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Interdisciplinary Sciences, Computational Life Sciences

Li Ma, Jialin Lv, Yujie Dong, Xinyong Zhang, Xi Li, Hui Zhang, Jingying Nong, Quan Zhang, Na Qin, Xinjie Yang, Jinghui Wang, Shucai Zhang
BACKGROUND: The mechanism of regulation of PD-L1 expression by ALK translocation remains unclear. We detected PD-L1 protein expression and its regulation in lung adenocarcinoma patients with EML4-ALK fusion gene. METHODS: PD-L1 and ALK expression at protein level in human lung adenocarcinoma cell lines and tumor tissue specimens was evaluated by immunohistochemistry analysis and Western blotting. The expression at DNA level and RNA level was indicated by quantitative real-time PCR analysis...
May 16, 2019: Interdisciplinary Sciences, Computational Life Sciences
Peng Song, Shafei Wu, Li Zhang, Xuan Zeng, Jinghui Wang
BACKGROUND: PD-1/PD-L1 inhibitors is the important drugs of immunotherapy for malignant tumors. PD-L1 expression is an important biomarker of selecting patients for ICIs therapy. However, the correlation of PD-L1 expression with clinicopathologic features in lung adenocarcinoma remains controversial. METHODS: PD-L1 expression was tested using clone SP263 by immunohistochemistry (IHC) on Ventana automated Benchmark in tissue micro-arrays (TMA) in lung adenocarcinoma...
May 11, 2019: Interdisciplinary Sciences, Computational Life Sciences
Xin Feng, Xubing Hao, Ruihao Xin, Xiaoqian Gao, Minge Liu, Fei Li, Yubo Wang, Ruoyao Shi, Shishun Zhao, Fengfeng Zhou
Autism was a spectrum of multiple complex diseases that required an interdisciplinary group of experts to make a diagnostic decision. Both genetic and environmental factors play essential roles in causing the onset of Autism. Therefore, this study hypothesized that methylomic biomarkers may facilitate the accurate Autism detection. A comprehensive series of biomarker detection algorithms were utilized to find the best methylomic biomarkers for the Autism detection using the methylomic data of the peripheral blood samples...
April 16, 2019: Interdisciplinary Sciences, Computational Life Sciences
Anil Kumar Tomar, Rahul Agarwal, Bishwajit Kundu
Acute lymphoblastic leukemia (ALL) is a hematologic tumor caused by cell cycle aberrations due to accumulating genetic disturbances in the expression of transcription factors (TFs), signaling oncogenes and tumor suppressors. Though survival rate in childhood ALL patients is increased up to 80% with recent medical advances, treatment of adults and childhood relapse cases still remains challenging. Here, we have performed bioinformatics analysis of 207 ALL patients' mRNA expression data retrieved from the ICGC data portal with an objective to mark out the decisive genes and pathways responsible for ALL pathogenesis and aggression...
April 10, 2019: Interdisciplinary Sciences, Computational Life Sciences
Carlos A C Bastos, Vera Afreixo, João M O S Rodrigues, Armando J Pinho, Raquel M Silva
Finding DNA sites with high potential for the formation of hairpin/cruciform structures is an important task. Previous works studied the distances between adjacent reversed complement words (symmetric word pairs) and also for non-adjacent words. It was observed that for some words a few distances were favoured (peaks) and that in some distributions there was strong peak regularity. The present work extends previous studies, by improving the detection and characterization of peak regularities in the symmetric word pairs distance distributions of the human genome...
March 25, 2019: Interdisciplinary Sciences, Computational Life Sciences
Jin Li, Ailing Fu, Le Zhang
Currently, molecular docking is becoming a key tool in drug discovery and molecular modeling applications. The reliability of molecular docking depends on the accuracy of the adopted scoring function, which can guide and determine the ligand poses when thousands of possible poses of ligand are generated. The scoring function can be used to determine the binding mode and site of a ligand, predict binding affinity and identify the potential drug leads for a given protein target. Despite intensive research over the years, accurate and rapid prediction of protein-ligand interactions is still a challenge in molecular docking...
March 15, 2019: Interdisciplinary Sciences, Computational Life Sciences
Shuaibin Lian, Tianliang Liu, Zaibao Zhang, Hongyu Yuan, Lei Wang, Lin Cheng
BACKGROUND: The gene order in a eukaryotic genome is not random. Some neighboring genes show specific similarities, while others become separated during evolution. Whole genome duplication events (WGDs) have been recognized as an important evolutionary force. The potential relationship between the separation of neighboring genes and WGDs needs to be investigated. In this study, we investigated whether there is a potential relationship between separated neighboring gene pairs and WGDs, and the mechanism by which neighboring genes are separated...
