This course is organized with support from the IAP “Belgian Medical Genomics Initiative”, SymBioSys and the Genomics Core.

For inquiries, please email Ms Narcisse Opdekamp ( narcisse.opdekamp@uzleuven.be ).

More at >> http://gc.uzleuven.be/

https://evomics.org/2024-workshop-on-genomics/

Address of the bookmark: https://evomics.org/2024-workshop-on-genomics/

1. Accelrys Software Solution Pvt Ltd.
12th Floor, Discover, ITPL, White Field, Bangalore-65.
www.accelrys.com

2. Apticraft Systems (P) Ltd.
142, Electronics Complex, Pardeshipura, Indore – 452010 (M.P.), India
www.apticraft.com

3. Aptuit Informatics
Plot No. 100-103, Export Promotion Industrial Park, White Field, Bangalore-560066
www.aptiuit.com

4. Bigtec
J. K. Towers, 8th Block, Sangam Circle,46th Cross, Bangalore-560082.
www.bigtec.org

5. Bijam Biosciences Private Limited
Nagarjuna Hills, Hyderabad 500 082, India
www.nagarjunagroup.com

6. Bio Base Databases India Pvt Ltd.
Crescent Towers, 4th Floor, No : 32/1, Crescent Road, Bnagalore – 560 001
www.biobase-international.com

7. BioImagene India Pvt. Ltd.
4th floor, C-Wing, Godrej Eternia, Shivajinagar, Pune-411005
www.bioimagene.com

8. BioInformatics Institute Of India – Noida
C-56 A/28, Sector -62, Noida – 201 301
www.bii.in

9. CLC bio India Pvt Ltd
#Plot No. 51, H.No. 8-3-214/51, Srinivasa Nagar (West) Ameerpet Hyderabad – 500 038
www.clcbio.com/india

10. CytoGenomics India (P) Ltd.
#3004, 12A Main HAL 2nd Stage, Bangalore 560008
www.silicocyte.com

11. Genotypic Technology
211, 6th Cross, 80ft Road, RMV II Stage, Bangalore 560094
www.genotypic.co.in

12. Genvea Biosciences
Dr. D. T. Singh, CSO, 53, Craig Rd. #04-01, Singapore-089691
www.genvea.com

13. Helix Info Systems
132 A, II Floor, Sterling Towers, IV Cross Street, Sterling Road, Nungambakkam, Chennai.
www.helixinfosystems.com

14. Jalaja Technologies Pvt. Ltd.,
21/1,Victoria Layout, Victoria Road, Bangalore-47
www.jalaja.com

15. Jubilant Biosys Ltd
#96, Industrial Subrub, 2nd Stage, Yeshwanthpur, Bangalore- 560022
Jubilant Organosys Ltd.
1A, Sector 16A, Noida – 201 301 (India)
www.jubl.com

16. Kshema Technologies
#1, Global Village, Mylasandra, Mysore Road, Bangalore-560 059.
www.mphasis.com

17. LabNetworx
B-704, Gitanjali Apartments, Vikas Marg Extension, New Delhi – 110 092
www.labnetworx.com

18. LabVantage Solutions Pvt. Ltd.
Bengal Intelligent Park, Building C, 2nd Floor, Sector V, Salt Lake Electronics Complex, Kolkata – 700 091
www.labvantage.com

19. LeadInvent, 
2nd Floor, Biotech Centre, University of Delhi, South Campus, Benito Juarez Road, New Delhi 110021, India
Contact no: +91 11 24119241
Email: contact@leadinvent.com
www.leadinvent.com

20. Mascon Life Sciences
B – 8/ 10, Vasant Vihar, New Delhi 110057, India
www.masconlifesciences.com

21. Molecular Connections P Ltd
Kandala Mansion, 2/2 Kariappa Road, Near Krishna Rao Park, Basavangudi, Bangalore – 4
www.molecularconnections.com

22.Novo Informatics Pvt. Ltd.
TBIU, 2nd Floor, Synergy Building, Indian Institute of Technology, Hauz Khas, New Delhi-16.
Contact: 91-11-26581524, 91-11-26581766(Extension: 28)
Email: info@novoinformatics.com
www.novoinformatics.com

23. Ocimum Biosolutions (India) Ltd
6th Floor, Reliance Classic, Road No.1 Banjara Hills, Hyderabad 500 034, India.
www.ocimumbio.com

24. Scube Scientific Software Solutions
613, Hemkunt Chambers, 89, Nehru Place, New Delhi -110 019
www.scribeindia.com

25. Siri Technologies Pvt Ltd.
38/C -23, South End Road, Basavanagudi, Bangalore-56004.
www.siritech.com

26. Strand Life Sciences Pvt. Ltd.
#237, Sir C. V. Raman Avenue, Raj Mahal Vilas, Bangalore 560 080 INDIA
www.strandls.com

