We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals;

Address of the bookmark: http://www.bx.psu.edu/miller_lab/car/

Courses

Old courses (2012-2014)

Metagenomics Workshop

2015 November - Uppsala
2016 November - Uppsala
2017 November - Uppsala

Introduction to Bioinformatics Using NGS Data

2015 February - Uppsala 
2015 May - Gothenburg
2015 September - Uppsala
2015 November - Lund
2016 January - Uppsala
2016 April - Linköping
2016 September - Uppsala
2016 November - Umeå
2017 January - Uppsala
2017 May - Gothenburg
2017 September - Lund
2017 November - Uppsala
2018 February - Uppsala

Introduction to Genome Annotation

2015 April - Uppsala
2016 April - Uppsala
2017 April - Uppsala
2018 May - Uppsala

De Novo Genome Assembly

2016 November - Uppsala
2017 November - Uppsala

RNA-seq course

2015 October - Uppsala
2016 April - Uppsala
2016 October - Uppsala
2017 March - Uppsala
2017 November - Uppsala
RNAseq tutorials

R Programming Foundations for Life Scientists

2016 November - Uppsala
2017 Mars - Uppsala

Single cell RNA sequencing analysis

2017 October - Uppsala

Address of the bookmark: https://scilifelab.github.io/courses/

Analysis of regulatory sequences (RSAT project)
Classification and analysis of mobile genetic elements (ACLAME project).
Analysis of molecular interaction networks (NeAT project)
Inference of metabolic pathways from genomic and post-genomic data
(metabolic pathfinding, see also metabolic pathfinding in NeAT)
Critical assesment of protein interactions (CAPRI)

Lab Page http://www.bigre.ulb.ac.be/

Workshops are conducted in regular intervals on Drug Designing, Protein Modeling and Simulation, Chemoinformatics, Bioinformatics etc.The workshops are highly beneficial for working professionals, students, researcher for enhancements of the skills in short duration.

More at https://pubmed.ncbi.nlm.nih.gov/20494974/

Address of the bookmark: http://www.sequenceontology.org/cgi-bin/soba.cgi

WALK-IN-INTERVIEW

A walk-in-Interview is proposed to be held at National Bureau of Animal Genetic Resources, Karnal (Haryana)-132001 at 11:30 AM on 18.12.2013 to select One RA and One SRF as per details given below:

1. One post of Research Associate under DBT sponsored Support under BIPP for the “SanGenix: A comprehensive Next Generation Sequence (NGS) data analysis solution” as Grants in AID. Thepost duration is Upto 31st March 2015 or earlier.

2. One post of Senior Research Fellow under NAIP (Component-4) Bioprospecting of genes and allele mining for abiotic stress tolerance. The post duration is Upto 31st March 2014 or earlier

Essential Qualifications: Ph.D. in Bioinformatics/ Computer Application or
First Class Masters degree in Bioinformatics/ Computer Application with two years experience as evidenced by Publications.

Desirable: Experience in the field of handling Next generation Sequencing Data.

Emolument: Rs. 22,000/- per month + HRA as per admissibility

Age Limit:

40 years for Men
45 years for women as on date of interview

Research Associate: ONE

Duration of engagement: Upto

31st March 2015 or earlier & Coterminus with the project

Responsibilities: To help the PI for Beta testing and development of the SanGenix Tool for NGS data.

Essential Qualifications: First Class Masters’ degree in Bioinformatics/Biotechnology.

Desirable: Experience in the field of Biotechnology/ Bioinformatics

Emoluments:

Rs. 16,000/- per month + HRA as per admissibility.
Senior Research Fellow: ONE
Duration of engagement: Upto 31st March 2014 or earlier & Coterminus with the project

Age Limit

35 years for men
40 years for women as on date of interview

Note: Relaxation in age will be admissible for SC/ST & OBC candidates as per Govt. of India /ICAR norms

1. The applicants must bring with them original documents and brief of research work done during post graduation along with a set of photocopy and latest two passport size photographs.
2. A panel of selected candidates will also be made which may be utilized for filling of positions of shorter durations in future if demand arises.
3. Experience certificate in original, if any 4. The above positions are purely on temporary basis and are co-terminus with the project. No TA/DA will be paid to attend the interview.
5. Any other clarifications can be had on the date of interview.
6. The Director’s decision will be final and binding on all respects.