March 14, 2019: Interdisciplinary Sciences, Computational Life Sciences
Antonino Aparo, Vincenzo Bonnici, Giovanni Micale, Alfredo Ferro, Dennis Shasha, Alfredo Pulvirenti, Rosalba Giugno
Many scientific applications entail solving the subgraph isomorphism problem, i.e., given an input pattern graph, find all the subgraphs of a (usually much larger) target graph that are structurally equivalent to that input. Because subgraph isomorphism is NP-complete, methods to solve it have to use heuristics. This work evaluates subgraph isomorphism methods to assess their computational behavior on a wide range of synthetic and real graphs. Surprisingly, our experiments show that, among the leading algorithms, certain heuristics based only on pattern graphs are the most efficient...
February 21, 2019: Interdisciplinary Sciences, Computational Life Sciences
Mei Kie Hon, Mohd Saberi Mohamad, Abdul Hakim Mohamed Salleh, Yee Wen Choon, Kauthar Mohd Daud, Muhammad Akmal Remli, Mohd Arfian Ismail, Sigeru Omatu, Richard O Sinnott, Juan Manuel Corchado
In recent years, metabolic engineering has gained central attention in numerous fields of science because of its capability to manipulate metabolic pathways in enhancing the expression of target phenotypes. Due to this, many computational approaches that perform genetic manipulation have been developed in the computational biology field. In metabolic engineering, conventional methods have been utilized to upgrade the generation of lactate and succinate in E. coli, although the yields produced are usually way below their theoretical maxima...
February 13, 2019: Interdisciplinary Sciences, Computational Life Sciences
Zhaoying Liao, Xiaonan Zhang, Yonghong Zhang, Donghong Peng
Tuberculosis (TB) is a global infectious disease and one of the ten leading causes of death worldwide. As TB incidence is seasonal, a reliable forecasting model that incorporates both seasonal and trend effects would be useful to improve the prevention and control of TB. In this study, the X12 autoregressive integrated moving average (X12-ARIMA) model was constructed by dividing the sequence into season term and trend term to forecast the two terms, respectively. Data regarding the TB report rate from January 2004 to December 2015 were included in the model, and the TB report data from January 2016 to December 2016 were used to validate the results...
February 8, 2019: Interdisciplinary Sciences, Computational Life Sciences
Morteza Hosseini, Diogo Pratas, Armando J Pinho
Advancement of protein sequencing technologies has led to the production of a huge volume of data that needs to be stored and transmitted. This challenge can be tackled by compression. In this paper, we propose AC, a state-of-the-art method for lossless compression of amino acid sequences. The proposed method works based on the cooperation between finite-context models and substitutional tolerant Markov models. Compared to several general-purpose and specific-purpose protein compressors, AC provides the best bit-rates...
February 5, 2019: Interdisciplinary Sciences, Computational Life Sciences
Jiong Wu, Linhui Chen, Chaobo Zheng, Shanhu Xu, Yuhai Gao, Junjun Wang
Alzheimer's disease (AD) is one of the most common types of dementia among the elderly. Previous studies had revealed that the dysregulation of lncRNAs played important roles in human diseases, including AD. However, there is still a lack of comprehensive analysis of differently expressed long non-coding RNAs (lncRNAs) in different distinct regions related to AD. In present study, we identified a total of 678, 593, 941, 1445, 1179, 466 differently expressed lncRNAs that were found in entorhinal cortex (EC), middle temporal gyrus(MTG), hippocampus (HIP), superior frontal gyrus (SFG), posterior cingulate (PC), cortex and primary visual cortex (VCX) AD samples, respectively...
February 4, 2019: Interdisciplinary Sciences, Computational Life Sciences
Noé Vázquez, Hugo López-Fernández, Cristina P Vieira, Florentino Fdez-Riverola, Jorge Vieira, Miguel Reboiro-Jato
Nowadays, bioinformatics is one of the most important areas in modern biology and the creation of high-quality scientific software supporting this recent research area is one of the core activities of many researchers. In this context, high-quality sequence datasets are needed to perform inferences on the evolution of species, genes, and gene families, or to get evidence for adaptive amino acid evolution, among others. Nevertheless, sequence data are very often spread over several databases, many useful genomes and transcriptomes are non-annotated, the available annotation is not for the desired coding sequence isoform, and/or is unlikely to be accurate...
