102 results match your criteria Journal of clinical bioinformatics[Journal]


Comparative efficacy and acceptability of five anti-tubercular drugs in treatment of multidrug resistant tuberculosis: a network meta-analysis.

J Clin Bioinforma 2015 28;5. Epub 2015 Apr 28.

Key Laboratory of Zoonosis, Ministry of Education, College of Basic Medicine, Jilin University, 126 Xinmin Street, Changchun, Jilin China.

Multidrug resistant tuberculosis (MDR-TB) is a serious form of tuberculosis (TB). There is no recognized effective treatment for MDR-TB, although there are a number of publications that have reported positive results for MDR-TB. We performed a network meta-analysis to assess the efficacy and acceptability of potential antitubercular drugs. Read More

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http://www.jclinbioinformatics.com/content/5/1/5
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http://dx.doi.org/10.1186/s13336-015-0020-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416256PMC
May 2015
5 Reads

Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine.

J Clin Bioinforma 2015 26;5. Epub 2015 Mar 26.

Genomics and Biomarkers Program, Hackensack University Medical Center, Hackensack, NJ 07601 USA ; John Theurer Cancer Center, Hackensack University Medical Center, D. Jurist Research Building, 40 Prospect Avenue, Hackensack, NJ 07601 USA.

As research laboratories and clinics collaborate to achieve precision medicine, both communities are required to understand mandated electronic health/medical record (EHR/EMR) initiatives that will be fully implemented in all clinics in the United States by 2015. Stakeholders will need to evaluate current record keeping practices and optimize and standardize methodologies to capture nearly all information in digital format. Collaborative efforts from academic and industry sectors are crucial to achieving higher efficacy in patient care while minimizing costs. Read More

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http://dx.doi.org/10.1186/s13336-015-0019-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381462PMC
April 2015
4 Reads

Metabolomics and partial least square discriminant analysis to predict history of myocardial infarction of self-claimed healthy subjects: validity and feasibility for clinical practice.

J Clin Bioinforma 2015 13;5. Epub 2015 Mar 13.

Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Bandar Puncak Alam, Puncak Alam Malaysia, Selangor 42300 Malaysia ; Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Bandar Puncak Alam, Selangor 42300 Malaysia.

Background: The dynamics of metabolomics in establishing a prediction model using partial least square discriminant analysis have enabled better disease diagnosis; with emphasis on early detection of diseases. We attempted to translate the metabolomics model to predict the health status of the Orang Asli community whom we have little information. The metabolite expressions of the healthy vs. Read More

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http://dx.doi.org/10.1186/s13336-015-0018-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371619PMC
March 2015
12 Reads
1 Citation

K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores.

J Clin Bioinforma 2015 3;5. Epub 2015 Mar 3.

Department of Genetic Medicine, Weill Cornell Medical College, New York, NY USA ; Genomic Core, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, 24144 Qatar.

Background: Network biology currently focuses primarily on metabolic pathways, gene regulatory, and protein-protein interaction networks. While these approaches have yielded critical information, alternative methods to network analysis will offer new perspectives on biological information. A little explored area is the interactions between domains that can be captured using domain co-occurrence networks (DCN). Read More

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http://dx.doi.org/10.1186/s13336-015-0016-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357223PMC
March 2015
2 Reads

Variations in genome-wide RNAi screens: lessons from influenza research.

J Clin Bioinforma 2015 3;5. Epub 2015 Mar 3.

Research Center for Emerging Viruses, China Medical University Hospital, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung, 40402 Taiwan ; China Medical University, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung, 40402 Taiwan.

Genome-wide RNA interference (RNAi) screening is an emerging and powerful technique for genetic screens, which can be divided into arrayed RNAi screen and pooled RNAi screen/selection based on different screening strategies. To date, several genome-wide RNAi screens have been successfully performed to identify host factors essential for influenza virus replication. However, the host factors identified by different research groups are not always consistent. Read More

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http://dx.doi.org/10.1186/s13336-015-0017-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350949PMC
March 2015
4 Reads

Copy number variation analysis based on AluScan sequences.

J Clin Bioinforma 2014 5;4(1):15. Epub 2014 Dec 5.

Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.

