A position for a doctoral candidate is available in Leila Taher’s new lab at the Institute for
Biomedical Informatics at Graz University of Technology (Austria, https://www.bioinfo.tugraz.at).
We develop and apply regulatory genomics and systems biology approaches to analyze large
genomic datasets. Our long-term goal is to gain novel insights into the mechanisms and
evolution of differential gene expression

Link:
https://www.tugraz.at/fileadmin/user_upload/tugrazExternal/1565e0f6-6c94-4077-a118-f84bc91c4b07/Stellenausschreibung_Bioinfo_FWF_Jan2020_EN.pdf

The BeadChip was developed in collaboration with leading ovine researchers from AgResearch, Baylor UCSC, CSIRO, and the USDA as part of the International Sheep Genomics Consortium. It features over 54,241 evenly spaced probes that target single nucleotide polymorphisms (SNPs). More than 18,000 of these markers were discovered through sequencing reduced representation libraries with the Illumina Genome Analyzer IIx. A set of 600 SNPs were identified by BAC end sequencing and validated with Illumina GoldenGate Genotyping Assays over 403 animals from 23 breeds. The remaining SNPs were derived from the draft ovine genome.

Read more @

http://res.illumina.com/documents/products/datasheets/datasheet_ovinesnp50.pdf

http://www.illumina.com/products/ovinesnp50_dna_analysis_kit.ilmn

Address of the bookmark: https://github.com/hugheslab/snpgenie

Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical for large error prone genomes which makes the assembly process produce an excessive number of false positive cycles.  Our solution is to search the graph in multicores shared memory parallel mode using graph decomposition then use filtering method to generate good quality SNPs.

https://arxiv.org/abs/1809.06700

https://github.com/redayounsi/2KP2P

/2kp2omp/bin/main_2kp2_K63_C2 -i fastq_files.txt -o fungus_bub.fasta -r stat_fungus.txt -c cov_fungus_hash.txt -k 63 -h 20 -b 100 -g 600 -l 100 -f 16 -t 5.0 -x 1 -v 0 -p 1 -y 1 -u 1

 

Address of the bookmark: https://github.com/redayounsi/2KP2P

The variant should be transmitted from its original location to another "geographically distinct population"—say, another country or a province of a large and populous country.
It should differ from its ancestor by at least one nucleotide.
At least 95% of its genetic code should have been sequenced at least five times from different samples.

Address of the bookmark: https://github.com/sbg/geck

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

NCBI Hackathon specifically looking for folks who have experience in computational virus hunting or adjacent fields to identify known, taxonomically-definable and novel viruses from a few hundred thousand metagenomic datasets that we’ll put on cloud infrastructure. This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. If this describes you, please apply! The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).

https://ncbiinsights.ncbi.nlm.nih.gov/2018/11/09/ncbi-sdsu-virus-hunting-data-science-hackathon-january-2019/

https://www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.html

Address of the bookmark: https://www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.html