February 2, 2019: Interdisciplinary Sciences, Computational Life Sciences
Noé Vázquez, Sara Rocha, Hugo López-Fernández, André Torres, Rui Camacho, Florentino Fdez-Riverola, Jorge Vieira, Cristina P Vieira, Miguel Reboiro-Jato
Protein-protein interaction (PPI) data is essential to elucidate the complex molecular relationships in living systems, and thus understand the biological functions at cellular and systems levels. The complete map of PPIs that can occur in a living organism is called the interactome. For animals, PPI data is stored in multiple databases (e.g., BioGRID, CCSB, DroID, FlyBase, HIPPIE, HitPredict, HomoMINT, INstruct, Interactome3D, mentha, MINT, and PINA2) with different formats. This makes PPI comparisons difficult to perform, especially between species, since orthologous proteins may have different names...
February 1, 2019: Interdisciplinary Sciences, Computational Life Sciences
Dino Franklin
MeCP2 is a protein highly expressed in the brain that participates in the genetic expression and RNA splicing regulation. MeCP2 binds preferably to methylated DNA and other nuclear corepressors to alter chromatin. MECP2 gene mutations can cause rett syndrome (RTT), a severe neurological disorder that affects around one in ten thousand girls. In this paper, Molecular Dynamics (MD) simulations were performed to scrutinize how the MeCP2 P152R mutation influences the protein binding to DNA. Also, the Umbrella Sampling technique was used to obtain the potential mean forces (PMFs) of both wild-type and mutated MeCP2 Methyl-CpG-binding domain (MBD) binding to both non-methylated and methylated DNA...
January 23, 2019: Interdisciplinary Sciences, Computational Life Sciences
Mouna Choura, Ahmed Rebaï
Intrinsically disordered proteins (IDPs) are often involved in diseases and have been shown to be promising targets for drug development. Here, we focus on the human disordered charged biased proteins (HDCBPs). We have investigated the association of the HDCBPs with diseases by integrating various sources that cover public sources of gene-disease associations and intensive literature mining. The results indicate that 95% of HDCBPs are associated with multiple diseases, including mainly various cancers, nervous, endocrine, immune, hematological, and respiratory systems diseases...
January 11, 2019: Interdisciplinary Sciences, Computational Life Sciences
Bo Hu, Xiao Chang, Xiaoping Liu
Complex diseases are generally caused by disorders of biological networks or/and mutations in multiple genes. The efficient and systematic identification of functional modules can not only supply effective diagnosis and treatment in clinic, but also benefit in further in-depth analysis of the pathological mechanism of complex diseases. In this study, we applied the method of differential network to identify functional modules between control and disease samples, which are different from most of the current approaches that focus on differential expression...
January 2, 2019: Interdisciplinary Sciences, Computational Life Sciences
Amani Al-Ajlan, Achraf El Allali
Accurate gene prediction in metagenomics fragments is a computationally challenging task due to the short-read length, incomplete, and fragmented nature of the data. Most gene-prediction programs are based on extracting a large number of features and then applying statistical approaches or supervised classification approaches to predict genes. In our study, we introduce a convolutional neural network for metagenomics gene prediction (CNN-MGP) program that predicts genes in metagenomics fragments directly from raw DNA sequences, without the need for manual feature extraction and feature selection stages...
December 27, 2018: Interdisciplinary Sciences, Computational Life Sciences
Kaja Gutowska, Dorota Formanowicz, Piotr Formanowicz
Many factors, such as endothelial dysfunction, inflammation and hemostatic disturbances, affect formation and progression of atherosclerotic plaque. In our study, we have focused on hemostatic disturbances with particular emphasis on the extrinsic pathways of coagulation. Thrombin is a main enzyme of coagulation and it is engaged in many different subprocesses. It leads to activation of factors of the coagulation cascade, transition of fibrinogen to fibrin monomer, endothelial damage, inflammation, activation of platelets and proliferation...
December 24, 2018: Interdisciplinary Sciences, Computational Life Sciences
Lina Teresa Gaudio, Pierangelo Veltri, Salvatore De Rosa, Ciro Indolfi, Gionata Fragomeni
Cardiovascular diseases are among the main causes of morbidity, disability, and mortality. Most of them occur because of an atherosclerotic plaque developing within a coronary artery, which can cause a narrowing of the vessel lumen (coronary stenosis) or even break it. It is, therefore, useful to evaluate the role of the stress state of the endothelial layer of the arterial tissue, both for the maintenance of the blood circulation and for the implications in presence of a pathology that can lead to thromboembolic complications...
December 7, 2018: Interdisciplinary Sciences, Computational Life Sciences
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