced warfarin dose prediction

Vitamin K antagonist (warfarin) is the most classical and widely used oral anticoagulant with assuring anticoagulant effect, wide clinical indications and low price. Warfarin dosage requirements of different p...

Authors: Yanyun Tao, Yuzhen Zhang and Bin Jiang

Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts

Bronchoscopy for suspected lung cancer has low diagnostic sensitivity, rendering many inconclusive results. The Bronchial Genomic Classifier (BGC) was developed to help with patient management by identifying t...

Authors: Yoonha Choi, Jianghan Qu, Shuyang Wu, Yangyang Hao, Jiarui Zhang, Jianchang Ning, Xinwu Yang, Lori Lofaro, Daniel G. Pankratz, Joshua Babiarz, P. Sean Walsh, Ehab Billatos, Marc E. Lenburg, Giulia C. Kennedy, Jon McAuliffe and Jing Huang

Stage-specific protein-domain mutational profile of invasive ductal breast cancer

Understanding the mechanisms underlying the malignant progression of cancer cells is crucial for early diagnosis and therapeutic treatment for cancer. Mutational heterogeneity of breast cancer suggests that ab...

Authors: Ting Yu, Kwok Pui Choi, Ee Sin Chen and Louxin Zhang

Genomic amplification of chromosome 20q13.33 is the early biomarker for the development of sporadic colorectal carcinoma

Colorectal carcinoma (CRC) is the third most common cancer in the world and also the third leading cause of cancer-related mortality in Taiwan. CRC tumorigenesis is a multistep process, starting from mutations...

Authors: Vo-Minh-Hoang Bui, Clément Mettling, Jonathan Jou and H. Sunny Sun

Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening

Advancements in transcriptomic profiling have led to the emergence of new challenges regarding data integration and interpretability. Variability between measurement platforms makes it difficult to compare bet...

Authors: Laura Moody, Hong Chen and Yuan-Xiang Pan

Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data

Treating cancer depends in part on identifying the mutations driving each patient’s disease. Many clinical laboratories are adopting high-throughput sequencing for assaying patients’ tumours, applying targeted...

Authors: Ali Karimnezhad, Gareth A. Palidwor, Kednapa Thavorn, David J. Stewart, Pearl A. Campbell, Bryan Lo and Theodore J. Perkins

Exploring the association of long noncoding RNA expression profiles with intracranial aneurysms, based on sequencing and related bioinformatics analysis

The present study aims to investigate the complete long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in Intracranial aneurysm (IA) patients and controls by RNA sequencing, which reveals...

Authors: Yi Sun, Yeying Wen, Qishuang Ruan, Le Yang, Shuna Huang, Xingyan Xu, Yingying Cai, Huangyuan Li and Siying Wu

Fraternal twins with Phelan-McDermid syndrome not involving the SHANK3 gene: case report and literature review

Phelan-McDermid syndrome (PMS, OMIM#606232), or 22q13 deletion syndrome, is a rare genetic disorder caused by deletion of the distal long arm of chromosome 22 with a variety of clinical features that display c...

Authors: Shan Li, Ke-wang Xi, Ting Liu, Ying Zhang, Meng Zhang, Li-dong Zeng and Juan Li

TOP2A and CENPF are synergistic master regulators activated in cervical cancer

Identification of master regulators (MRs) using transcriptome data in cervical cancer (CC) could help us to develop biomarkers and find novel drug targets to fight this disease.

Authors: Beiwei Yu, Long Chen, Weina Zhang, Yue Li, Yibiao Zhang, Yuan Gao, Xianlin Teng, Libo Zou, Qian Wang, Hongtao Jia, Xiangtao Liu, Hui Zheng, Ping Hou, Hongyan Yu, Ying Sun, Zhiqin Zhang…

A novel phenotype of 13q12.3 microdeletion characterized by epilepsy in an Asian child: a case report

The microdeletion of chromosome 13 has been rarely reported. Here, we report a 14-year old Asian female with a de novo microdeletion on 13q12.3.

Authors: Mina Wang, Bin Li, Zehuan Liao, Yu Jia and Yuanbo Fu

Highly multiplexed quantifications of 299 somatic mutations in colorectal cancer patients by automated MALDI-TOF mass spectrometry

Detection of somatic mutations in tumor tissues helps to understand tumor biology and guide treatment selection. Methods such as quantitative PCR can analyze a few mutations with high efficiency, while next ge...