Advertisement: http://210.212.93.85/rasrfadvertise.pdf

More at https://boards.greenhouse.io/twistbioscience/jobs/3135495?gh_src=9ecc0b941us

Classificier of reads from metagenomic sequencing experiments.

•  Kawulok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE, 2015; 10(4):1–23,

CoMSA

Compressor of multiple sequence alignments of proteins.

•  Deorowicz, S., Walczyszyn, J., Debudaj-Grabysz, A., CoMSA: compression of protein multiple sequence alignment files, Bioinformatics, 2019; 35(2):22–234,

DSRC

Compressor of sequencing reads.

•  Roguski, L., Deorowicz, S., DSRC 2: Industry-oriented compression of FASTQ files, Bioinformatics, 2014; 30(15):2213–2215,
•  Deorowicz, S., Grabowski, Sz., Compression of DNA sequences in FASTQ format, Bioinformatics, 2011; 27(6):860–862,

FAMSA

Multiple sequence alignment designed for huge families of proteins (even containing hundreds of thousands of sequences).

•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., FAMSA: Fast and accurate multiple sequence alignment of huge protein families, Scientific Reports, 2016; 6(33964):

FaStore

Compressor of FASTQ files.

•  Roguski, L., Ochoa, I., Hernaez, M., Deorowicz, S., FaStore - a space-saving solution for raw sequencing data, Bioinformatics, 2018; 34(16):2748–2756,

FQSqueezer

Experimental high-end compressor of FASTQ files.

•  Deorowicz, S., FQSqueezer: k-mer-based compression of sequencing data, Scientific Reports, 2020; 10(578):

GDC

Compressor of collections of genome sequences.

•  Deorowicz, S., Danek, A., Niemiec, M., GDC 2: Compression of large collections of genomes, Scientific Reports, 2015; 5(11565):1–12,
•  Deorowicz, S., Grabowski, Sz., Robust relative compression of genomes with random access, Bioinformatics, 2011; 27(21):2979–2986,

GTC

Genotype databases compressor with support for fast queries.

•  Danek, A., Deorowicz, S., GTC: how to maintain huge genotype collections in a compressed form, Bioinformatics, 2018; 34(11):1834–1840,

GTShark

Genotypes compressor.

•  Deorowicz, S., Danek, A., GTShark: Genotype compression in large projects, Bioinformatics, 2019; 35(22):4791–4793,

KMC

Memory frugal k-mer counter.

•  Kokot, M., Długosz, M., Deorowicz, S., KMC 3: counting and manipulating k -mer statistics, Bioinformatics, 2017; 33(17):2759–2761,
•  Deorowicz, S., Kokot, M., Grabowski, Sz., Debudaj-Grabysz, A., KMC 2: Fast and resource-frugal k-mer counting, Bioinformatics, 2015; 31(10):1569–1576,
•  Deorowicz, S., Debudaj-Grabysz, A., Grabowski, Sz., Disk-based k-mer counting on a PC, BMC Bioinformatics, 2013; 14():Article no. 160,

Kmer-db

Tool for estimation of evolutionary distances in a collection of genomes.

•  Deorowicz, S., Gudys, A., Dlugosz, M., Kokot, M., Danek, A., Kmer-db: instant evolutionary distance estimation, Bioinformatics, 2019; 35(1):133–136,

MuGI

Index allowing queries for a collection of multiple genome sequences.

•  Danek, A., Deorowicz, S., Grabowski, Sz., Indexes of Large Genome Collections on a PC, PLOS ONE, 2014; 9(10):e109384,

ORCOM

Experimental compressor of sequencing reads.

•  Grabowski, Sz., Deorowicz, S., Roguski, L., Disk-based compression of data from genome sequencing, Bioinformatics, 2014; 31(9):1389–1395,

PgSA

Index allowing queries for a collection of sequencing reads.