Background: AluScan combines inter-Alu PCR using multiple Alu-based primers with opposite orientations and next-generation sequencing to capture a huge number of Alu-proximal genomic sequences for investigation. Its requirement of only sub-microgram quantities of DNA facilitates the examination of large numbers of samples. However, the special features of AluScan data rendered difficult the calling of copy number variation (CNV) directly using the calling algorithms designed for whole genome sequencing (WGS) or exome sequencing. Read More

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http://dx.doi.org/10.1186/s13336-014-0015-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273479PMC
January 2015
16 Reads

Semi-automated literature mining to identify putative biomarkers of disease from multiple biofluids.

J Clin Bioinforma 2014 23;4:13. Epub 2014 Oct 23.

Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA ; Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA ; Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.

Background: Computational methods for mining of biomedical literature can be useful in augmenting manual searches of the literature using keywords for disease-specific biomarker discovery from biofluids. In this work, we develop and apply a semi-automated literature mining method to mine abstracts obtained from PubMed to discover putative biomarkers of breast and lung cancers in specific biofluids.

Methodology: A positive set of abstracts was defined by the terms 'breast cancer' and 'lung cancer' in conjunction with 14 separate 'biofluids' (bile, blood, breastmilk, cerebrospinal fluid, mucus, plasma, saliva, semen, serum, synovial fluid, stool, sweat, tears, and urine), while a negative set of abstracts was defined by the terms '(biofluid) NOT breast cancer' or '(biofluid) NOT lung cancer. Read More

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http://dx.doi.org/10.1186/2043-9113-4-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4215335PMC
November 2014
2 Reads

Extraction of echocardiographic data from the electronic medical record is a rapid and efficient method for study of cardiac structure and function.

J Clin Bioinforma 2014 20;4:12. Epub 2014 Sep 20.

Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA ; Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.

Background: Measures of cardiac structure and function are important human phenotypes that are associated with a range of clinical outcomes. Studying these traits in large populations can be time consuming and costly. Utilizing data from large electronic medical records (EMRs) is one possible solution to this problem. Read More

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http://dx.doi.org/10.1186/2043-9113-4-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177384PMC
October 2014
17 Reads

Meta-analyses of 4 CFTR variants associated with the risk of the congenital bilateral absence of the vas deferens.

J Clin Bioinforma 2014 21;4:11. Epub 2014 Aug 21.

Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.

Aims: The aim of our study was to evaluate the relationship between four CFTR variations and the congenital bilateral absence of the vas deferens (CBAVD).

Methods: A systematic search was performed in the literature databases for the case-control studies of CFTR variations with the risk of CBAVD. A total of 29 studies among 1139 controls and 1562 CBAVD patients were gathered for the meta-analyses of three commonly tecsted variations (5T, ΔF508 and M470V) with CBAVD. Read More

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http://dx.doi.org/10.1186/2043-9113-4-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147875PMC
August 2014
12 Reads

Tools to identify linear combination of prognostic factors which maximizes area under receiver operator curve.

J Clin Bioinforma 2014 4;4:10. Epub 2014 Jul 4.

Company for Applied Informatics, Republicii 101-102, 400015 Cluj-Napoca, Romania.

Background: The linear combination of variables is an attractive method in many medical analyses targeting a score to classify patients. In the case of ROC curves the most popular problem is to identify the linear combination which maximizes area under curve (AUC). This problem is complete closed when normality assumptions are met. Read More

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http://dx.doi.org/10.1186/2043-9113-4-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099021PMC
July 2014
2 Reads

comoR: a software for disease comorbidity risk assessment.

J Clin Bioinforma 2014 23;4. Epub 2014 May 23.

Computer Laboratory, University of Cambridge, William Gates Building, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK.

Background: The diagnosis of comorbidities, which refers to the coexistence of different acute and chronic diseases, is difficult due to the modern extreme specialisation of physicians. We envisage that a software dedicated to comorbidity diagnosis could result in an effective aid to the health practice.

Results: We have developed an R software comoR to compute novel estimators of the disease comorbidity associations. Read More

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http://dx.doi.org/10.1186/2043-9113-4-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081507PMC
July 2014
4 Reads

Interpretation for scales of measurement linking with abstract algebra.

J Clin Bioinforma 2014 10;4. Epub 2014 Jun 10.

Department of Psychiatry, Tokyo Women's Medical University, Tokyo, Japan.

THE STEVENS CLASSIFICATION OF LEVELS OF MEASUREMENT INVOLVES FOUR TYPES OF SCALE: "Nominal", "Ordinal", "Interval" and "Ratio". This classification has been used widely in medical fields and has accomplished an important role in composition and interpretation of scale. With this classification, levels of measurements appear organized and validated. Read More

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http://dx.doi.org/10.1186/2043-9113-4-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075994PMC
July 2014
2 Reads

Estimating age-dependent per-encounter chlamydia trachomatis acquisition risk via a Markov-based state-transition model.