Authors: Chang Xu, Danli Peng, Jialu Li, Meihua Chen, Yujie Hu, Mingliang Hou, Qingjuan Shang, Qi Liang, Jie Li, Wenfeng Li, Xiaoli Wu, Changbao Liu, Wanle Hu, Mao Cai, Huxiang Zhang, Guorong Chen…

Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy

Angiogenesis is an important parameter in the development of diabetic retinopathy (DR), and it is indicative of an early stage evolving into a late phase. Therefore, examining the role of angiogenic factors in...

Authors: Chufeng Gu, Thashi Lhamo, Chen Zou, Chuandi Zhou, Tong Su, Deji Draga, Dawei Luo, Zhi Zheng, Lili Yin and Qinghua Qiu

Mosaic chromosome 18 anomaly delineated in a child with dysmorphism using a three-pronged cytogenetic techniques approach: a case report

A plethora of cases are reported in the literature with iso- and ring-chromosome 18. However, co-occurrence of these two abnormalities in an individual along with a third cell line and absence of numerical ano...

Authors: Harsh Sheth, Sunil Trivedi, Thomas Liehr, Ketan Patel, Deepika Jain, Jayesh Sheth and Frenny Sheth

Identification of key genes and functions of circulating tumor cells in multiple cancers through bioinformatic analysis

Circulating tumor cells (CTCs) play a key role in cancer progression, especially metastasis, due to the rarity and heterogeneity of CTCs, fewer researches have been conducted on them at the molecular level. Ho...

Authors: Yibing Guan, Fangshi Xu, Yiyuan Wang, Juanhua Tian, Ziyan Wan, Zhenlong Wang and Tie Chong

The similarity of inherited diseases (II): clinical and biological similarity between the phenotypic series

Despite being caused by mutations in different genes, diseases in the same phenotypic series are clinically similar, as reported in Part I of this study. Here, in Part II, we hypothesized that the phenotypic s...

Authors: Alessio Gamba, Mario Salmona, Laura Cantù and Gianfranco Bazzoni

Whole-exome sequencing reveals potential mechanisms of drug resistance to FGFR3-TACC3 targeted therapy and subsequent drug selection: towards a personalized medicine

Drug resistance is a major obstacle to effective cancer therapy. In order to detect the change in tumor genomic states under drug selection pressure, we use next-generation sequencing technology to investigate...

Authors: Zhou Tong, Cong Yan, Yu-An Dong, Ming Yao, Hangyu Zhang, Lulu Liu, Yi Zheng, Peng Zhao, Yimin Wang, Weijia Fang, Feifei Zhang and Weiqin Jiang

Transcription factor expression as a predictor of colon cancer prognosis: a machine learning practice

Colon cancer is one of the leading causes of cancer deaths in the USA and around the world. Molecular level characters, such as gene expression levels and mutations, may provide profound information for precis...

Authors: Jiannan Liu, Chuanpeng Dong, Guanglong Jiang, Xiaoyu Lu, Yunlong Liu and Huanmei Wu

Expression correlation attenuates within and between key signaling pathways in chronic kidney disease

Compared to the conventional differential expression approach, differential coexpression analysis represents a different yet complementary perspective into diseased transcriptomes. In particular, global loss o...

Authors: Hui Yu, Danqian Chen, Olufunmilola Oyebamiji, Ying-Yong Zhao and Yan Guo

High dimensional model representation of log likelihood ratio: binary classification with SNP data

Developing binary classification rules based on SNP observations has been a major challenge for many modern bioinformatics applications, e.g., predicting risk of future disease events in complex conditions suc...

Authors: Ali Foroughi pour, Maciej Pietrzak, Lara E. Sucheston-Campbell, Ezgi Karaesmen, Lori A. Dalton and Grzegorz A. Rempała

Integrative network analysis identifies potential targets and drugs for ovarian cancer

Though accounts for 2.5% of all cancers in female, the death rate of ovarian cancer is high, which is the fifth leading cause of cancer death (5% of all cancer death) in female. The 5-year survival rate of ova...

Authors: Tianyu Zhang, Liwei Zhang and Fuhai Li

LncRNA and transcriptomic analysis of fetal membrane reveal potential targets involved in oligohydramnios

The multiple causes of oligohydramnios make it challenging to study. Long noncoding RNAs (lncRNAs) are sets of RNAs that have been proven to function in multiple biological processes. The purpose of this study...

Authors: Yu-hua Ou, Yu-kun Liu, Li-qiong Zhu, Man-qi Chen, Xiao-chun Yi, Hui Chen and Jian-ping Zhang

Transcriptome analysis of peripheral whole blood identifies crucial lncRNAs implicated in childhood asthma

Asthma is a chronic disorder of both adults and children affecting more than 300 million people heath worldwide. Diagnose and treatment for asthma, particularly in childhood asthma have always remained a great...

Authors: Peiyan Zheng, Chen Huang, Dongliang Leng, Baoqing Sun and Xiaohua Douglas Zhang

A sporadic case of congenital aniridia caused by pericentric inversion inv(11)(p13q14) associated with a 977 kb deletion in the 11p13 region

Because of the significant occurrence of “WAGR-region” deletions among de novo mutations detected in congenital aniridia, DNA diagnosis is critical for all sporadic cases of aniridia due to its help in making ...

Authors: Tatyana A. Vasilyeva, Andrey V. Marakhonov, Marina E. Minzhenkova, Zhanna G. Markova, Nika V. Petrova, Natella V. Sukhanova, Philipp A. Koshkin, Denis V. Pyankov, Ilya V. Kanivets, Sergey A. Korostelev, Irina A. Krynskaya, Nadezhda V. Shilova, Sergey I. Kutsev, Vitaly V. Kadyshev and Rena A. Zinchenko

miRNAs expression signature potentially associated with lymphatic dissemination in locally advanced prostate cancer

Prostate cancer is one of the most common and socially significant cancers among men. The aim of our study was to reveal changes in miRNA expression profiles associated with lymphatic dissemination in prostate...

Authors: Elena A. Pudova, George S. Krasnov, Kirill M. Nyushko, Anastasiya A. Kobelyatskaya, Maria V. Savvateeva, Andrey A. Poloznikov, Daniyar R. Dolotkazin, Kseniya M. Klimina, Zulfiya G. Guvatova, Sergey A. Simanovsky, Nataliya S. Gladysh, Artemy T. Tokarev, Nataliya V. Melnikova, Alexey A. Dmitriev, Boris Y. Alekseev, Andrey D. Kaprin…

Medical genomics at the Systems Biology and Bioinformatics (SBB-2019) school

Authors: Yuriy L. Orlov, Elena N. Voropaeva, Ming Chen and Ancha V. Baranova

Multiple paragangliomas: a case report

Carotid and vagal paragangliomas (CPGLs and VPGLs) are rare neoplasms that arise from the paraganglia located at the bifurcation of carotid arteries and vagal trunk, respectively. Both tumors can occur jointly...

Authors: Vladislav S. Pavlov, Dmitry V. Kalinin, Elena N. Lukyanova, Alexander L. Golovyuk, Maria S. Fedorova, Elena A. Pudova, Maria V. Savvateeva, Anastasiya V. Lipatova, Zulfiya G. Guvatova, Andrey D. Kaprin, Marina V. Kiseleva, Tatiana B. Demidova, Sergey A. Simanovsky, Nataliya V. Melnikova, Alexey A. Dmitriev, George S. Krasnov…

Mutation profiling in eight cases of vagal paragangliomas

Vagal paragangliomas (VPGLs) belong to a group of rare head and neck neuroendocrine tumors. VPGLs arise from the vagus nerve and are less common than carotid paragangliomas. Both diagnostics and therapy of the...

Authors: Anna V. Kudryavtseva, Dmitry V. Kalinin, Vladislav S. Pavlov, Maria V. Savvateeva, Maria S. Fedorova, Elena A. Pudova, Anastasiya A. Kobelyatskaya, Alexander L. Golovyuk, Zulfiya G. Guvatova, George S. Razmakhaev, Tatiana B. Demidova, Sergey A. Simanovsky, Elena N. Slavnova, Andrey А. Poloznikov, Andrey P. Polyakov, Nataliya V. Melnikova…

Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments

Machine learning (ML) methods still have limited applicability in personalized oncology due to low numbers of available clinically annotated molecular profiles. This doesn’t allow sufficient training of ML cla...

Authors: Nicolas Borisov, Maxim Sorokin, Victor Tkachev, Andrew Garazha and Anton Buzdin

Genome scale analysis of pathogenic variants targetable for single base editing

Single nucleotide variants account for approximately 90% of all known pathogenic variants responsible for human diseases. Recently discovered CRISPR/Cas9 base editors can correct individual nucleotides without...