•  Kowalski, T., Grabowski, Sz., Deorowicz, S., Indexing arbitrary-length k-mers in sequencing reads, PLOS ONE, 2015; 10(7):1–16,

QuickProbs

Multiple sequence alignment designed especially for GPU.

•  Gudys, A., Deorowicz, S., QuickProbs 2: towards rapid construction of high-quality alignments of large protein families, Scientific Reports, 2017; 7(41553):
•  Gudys, A., Deorowicz, S., QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors, PLOS ONE, 2014; 9(2):e88901,

RECKONER

Read error corrector.

•  Maciej Długosz, M., Deorowicz, S., RECKONER: read error corrector based on KMC, Bioinformatics, 2017; 33(7):1086–1089,

TGC

Compressor of collections of genomes given in Variant Call Format (VCF) files.

•  Deorowicz, S., Danek, A., Grabowski, Sz., Genome compression: a novel approach for large collections, Bioinformatics, 2013; 29(20):2572–2578,

VCFShark

Compressor of VCF files.

•  Deorowicz, S., Danek, A., GTShark: Genotype compression in large projects, biorxiv.org, 2020; ():

Whisper

Experimental mapper of whole genome sequencing data.

•  Deorowicz, S., Gudys, A., Whisper 2: indel-sensitive short read mapping, bioRxiv.org, 2019; :
•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz., Whisper: read sorting allows robust robust mapping of DNA sequencing data, Bioinformatics, 2019; 35(12):2043–2050,
•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz., Robust mapping of whole genome sequencing data, Poster at The Biology of Genomes Conference, 2017;

This is a fixed term post for 36 months.

We wish to recruit a highly motivated, postdoctoral scientist to carry out a BBSRC funded project in the laboratory of Dr. Denis Larkin. The project is focused on developing and applying new algorithms to study genome and chromosome evolution in birds, mammals and other vertebrate species using whole-genome sequences and existing algorithms. The post holder will use cutting edge computational and laboratory approaches to generate chromosomal assemblies for sequenced genomes, study chromosomal structures and genome differences between bird and other vertebrate species in attempt to identify species- and clade-specific genome signatures.

Applicants must have a Ph.D. and a track record of success, as indicated by first-author publications in international journals. They must possess excellent organisation skills and be capable of individual initiative and of interacting as part of a team. Applicants with extensive practical experience in bioinformatics or computer science, programming, visualization, handling of large data sets, high-performance computing are encouraged to apply. The post will involve collaboration with a wide range of academic partners both within the UK, EU and worldwide. In addition to leading their own project the post holder will have opportunities to contribute to multiple international genome initiatives.

Experience in programming, bioinformatics and comparative genome analysis is essential. Applicants should have a minimum of a degree and preferably a higher degree in a relevant subject.

The Royal Veterinary College has the largest range of veterinary, para-veterinary and animal science undergraduate and postgraduate courses of any veterinary school in the world and is one of the largest veterinary schools in Europe.

Prospective applicants are encouraged to contact Dr. Denis Larkin, Comparative Biomedical Sciences Department on +442071211906 or email: dlarkin@rvc.ac.uk

We offer a generous reward package.

For further information and to apply on-line please visit our website: www.rvc.ac.uk
Job reference CBS-0025-14A

Closing date: 4 July 2014
Interviews are likely to be held in July 2014

We promote equality of opportunity and diversity within the workplace and welcome applications from all sections of the community.

Current computational interests:

Systematic analysis of genetic epistasis to identify redundant or compensatory systems and to reveal order of action in genetic pathways.
Using knockout, knockdown, or overexpression, or other perturbation experiments in combinations of genes in S. cerevisiae, C. elegans or mouse.
Using genome-scale genotyping of natural polymorphisms in S. cerevisiae and human populations.
Alternative splicing and its relationship to protein interaction networks.
Integrating large-scale studies including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns to quantitatively assign function to genes and guide experimentation.

More at http://llama.mshri.on.ca/index.html