J Clin Bioinforma 2014 25;4. Epub 2014 Apr 25.

Division of Biostatistics, School of Medicine, Indiana University, 340 W 10th Street, Indianapolis, IN 46202, USA.

Background: Chlamydial infection is a common bacterial sexually transmitted infection worldwide, caused by C. trachomatis. The screening for C. Read More

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http://jclinbioinformatics.biomedcentral.com/articles/10.118
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http://dx.doi.org/10.1186/2043-9113-4-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022339PMC
May 2014
7 Reads

A novel tree-based procedure for deciphering the genomic spectrum of clinical disease entities.

J Clin Bioinforma 2014 16;4. Epub 2014 Apr 16.

Abirisk consortium WP4, 14-16 Avenue Paul-Vaillant-Couturier, 94807 Villejuif, France ; Inserm U669, 14-16 Avenue Paul-Vaillant-Couturier, 94807 Villejuif, France ; Faculty of Medicine Paris-Sud, 63 rue Gabriel Peri, 94276 Le Kremlin-Bicêtre, France ; Assistance Publique - Hôpitaux de Paris, Hôpital Paul Brousse, Villejuif, France.

Background: Dissecting the genomic spectrum of clinical disease entities is a challenging task. Recursive partitioning (or classification trees) methods provide powerful tools for exploring complex interplay among genomic factors, with respect to a main factor, that can reveal hidden genomic patterns. To take confounding variables into account, the partially linear tree-based regression (PLTR) model has been recently published. Read More

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http://dx.doi.org/10.1186/2043-9113-4-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4129184PMC
September 2014
2 Reads

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

J Clin Bioinforma 2014 Mar 31;4(1). Epub 2014 Mar 31.

Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.

Background: A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events.

Results: We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. Read More

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http://dx.doi.org/10.1186/2043-9113-4-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230720PMC
March 2014
8 Reads

A novel molecular typing method of Mycobacteria based on DNA barcoding visualization.

J Clin Bioinforma 2014 Feb 20;4(1). Epub 2014 Feb 20.

Department of Pathogenobiology, Basic Medical College of Jilin University, Changchun, Jilin, China.

Different subtypes of Mycobacterium tuberculosis (MTB) may induce diverse severe human infections, and some of their symptoms are similar to other pathogenes, e.g. Nontuberculosis mycobacteria (NTM). Read More

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http://dx.doi.org/10.1186/2043-9113-4-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931916PMC
February 2014
1 Read

Development of detection method for novel fusion gene using GeneChip exon array.

J Clin Bioinforma 2014 Feb 18;4(1). Epub 2014 Feb 18.

Genome Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.

Background: Fusion genes have been recognized to play key roles in oncogenesis. Though, many techniques have been developed for genome-wide analysis of fusion genes, a more efficient method is desired.

Results: We introduced a new method of detecting the novel fusion gene by using GeneChip Exon Array that enables exon expression analysis on a whole-genome scale and TAIL-PCR. Read More

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http://jclinbioinformatics.biomedcentral.com/articles/10.118
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http://dx.doi.org/10.1186/2043-9113-4-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937068PMC
February 2014
5 Reads

Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference.

J Clin Bioinforma 2014 Jan 24;4(1). Epub 2014 Jan 24.

Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano Bicocca, Viale Sarca 336, U14, 20126 Milan, Italy.

Background: Copy number alterations (CNAs) represent an important component of genetic variations. Such alterations are related with certain type of cancer including those of the pancreas, colon, and breast, among others. CNAs have been used as biomarkers for cancer prognosis in multiple studies, but few works report on the relation of CNAs with the disease progression. Read More

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http://dx.doi.org/10.1186/2043-9113-4-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931674PMC
January 2014
11 Reads

Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.

J Clin Bioinforma 2014 Jan 13;4(1). Epub 2014 Jan 13.

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.

Background: The human body plays host to a vast array of bacteria, found in oral cavities, skin, gastrointestinal tract and the vagina. Some bacteria are harmful while others are beneficial to the host. Despite the availability of many methods to identify bacteria, most of them are only applicable to specific and cultivable bacteria and are also tedious. Read More

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http://jclinbioinformatics.biomedcentral.com/articles/10.118
Publisher Site
http://dx.doi.org/10.1186/2043-9113-4-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901789PMC
January 2014
9 Reads

SN algorithm: analysis of temporal clinical data for mining periodic patterns and impending augury.

