http://www.atherosclerosis-journal.com/article/S0021-9150(18)30024-8/fulltext DOI: http://dx.doi.org/10.1016/j.atherosclerosis.2018.01.024 Atherosclerosis, manuscript in the press, accepted 16 January, 2028 Thidathip Wongsurawat, Chin Cheng Woo, Antonis Giannakakis, Xiao Yun Lin, Esther Sok Hwee Cheow, Chuen Neng Lee, Mark Richards, Siu Kwan Sze, Intawat Nookaew, Vladimir A. Kuznetsov’Correspondence information about the author Vladimir A. Kuznetsov, Vitaly Sorokin Abstract Background and aims: We aim to […]
Publications
Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D
Introduction: The genome of the most well studied eukaryotic model organism, Saccharomyces cerevisiae strain S288c, was sequenced and released in 1996; it was the first complete, high quality genome sequence of an eukaryal organism (1). Since then, the development ofDNAsequencing technologies has yielded scientific breakthroughs that enable us to obtain and analyze genomic DNA sequences […]
Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)
http://onlinelibrary.wiley.com/doi/10.1002/ece3.3638/full Ecology and Evolution, (2018), 8:185-196. DOI: 10.1002/ece3.3638 Michael S. Robeson II, Kamil Khanipov, George Golovko, Samantha M. Wisely, Michael D. White, Michael Bodenchuck, Timothy J. Smyser, Yuriy Fofanov, Noah Fierer, Antoinette J. Piaggio Abstract Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to […]
13: The Role of Axiomatically-Rich Ontologies in Transforming Medical Data to Knowledge
Stud Health Technol Inform. 2018;249:38-49 Brochhausen M, Bona J, Blobel B Abstract In the biomedical domain, there exist a number of common data models (CDM) that have experienced wide uptake. However, none of these has emerged as the common model. Recently, the demand for integrating and analyzing increasingly large data sets in clinical and translational research […]
Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics
https://doi.org/10.1016/j.ygeno.2017.03.001 Subazini Thankaswamy-Kosalai, Partho Sen, Intawat Nookaew Abstract Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, […]
Insights from Comparative Genomics of the Genus Salmonella
Submitted: May 5th 2016 | Reviewed: December 1st 2016 | Published: April 5th 2017 | DOI: 10.5772/67131 Trudy M. Wassenaar, Se-Ran Jun, Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew, Katrina Schlum, Michael R. Leuze and David W. Ussery Abstract Comparative genomics have become a standard approach to gain insights into the inter – relationships of microorganisms. […]
Host diabetes status is the major regulator of gut microbiome in the UCD-T2DM Rat
The FASEB Journal 31 (1 Supplement), 138.1-138.1(2017) Brian Piccolo, James Graham, Umesh Wankhade, Intawat Nookaew, Kartik Shankar, Peter Havel, Sean Adams Abstract There is strong evidence in humans and in animal models that the gut microbiome is altered in obesity and/or the insulin resistant condition. Poor metabolic health is often linked to overnutrition and poor-quality […]
Bi-allelic inactivation is more prevalent at relapse in multiple myeloma, identifying RB1 as an independent prognostic marker
Received: 27 December 2016 | Accepted: 13 January 2017 | Published: 24 February 2017 | DOI: https://doi.org/10.1038/bcj.2017.12 Chavan SS, He J, Tytarenko R, Deshpande S, Patel P, Bailey M, Stein CK, Stephens O, Weinhold N, Petty N, Stewart D, Rasche L, Bauer M, Ashby C, Peterson EA, Ali S, Ross J, Miller VA, Stephens P, […]
GSAR: Bioconductor package for Gene Set analysis in R
BMC Bioinformatics BMC series | DOI: https://doi.org/10.1186/s12859-017-1482-6 Yasir Rahmatallah, Boris Zybailov, Frank Emmert-Streib, Galina Glazko Abstract Gene set analysis (in a form of functionally related genes or pathways) has become the method of choice for analyzing omics data in general and gene expression data in particular. There are many statistical methods that either summarize gene-level […]
Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer
Sci Rep. 2017 Jan 19;7:40712. doi: 10.1038/srep40712. PubMed PMID: 28102365; PubMed Central PMCID: PMC5244389 Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery & Intawat Nookaew Abstract The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained […]