BOL: Related items

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

BioJoker — Sun, 20 Jan 2019 06:34:36 -0600

ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome.

Address of the bookmark: https://github.com/shinout/clipcrop

vsFilt: A tool to improve virtual screening by structural filtration of docking poses

Neel — Wed, 25 Nov 2020 02:39:16 -0600

The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition, including hydrogen and halogen bonds, ionic interactions, hydrophobic contacts, π-stacking, and cation-π interactions. The web-server can process large libraries of up to 150’000 docked ligand poses. The results are web-based and can be operated on-line using the built-in HTML5 interactive analysis tools, or can be downloaded for a local use. The vsFilt is freely available on-line, no login required.

Address of the bookmark: https://biokinet.belozersky.msu.ru/vsfilt

Severus: a somatic structural variation (SV) caller for long reads

LEGE — Sun, 31 Mar 2024 02:41:27 -0500

Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT). It is designed for matching tumor/normal analysis, supports multiple tumor samples, and produces accurate and complete somatic and germline calls. Severus takes advantage of long-read phasing and uses the breakpoint graph framework to model complex chromosomal rearrangements.

If you use Severus, please cite https://www.medrxiv.org/content/10.1101/2024.03.22.24304756v1

Address of the bookmark: https://github.com/KolmogorovLab/Severus

truvari: Structural variant comparison tool for VCFs

Jit — Tue, 30 Jun 2020 21:30:44 -0500

Structural variant comparison tool for VCFs

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

Resolving the complexity of the human genome using single-molecule sequencing

Rahul Agarwal — Sat, 11 Jul 2015 12:47:34 -0500

The human genome is arguably the most complete mammalian reference assembly yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. The results in this paper https://www.genomeweb.com/sequencing/team-uses-single-molecule-sequencing-close-gaps-chart-complexity-human-reference suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology.

Address of the bookmark: http://www.nature.com/nature/journal/v517/n7536/full/nature13907.html

Queensland Centre for Medical Genomics, Grimmond Lab

Sun, 14 Jul 2013 11:58:34 -0500

Queensland Centre for Medical Genomics

Research Area:
pancreatic cancer; ovarian cancer; prostate cancer; bowel cancer; brain cancer; endometrial cancer; breast cancer; personalised medicine; high-throughput genomics

Link @ http://www.imb.uq.edu.au/sean-grimmond

Lateral Gene Transfer Is Enriched in Cancer Samples

Jitendra Narayan — Mon, 22 Jul 2013 05:13:06 -0500

There has been always a confusion on cancer and bacteria relationship. This is the first paper which shows lateral gene transfer causes cancer.

Find more at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003107

Cancer's origins revealed

Jitendra Narayan — Thu, 15 Aug 2013 13:06:56 -0500

Researchers have provided the first comprehensive compendium of mutational processes that drive tumour development. Together, these mutational processes explain most mutations found in 30 of the most common cancer types. This new understanding of cancer development could help to treat and prevent a wide-range of cancers.

More at >> http://www.sanger.ac.uk/about/press/2013/130814.html

Giovanni Parmigiani Lab

Fri, 20 Sep 2013 13:21:41 -0500

Scientific Interests:

Models and software for predicting who is at risk of carrying genetic variants that confer susceptibility to cancer. Application to breast, ovarian, colorectal, pancreatic and skin cancer.

Statistical methods for the analysis of high throughput genomic data: analysis of cancer genome sequencing projects; integration of genomic information across technologies; cross-study validation of genomics results.

Statistical methods for comparative effectiveness research: comprehensive models for lifetime history of chronic disease outcomes; Bayesian meta-analysis; Bayesian causal inference; decision analysis.

Bayesian modeling and computation: multilevel models; decision theoretic approaches to inference; sequential experimental design and their application to adaptive and multistage studies in clinical and epidemiological research.

http://bcb.dfci.harvard.edu/~gp/index.html

http://scholar.google.com/citations?user=OlpYP3UAAAAJ&hl=en

04- Informatics Approach to Cancer - Interview with Dr. Joel Saltz

Mon, 07 Oct 2013 14:35:43 -0500

For additional information visit http://www.cancerquest.org/joel-saltz-interview. Dr. Joel Saltz is a Professor in the Departments of Pathology, Biostatistics and Bioinformatics, and Mathematics and Computer Science at Emory University. Dr. Saltz's research on bioinformatics spans several disciplines. One project involves applying computer analysis to medical imaging to yield better results for patients. As an example, a computer program may able to help doctors detect small cancers in a CT scan or mammogram. In this interview segment, Dr. Saltz discusses the informatics approach to cancer. To learn more about cancer and watch additional interviews, please visit the CancerQuest website at http://www.cancerquest.org.