J Clin Bioinforma 2013 Nov 28;3(1):24. Epub 2013 Nov 28.

Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, H,P, India.

Background: EHR (Electronic Health Record) system has led to development of specialized form of clinical databases which enable storage of information in temporal prospective. It has been a big challenge for mining this form of clinical data considering varied temporal points. This study proposes a conjoined solution to analyze the clinical parameters akin to a disease. Read More

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http://dx.doi.org/10.1186/2043-9113-3-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177143PMC
November 2013
1 Read

Mathematical models for translational and clinical oncology.

J Clin Bioinforma 2013 Nov 7;3(1):23. Epub 2013 Nov 7.

Biocenter, Division of Bioinformatics, Innsbruck Medical University, Innrain 80, 6020 Innsbruck, Austria.

In the context of translational and clinical oncology, mathematical models can provide novel insights into tumor-related processes and can support clinical oncologists in the design of the treatment regime, dosage, schedule, toxicity and drug-sensitivity. In this review we present an overview of mathematical models in this field beginning with carcinogenesis and proceeding to the different cancer treatments. By doing so we intended to highlight recent developments and emphasize the power of such theoretical work. Read More

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http://dx.doi.org/10.1186/2043-9113-3-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828625PMC
November 2013
5 Reads

PROGgene: gene expression based survival analysis web application for multiple cancers.

J Clin Bioinforma 2013 Oct 28;3(1):22. Epub 2013 Oct 28.

Thomas Jefferson University Hospitals, 117 S 11th Street, Suite 207, Philadelphia, PA 19107, USA.

Background: Identification of prognostic mRNA biomarkers has been done for various cancer types. The data that are published from such studies are archived in public repositories. There are hundreds of such datasets available for multiple cancer types in public repositories. Read More

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http://dx.doi.org/10.1186/2043-9113-3-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875898PMC
October 2013
39 Reads

In silico analysis of the molecular machinery underlying aqueous humor production: potential implications for glaucoma.

J Clin Bioinforma 2013 Oct 28;3(1):21. Epub 2013 Oct 28.

Department of Clinical and Molecular Ophthalmogenetics the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, the Netherlands.

Background: The ciliary body epithelia (CBE) of the eye produce the aqueous humor (AH). The equilibrium between the AH production by the CBE and the outflow through the trabecular meshwork ultimately determines the intraocular pressure (IOP). An increased IOP is a major risk factor for primary open angle glaucoma (POAG). Read More

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http://jclinbioinformatics.biomedcentral.com/articles/10.118
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http://dx.doi.org/10.1186/2043-9113-3-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875900PMC
October 2013
2 Reads

A systematic analysis of a mi-RNA inter-pathway regulatory motif.

J Clin Bioinforma 2013 Oct 24;3(1):20. Epub 2013 Oct 24.

Department of Control and Computer Engineering, Politecnico di Torino, Torino, IT, Italy.

Background: The continuing discovery of new types and functions of small non-coding RNAs is suggesting the presence of regulatory mechanisms far more complex than the ones currently used to study and design Gene Regulatory Networks. Just focusing on the roles of micro RNAs (miRNAs), they have been found to be part of several intra-pathway regulatory motifs. However, inter-pathway regulatory mechanisms have been often neglected and require further investigation. Read More

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http://dx.doi.org/10.1186/2043-9113-3-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875894PMC
October 2013
3 Reads

Comparative analysis of differential network modularity in tissue specific normal and cancer protein interaction networks.

J Clin Bioinforma 2013 Oct 6;3(1):19. Epub 2013 Oct 6.

Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna 9208, Bangladesh.

Background: Large scale understanding of complex and dynamic alterations in cellular and subcellular levels during cancer in contrast to normal condition has facilitated the emergence of sophisticated systemic approaches like network biology in recent times. As most biological networks show modular properties, the analysis of differential modularity between normal and cancer protein interaction networks can be a good way to understand cancer more significantly. Two aspects of biological network modularity e. Read More

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http://dx.doi.org/10.1186/2043-9113-3-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852839PMC
October 2013
19 Reads

Using biomarkers to predict progression from clinically isolated syndrome to multiple sclerosis.

J Clin Bioinforma 2013 Oct 3;3(1):18. Epub 2013 Oct 3.

Department of Medicine, Vanderbilt University School of Medicine, MCN T3219, 1161 21st Avenue South, Nashville, TN, 37232-2681, USA.

Background: Detection of brain lesions disseminated in space and time by magnetic resonance imaging remains a cornerstone for the diagnosis of clinically definite multiple sclerosis. We have sought to determine if gene expression biomarkers could contribute to the clinical diagnosis of multiple sclerosis.

Methods: We employed expression levels of 30 genes in blood from 199 subjects with multiple sclerosis, 203 subjects with other neurologic disorders, and 114 healthy control subjects to train ratioscore and support vector machine algorithms. Read More

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http://dx.doi.org/10.1186/2043-9113-3-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3850501PMC
October 2013
3 Reads

The multiple roles of microRNA-155 in oncogenesis.

J Clin Bioinforma 2013 Sep 28;3(1):17. Epub 2013 Sep 28.

Yale Center for Medical Informatics, Yale University, Suite 505, 300 George Street, New Haven, USA.

The microRNA miR-155 is prominent in cancer biology. Among microRNAs that have been linked to cancer, it is the most commonly overexpressed in malignancies (PNAS 109:20047-20052, 2012). Since its discovery, miR-155 has been implicated in promoting cancers of the breast, lung, liver, and lymphatic system. Read More

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http://dx.doi.org/10.1186/2043-9113-3-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849775PMC
September 2013
3 Reads

Potential identification of pediatric asthma patients within pediatric research database using low rank matrix decomposition.

J Clin Bioinforma 2013 Sep 28;3(1):16. Epub 2013 Sep 28.

Biomedical Informatics Core, Children's Foundation Research Institute, Department of Pediatrics, The University of Tennessee Health Science Center, 50 N, Dunlap, 38013, Memphis, TN, USA.

Asthma is a prevalent disease in pediatric patients and most of the cases begin at very early years of life in children. Early identification of patients at high risk of developing the disease can alert us to provide them the best treatment to manage asthma symptoms. Often evaluating patients with high risk of developing asthma from huge data sets (e. Read More

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http://dx.doi.org/10.1186/2043-9113-3-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3850459PMC
September 2013
3 Reads

Automated analysis of immunoglobulin genes from high-throughput sequencing: life without a template.

J Clin Bioinforma 2013 Aug 27;3(1):15. Epub 2013 Aug 27.

The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.

Background: Immunoglobulin (that is, antibody) and T cell receptor genes are created through somatic gene rearrangement from gene segment libraries. Immunoglobulin genes are further diversified by somatic hypermutation and selection during the immune response. Studying the repertoires of these genes yields valuable insights into immune system function in infections, aging, autoimmune diseases and cancers. Read More

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http://dx.doi.org/10.1186/2043-9113-3-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846367PMC
August 2013
3 Reads

Plot protein: visualization of mutations.

Authors:
Tychele Turner

J Clin Bioinforma 2013 Jul 22;3(1):14. Epub 2013 Jul 22.

Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N, Broadway, MRB 572, Baltimore, MD 21205, USA.

Background: Next-generation sequencing has enabled examination of variation at the DNA sequence level and can be further enhanced by evaluation of the variants at the protein level. One powerful method is to visualize these data often revealing patterns not immediately apparent in a text version of the same data. Many investigators are interested in knowing where their amino acid changes reside within a protein. Read More

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http://dx.doi.org/10.1186/2043-9113-3-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724591PMC
July 2013
1 Read

High-throughput identification of reference genes for research and clinical RT-qPCR analysis of breast cancer samples.

J Clin Bioinforma 2013 Jul 22;3(1):13. Epub 2013 Jul 22.

SRC Bioclinicum, Moscow, Russia.

Background: Quantification and normalization of RT-qPCR data critically depends on the expression of so called reference genes. Our goal was to develop a strategy for the selection of reference genes that utilizes microarray data analysis and combines known approaches for gene stability evaluation and to select a set of appropriate reference genes for research and clinical analysis of breast samples with different receptor and cancer status using this strategy.

Methods: A preliminary search of reference genes was based on high-throughput analysis of microarray datasets. Read More

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http://dx.doi.org/10.1186/2043-9113-3-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726509PMC
July 2013
13 Reads

Multiple samples aCGH analysis for rare CNVs detection.