Authors: Alexander V. Lavrov, Georgi G. Varenikov and Mikhail Yu Skoblov

Epigenetic loci for blood pressure are associated with hypertensive target organ damage in older African Americans from the genetic epidemiology network of Arteriopathy (GENOA) study

Hypertension is a major modifiable risk factor for arteriosclerosis that can lead to target organ damage (TOD) of heart, kidneys, and peripheral arteries. A recent epigenome-wide association study for blood pr...

Authors: Minjung Kho, Wei Zhao, Scott M. Ratliff, Farah Ammous, Thomas H. Mosley, Lulu Shang, Sharon L. R. Kardia, Xiang Zhou and Jennifer A. Smith

Exosomal microRNAs are novel circulating biomarkers in cigarette, waterpipe smokers, E-cigarette users and dual smokers

Electronic cigarettes (e-cigs) vaping, cigarette smoke, and waterpipe tobacco smoking are associated with various cardiopulmonary diseases. microRNAs are present in higher concentration in exosomes that play a...

Authors: Kameshwar P. Singh, Krishna P. Maremanda, Dongmei Li and Irfan Rahman

A 15q25.2 microdeletion phenotype for premature ovarian failure in a Chinese girl: a case report and review of literature

Proximal microdeletions on chromosome 15q25.2 are very rare, and are associated with neurodevelopmental delay, inguinal hernia, chest deformities, and anemia. The minimum length missed so far is 1.4 Mb. Howeve...

Authors: Zhen Chen, Hong Chen, Ke Yuan and Chunlin Wang

Comparative transcriptome analysis of human skeletal muscle in response to cold acclimation and exercise training in human volunteers

Cold acclimation and exercise training were previously shown to increase peripheral insulin sensitivity in human volunteers with type 2 diabetes. Although cold is a potent activator of brown adipose tissue, th...

Authors: Emmani B. M. Nascimento, Roland W. J. Hangelbroek, Guido J. E. J. Hooiveld, Joris Hoeks, Wouter D. Van Marken Lichtenbelt, Matthijs H. C. Hesselink, Patrick Schrauwen and Sander Kersten

Integrative genomics analysis of various omics data and networks identify risk genes and variants vulnerable to childhood-onset asthma

Childhood-onset asthma is highly affected by genetic components. In recent years, many genome-wide association studies (GWAS) have reported a large group of genetic variants and susceptible genes associated wi...

Authors: Xiuqing Ma, Peilan Wang, Guobing Xu, Fang Yu and Yunlong Ma

Machine learning based refined differential gene expression analysis of pediatric sepsis

Differential expression (DE) analysis of transcriptomic data enables genome-wide analysis of gene expression changes associated with biological conditions of interest. Such analysis often provides a wide list ...

Authors: Mostafa Abbas and Yasser EL-Manzalawy

Constructing cancer patient-specific and group-specific gene networks with multi-omics data

Cancer is a complex and heterogeneous disease with many possible genetic and environmental causes. The same treatment for patients of the same cancer type often results in different outcomes in terms of effica...

Authors: Wook Lee, De-Shuang Huang and Kyungsook Han

A machine learning framework for genotyping the structural variations with copy number variant

Genotyping of structural variation is an important computational problem in next generation sequence data analysis. However, in cancer genomes, the copy number variant(CNV) often coexists with other types of s...

Authors: Tian Zheng, Xiaoyan Zhu, Xuanping Zhang, Zhongmeng Zhao, Xin Yi, Jiayin Wang and Hongle Li

A novel neoantigen discovery approach based on chromatin high order conformation

High-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify ...

Authors: Yi Shi, Mingxuan Zhang, Luming Meng, Xianbin Su, Xueying Shang, Zehua Guo, Qingjiao Li, Mengna Lin, Xin Zou, Qing Luo, Yaoliang Yu, Yanting Wu, Lintai Da, Tom Weidong Cai, Guang He and Ze-Guang Han

Association of blood pressure with cognitive function at midlife: a Mendelian randomization study

Whether high blood pressure has a causal effect on cognitive function as early as middle age is unclear. We investigated whether high blood pressure (BP) causally impairs cognitive function at midlife using Me...

Authors: Daokun Sun, Emy A. Thomas, Lenore J. Launer, Stephen Sidney, Kristine Yaffe and Myriam Fornage

Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

Advanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture...

Authors: Thomas W. Winkler, Felix Grassmann, Caroline Brandl, Christina Kiel, Felix Günther, Tobias Strunz, Lorraine Weidner, Martina E. Zimmermann, Christina A. Korb, Alicia Poplawski, Alexander K. Schuster, Martina Müller-Nurasyid, Annette Peters, Franziska G. Rauscher, Tobias Elze, Katrin Horn…

Unraveling the molecular heterogeneity in type 2 diabetes: a potential subtype discovery followed by metabolic modeling

Type 2 diabetes mellitus (T2DM) is a complex multifactorial disease with a high prevalence worldwide. Insulin resistance and impaired insulin secretion are the two major abnormalities in the pathogenesis of T2...

Authors: Maryam Khoshnejat, Kaveh Kavousi, Ali Mohammad Banaei-Moghaddam and Ali Akbar Moosavi-Movahedi

HDNA methylation data-based molecular subtype classification related to the prognosis of patients with hepatocellular carcinoma

DNA methylation is a common chemical modification of DNA in the carcinogenesis of hepatocellular carcinoma (HCC).

Authors: Hui He, Di Chen, Shimeng Cui, Gang Wu, Hailong Piao, Xun Wang, Peng Ye and Shi Jin

Haplotyping by linked-read sequencing (HLRS) of the genetic disease carriers for preimplantation genetic testing without a proband or relatives

In order to mitigate the risk of allele dropout (ADO) and ensure the accuracy of preimplantation genetic testing for monogenic disease (PGT-M), it is necessary to construct parental haplotypes. Typically, hapl...

Authors: Qing Li, Yan Mao, Shaoying Li, Hongzi Du, Wenzhi He, Jianchun He, Lingyin Kong, Jun Zhang, Bo Liang and Jianqiao Liu

Breast and prostate cancers harbor common somatic copy number alterations that consistently differ by race and are associated with survival

Pan-cancer studies of somatic copy number alterations (SCNAs) have demonstrated common SCNA patterns across cancer types, but despite demonstrable differences in aggressiveness of some cancers by race, pan-can...

Authors: Yalei Chen, Sudha M. Sadasivan, Ruicong She, Indrani Datta, Kanika Taneja, Dhananjay Chitale, Nilesh Gupta, Melissa B. Davis, Lisa A. Newman, Craig G. Rogers, Pamela L. Paris, Jia Li, Benjamin A. Rybicki and Albert M. Levin

Comparative transcriptome analysis of Parkinson’s disease and Hutchinson-Gilford progeria syndrome reveals shared susceptible cellular network processes

Parkinson’s Disease (PD) and Hutchinson-Gilford Progeria Syndrome (HGPS) are two heterogeneous disorders, which both display molecular and clinical alterations associated with the aging process. However, simil...

Authors: Diana M. Hendrickx and Enrico Glaab

Clinical, genomics and networking analyses of a high-altitude native American Ecuadorian patient with congenital insensitivity to pain with anhidrosis: a case report

Congenital insensitivity to pain with anhidrosis (CIPA) is an extremely rare autosomal recessive disorder characterized by insensitivity to pain, inability to sweat and intellectual disability. CIPA is caused ...

Authors: Andrés López-Cortés, Ana Karina Zambrano, Patricia Guevara-Ramírez, Byron Albuja Echeverría, Santiago Guerrero, Eliana Cabascango, Andy Pérez-Villa, Isaac Armendáriz-Castillo, Jennyfer M. García-Cárdenas, Verónica Yumiceba, Gabriela Pérez-M, Paola E. Leone and César Paz-y-Miño

Bioinformatic analysis revealing mitotic spindle assembly regulated NDC80 and MAD2L1 as prognostic biomarkers in non-small cell lung cancer development

Lung cancer has been the leading cause of tumor related death, and 80% ~ 85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the ...

Authors: Rong Wei, Ziyue Wang, Yaping Zhang, Bin Wang, Ningning Shen, Li E, Xin Li, Lifang Shang, Yangwei Shang, Wenpeng Yan, Xiaoqin Zhang, Wenxia Ma and Chen Wang

Fusion transcript detection using spatial transcriptomics

Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high sp...

Authors: Stefanie Friedrich and Erik L. L. Sonnhammer