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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
About me
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Posts
Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
portfolio
publications
Immune DNA signature of T-cell infiltration in breast tumor exomes
Published in Scientific Reports, 2016
This paper describes a method to identify CDR3 reads in a breast tumor exome and validate it using deep TCRB sequencing in 1,078 TCGA breast cancer exomes.
Download here
Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States
Published in Annals of the New York Academy of Sciences, 2016
This paper investigates the common practices in accessing biomedical data and ethical aspects of genome privacy
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PREMIX: Privacy-preserving EstiMation of individual admixture
Published in AMIA Annual Symposium Proceedings, 2017
This paper describes a framework: PRivacy-preserving EstiMation of Individual admiXture (PREMIX) using Intel software guard extensions (SGX).
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An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
Published in BMC Bioinformatics, 2017
In this study, we evaluated the performance of the most recent and commonly used CNV detection tools for WES data in cancer to address their limitations and provide guidelines for developing new ones. We focused on the tools that have been designed or have the ability to detect cancer somatic aberrations.
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Creating a scalable deep learning based Named Entity Recognition Model for biomedical textual data by repurposing BioSample free-text annotations
Published in BioRxiv, 2018
This paper evaluated the potential of using natural language processing method to find namely data sets consisting of short-phrases and long sentences in biomedical metadata.
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Integrative genomic analysis of mouse and human hepatocellular carcinoma
Published in PNAS (Proceedings of the National Academy of Sciences of the United States of America), 2018
Hepatocellular carcinoma (HCC) research has been hampered by the absence of consensus mouse models with clearly defined molecular features faithfully recapitulating human HCC. Here we tackle this gap by implementing a cross-species comparative analysis between a large cohort of patients and four diverse mouse models focused on clinically and therapeutically relevant aspects of genomic and transcriptomic profiles and propose two of these models as valid for the study of different stages of human HCC.
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Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive
Published in Pacific Symposium on Biocomputing, 2019
This study provides a rich database of known human variants across SRA samples that can support future meta-analyses of human sequence variation.
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Food-Intake Normalization of Dysregulated Fatty Acids in Women with Anorexia Nervosa
Published in Nutrients, 2019
This paper describes the investigation of the effect of abnomal metabolism of fatty acids (FAs) to anorexia nervosa (AN) patients. We found that intake and AN status modified the correlations of FAs with body mass index (BMI), depression, and anxiety. Specifically, FAs dysregulations correlate with worsened symptoms of AN.
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talks
Tutorial 1 on Relevant Topic in Your Field
Published in University 1, Department, 2013
This is a description of your workshop, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Talk 2 on Relevant Topic in Your Field
Published in University 1, Department, 2014
This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published in University 1, Department, 2014
This is a conference proceedings talk, for when you give a talk at a conference that archives talks as publications. When the talk_type variable is set to “Conference proceedings talk”, this talk will appear in the Talks page in /talks/, but it will not appear in the Talks section in the /cv/ page. The reason for this is that the conference proceedings talk should have a seprate publications .md file in the /_publications/ folder, which will go in the publications section. You can change this behavior by modifying the /_pages/cv.md file.
An Introduction to Testing
Published in Test University, Department of Testing Science, 2016
This talk is an introduction to Testing.
teaching
Teaching experience 1
Published in University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Published in University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.