J Clin Bioinforma 2013 Jun 11;3(1):12. Epub 2013 Jun 11.

Institute of Informatics, University of Warsaw, Warsaw, Poland.

Background: DNA copy number variations (CNV) constitute an important source of genetic variability. The standard method used for CNV detection is array comparative genomic hybridization (aCGH).

Results: We propose a novel multiple sample aCGH analysis methodology aiming in rare CNVs detection. Read More

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http://dx.doi.org/10.1186/2043-9113-3-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691624PMC
June 2013
39 Reads

Protein co-expression network analysis (ProCoNA).

J Clin Bioinforma 2013 Jun 1;3(1):11. Epub 2013 Jun 1.

Division of Bioinformatics and Computational Biology, Oregon Health & Science University, 3181 S,W, Sam Jackson Park Rd, Portland, OR 97239, USA.

Background: Biological networks are important for elucidating disease etiology due to their ability to model complex high dimensional data and biological systems. Proteomics provides a critical data source for such models, but currently lacks robust de novo methods for network construction, which could bring important insights in systems biology.

Results: We have evaluated the construction of network models using methods derived from weighted gene co-expression network analysis (WGCNA). Read More

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http://dx.doi.org/10.1186/2043-9113-3-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695838PMC
June 2013
5 Reads

An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples.

J Clin Bioinforma 2013 May 3;3(1):10. Epub 2013 May 3.

Pharma Research and Early Development (pRED), Roche Diagnostics GmbH, TR-H, Bldg 231/206a, Nonnenwald 2, 82377 Penzberg, Germany.

Background: Whole genome microarray gene expression profiling is the 'gold standard' for the discovery of prognostic and predictive genetic markers for human cancers. However, suitable research material is lacking as most diagnostic samples are preserved as formalin-fixed, paraffin-embedded tissue (FFPET). We tested a new workflow and data analysis method optimized for use with FFPET samples. Read More

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http://dx.doi.org/10.1186/2043-9113-3-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660273PMC
May 2013
3 Reads

A diagnostic methodology for Alzheimer's disease.

J Clin Bioinforma 2013 Apr 25;3(1). Epub 2013 Apr 25.

Systems Biology Lab, University of Florida, Gainesville, FL, 32611, USA.

Background: Like all other neurodegenerative diseases, Alzheimer's disease (AD) remains a very challenging and difficult problem for diagnosis and therapy. For many years, only historical, behavioral and psychiatric measures have been available to AD cases. Recently, a definitive diagnostic framework, using biomarkers and imaging, has been proposed. Read More

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http://dx.doi.org/10.1186/2043-9113-3-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660190PMC
April 2013
1 Read

Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays.

J Clin Bioinforma 2013 Apr 18;3(1). Epub 2013 Apr 18.

Center for Computational Science, University of Miami, Miami, FL, USA.

Background: Exploring stromal changes associated with tumor growth and development is a growing area of oncologic research. In order to study molecular changes in the stroma it is recommended to separate tumor tissue from stromal tissue. This is relevant to xenograft models where tumors can be small and difficult to separate from host tissue. Read More

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http://dx.doi.org/10.1186/2043-9113-3-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667020PMC
April 2013
1 Read

TUMIR: an experimentally supported database of microRNA deregulation in various cancers.

J Clin Bioinforma 2013 Apr 17;3(1). Epub 2013 Apr 17.

Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), National Laboratory of Medical Molecular Biology, Beijing, 100005, PR China.

Background: MicroRNAs were found to play an important role in cancers and several literatures exist to describe the relationship between microRNA and cancer, but the expression pattern was still faintly. There is a need for a comprehensive collection and summary of the interactions under experimental support.

Description: TUMIR (http://www. Read More

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http://dx.doi.org/10.1186/2043-9113-3-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640893PMC
April 2013
2 Reads

MicroRNAs: an emerging science in cancer epigenetics.

J Clin Bioinforma 2013 Mar 16;3(1). Epub 2013 Mar 16.

Department of Biology, University of Alabama Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.

MicroRNAs (miRNAs) are remarkable molecules that appear to have a fundamental role in the biology of the cell. They constitute a class of non-protein encoding RNA molecules which have now emerged as key players in regulating the activity of mRNA. miRNAs are small RNAmolecules around 22 nucleotides in length, which affect the activity of specific mRNA, directly degrading it and/or preventing its translation into protein. Read More

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http://dx.doi.org/10.1186/2043-9113-3-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608239PMC
March 2013
13 Reads

Improved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer.

J Clin Bioinforma 2013 Feb 14;3(1). Epub 2013 Feb 14.

Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, 415 Chien-Kung Road, Kaohsiung 80778, Taiwan.

Background: Single nucleotide polymorphisms (SNPs) in genes derived from distinct pathways are associated with a breast cancer risk. Identifying possible SNP-SNP interactions in genome-wide case-control studies is an important task when investigating genetic factors that influence common complex traits; the effects of SNP-SNP interaction need to be characterized. Furthermore, observations of the complex interplay (interactions) between SNPs for high-dimensional combinations are still computationally and methodologically challenging. Read More

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http://dx.doi.org/10.1186/2043-9113-3-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626712PMC
February 2013
1 Read

Cystic fibrosis testing in a referral laboratory: results and lessons from a six-year period.

J Clin Bioinforma 2013 Jan 23;3(1). Epub 2013 Jan 23.

ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.

Unlabelled:

Background: The recent introduction of high throughput sequencing technologies into clinical genetics has made it practical to simultaneously sequence many genes. In contrast, previous technologies limited sequencing based tests to only a handful of genes. While the ability to more accurately diagnose inherited diseases is a great benefit it introduces specific challenges. Read More

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http://dx.doi.org/10.1186/2043-9113-3-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563502PMC
January 2013
5 Reads

A ceRNA analysis on LMNA gene focusing on the Hutchinson-Gilford progeria syndrome.

J Clin Bioinforma 2013 Jan 14;3(1). Epub 2013 Jan 14.

Section of Endocrinology, Diabetology & Metabolism, Dipartimento Biomedico di Medicina Interna e Specialistica (Di,Bi,M,I,S,), University of Palermo, Piazza delle Cliniche 2, Palermo, 90127, Italy.

Unlabelled:

Background: Hutchinson-Gilford progeria syndrome is a rare dominant human disease of genetic origin. The average life expectancy is about 20 years, patients' life quality is still very poor and no efficient therapy has yet been developed. It is caused by mutation of the LMNA gene, which results in accumulation in the nuclear membrane of a particular splicing form of Lamin-A called progerin. Read More

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http://dx.doi.org/10.1186/2043-9113-3-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563501PMC
January 2013
1 Read

Availability of MudPIT data for classification of biological samples.

J Clin Bioinforma 2013 Jan 14;3(1). Epub 2013 Jan 14.

, Institute for Biomedical Technologies (ITB-CNR), via F.lli Cervi 93, Segrate (Milan), Italy.

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Background: Mass spectrometry is an important analytical tool for clinical proteomics. Primarily employed for biomarker discovery, it is increasingly used for developing methods which may help to provide unambiguous diagnosis of biological samples. In this context, we investigated the classification of phenotypes by applying support vector machine (SVM) on experimental data obtained by MudPIT approach. Read More

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http://dx.doi.org/10.1186/2043-9113-3-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563498PMC
January 2013
3 Reads

PROGmiR: a tool for identifying prognostic miRNA biomarkers in multiple cancers using publicly available data.

J Clin Bioinforma 2012 Dec 28;2(1):23. Epub 2012 Dec 28.

Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN, 46202, USA.

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Background: Identification of prognostic biomarkers is hallmark of cancer genomics. Since miRNAs regulate expression of multiple genes, they act as potent biomarkers in several cancers. Identification of miRNAs that are prognostically important has been done sporadically, but no resource is available till date that allows users to study prognostics of miRNAs of interest, utilizing the wealth of available data, in major cancer types. Read More

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http://jclinbioinformatics.biomedcentral.com/articles/10.118
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http://dx.doi.org/10.1186/2043-9113-2-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564827PMC
December 2012
4 Reads

mCOPA: analysis of heterogeneous features in cancer expression data.

J Clin Bioinforma 2012 Dec 10;2(1):22. Epub 2012 Dec 10.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia.

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Background: Cancer outlier profile analysis (COPA) has proven to be an effective approach to analyzing cancer expression data, leading to the discovery of the TMPRSS2 and ETS family gene fusion events in prostate cancer. However, the original COPA algorithm did not identify down-regulated outliers, and the currently available R package implementing the method is similarly restricted to the analysis of over-expressed outliers. Here we present a modified outlier detection method, mCOPA, which contains refinements to the outlier-detection algorithm, identifies both over- and under-expressed outliers, is freely available, and can be applied to any expression dataset. Read More

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http://dx.doi.org/10.1186/2043-9113-2-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553066PMC
December 2012
1 Read

Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays.

J Clin Bioinforma 2012 Nov 26;2(1):21. Epub 2012 Nov 26.

Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bangalore, 560100, India.

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Background: Second generation RNA sequencing technology (RNA-seq) offers the potential to interrogate genome-wide differential RNA splicing in cancer. However, since short RNA reads spanning spliced junctions cannot be mapped contiguously onto to the chromosomes, there is a need for methods to profile splicing from RNA-seq data. Before the invent of RNA-seq technologies, microarrays containing probe sequences representing exon-exon junctions of known genes have been used to hybridize cellular RNAs for measuring context-specific differential splicing. Read More

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http://dx.doi.org/10.1186/2043-9113-2-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3533750PMC
November 2012
2 Reads

Using gene expression data to identify certain gastro-intestinal diseases.

J Clin Bioinforma 2012 Nov 21;2(1):20. Epub 2012 Nov 21.

Department of Mathematics, Vanderbilt University, Nashville, TN, USA.

Background: Inflammatory bowel diseases, ulcerative colitis and Crohn's disease are considered to be of autoimmune origin, but the etiology of irritable bowel syndrome remains elusive. Furthermore, classifying patients into irritable bowel syndrome and inflammatory bowel diseases can be difficult without invasive testing and holds important treatment implications. Our aim was to assess the ability of gene expression profiling in blood to differentiate among these subject groups. Read More

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http://dx.doi.org/10.1186/2043-9113-2-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599448PMC
November 2012
5 Reads

Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection.

J Clin Bioinforma 2012 Nov 19;2(1):19. Epub 2012 Nov 19.

Department of Bioinformatics, Erasmus University Medical Center, Molewaterplein 50, Rotterdam, The Netherlands.

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Background: Next generation sequencing provides clinical research scientists with direct read out of innumerable variants, including personal, pathological and common benign variants. The aim of resequencing studies is to determine the candidate pathogenic variants from individual genomes, or from family-based or tumor/normal genome comparisons. Whilst the use of appropriate controls within the experimental design will minimize the number of false positive variations selected, this number can be reduced further with the use of high quality whole genome reference data to minimize false positives variants prior to candidate gene selection. Read More

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http://dx.doi.org/10.1186/2043-9113-2-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549785PMC
November 2012
13 Reads

The H-factor as a novel quality metric for homology modeling.

J Clin Bioinforma 2012 Nov 2;2(1):18. Epub 2012 Nov 2.

Computer Science Department, University of California Davis, 451 East Health Sciences Drive, Room 4337, Genome Center, GBSF, Davis, CA, 95616, USA.

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Background: Drug discovery typically starts with the identification of a potential target that is then tested and validated either through high-throughput screening against a library of drug compounds or by rational drug design. When the putative target is a protein, the latter approach requires the knowledge of its structure. Finding the structure of a protein is however a difficult task. Read More

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http://dx.doi.org/10.1186/2043-9113-2-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502507PMC
November 2012
2 Reads

Modeling autism: a systems biology approach.

J Clin Bioinforma 2012 Oct 8;2(1):17. Epub 2012 Oct 8.

Systems Engineering and Computer Engineering, University of Houston - Clear Lake, 2700 Bay Area Bvd, Houston, TX, 77058, USA.

Autism is the fastest growing developmental disorder in the world today. The prevalence of autism in the US has risen from 1 in 2500 in 1970 to 1 in 88 children today. People with autism present with repetitive movements and with social and communication impairments. Read More

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http://dx.doi.org/10.1186/2043-9113-2-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3507704PMC
October 2012
5 Reads

Cancer classification: Mutual information, target network and strategies of therapy.

J Clin Bioinforma 2012 Oct 2;2(1):16. Epub 2012 Oct 2.

System Biology Lab, University of Florida, Florida, USA.

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Background: Cancer therapy is a challenging research area because side effects often occur in chemo and radiation therapy. We intend to study a multi-targets and multi-components design that will provide synergistic results to improve efficiency of cancer therapy.

Methods: We have developed a general methodology, AMFES (Adaptive Multiple FEature Selection), for ranking and selecting important cancer biomarkers based on SVM (Support Vector Machine) classification. Read More

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http://dx.doi.org/10.1186/2043-9113-2-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3524788PMC
October 2012
1 Read