27. SooryaKiran Bioinformatics (P) Ltd
TBIC-13, Tejaswini Building, Technopark, Thriruvananthapuram- 695 584, Keralam, India

Ph: +91 471 4060979,+91 9895404104
Email: reachus@sooryakiran.com
http://www.sooryakiran.com

28. Systat Software Asia Pacific
4th Floor, Block 1, Shankar Narayan Building, No.25, MG Road, Bangalore – 560001
www.systat.com

29. ABC Genomics (India) Pvt. Ltd.
Biotech Park, Sector G, Jankipuram, Kursi Road, Lucknow-226021, U.P., INDIA
Tel +91-522-4068579, Email: director@abcgenomics.com
www.abcgenomics.com

30. en-GENE-ier's Core Technology Services,
1/340, Virat Khand, Gomtinagar, 
(Near Maharaja Agrasen Public School)
lucknow-226010, U.P., India.
http://www.bio.egicore.com/

Best of luck for your job hunts :).

About the person:

Essential criteria:

Hold or be about to obtain* a PhD in Computational biology, Bioinformatics, computing science or related subjects. (*must be obtained within 3 months of the closing date for the post) or MSc equivalent with at least 3 years' work experience in a relevant role.
Significant relevant research experience in genomics or work experience in a relevant technical/scientific role.
Significant experience in managing and analysing NGS data and other big data.
Experience in developing and maintaining analysis pipelines.
Experience working with Linux/UNIX environments.
Proficiency with python, bash, R and/or equivalent languages.
To be successful at shortlisting stage, please ensure you clearly evidence in your application how you meet the essential and, where applicable, desirable criteria listed in the Candidate Information document linked on our website.

More at https://hrwebapp.qub.ac.uk/tlive_webrecruitment/wrd/run/ETREC107GF.open

The project involves identification and characterization of transcription factors (TFs) from the Arabidopsis shoot apical meristem stem cell niche using genomic approaches and construction of a gene regulatory network for the identified TFs.

Positions: 1

Duration: 1 year but extendable up to three years based on performance and availability of funds.

Emoluments: As per DST rules.

Essential Qualifications: M.Sc. in any branch of life sciences with excellent academic record with CSIR-UGC NET or DBT-JRF. Candidate having previous work experience in the area of bioinformatics, molecular biology and genetics is preferred, but not required.

How to Apply: Applicants are requested to send a cover letter outlining previous research experiences and reasons for joining this position. Please send your complete bio-data including the cover letter as PDF attachment by email to Dr. Ram Yadav at ryadav@iisermohali.ac.in

Last date of submission is 17.00 IST, August 10, 2013.

Advertisement: www.iisermohali.ac.in/project_openings.html#29

We are looking for a highly motivated candidate with a PhD degree in
Bioinformatics or a related field. Candidates are expected to have a
strong background in evolutionary biology and/or comparative functional
genomics. Additional experiences in single cell functional genomics
analyses, statistics and computational data analyses are a plus, as is
an interest in comparative developmental (EvoDevo) questions.

We offer a dynamic and interactive research environment with state-of-the
art research facilities, good research funding and internationally
competitive salaries.

The Tschopp lab (www.evolution.unibas.ch/tschopp/research/)
studies the gene regulatory mechanisms of cell type
specification and evolution in vertebrates. See also our
preprints at https://doi.org/10.1101/2024.03.26.586769 and
https://doi.org/10.1101/2024.11.28.625862 Applications should include
a motivation letter, a CV, a list of publications, a statement about
research interests, as well as the names and contact details of at
least two referees. Applications (in the form of a single .pdf file)
should be sent to Patrick Tschopp (patrick.tschopp@unibas.ch); review
of applications will begin on January 1st 2025, and will continue until
the position is filled.

Patrick Tschopp

Genomics in India
www.ganitlabs.in
www.sandor.co.in
www.igib.res.in
www.genotypic.co.in
www.ocimumbio.com
www.abcgenomics.com
www.xcelrisgenomics.com
www.ayugen.com
www.geneombiotech.com

1. RNA-Seq Analysis Pipelines

RNA-seq is one of the most popular techniques for studying RNA. These tools streamline processing raw sequence data:

• FASTQC: For quality control of raw RNA-seq reads.
• Trimmomatic: For trimming and filtering RNA-seq reads.
• HISAT2/STAR: High-performance aligners for RNA-seq reads.
• FeatureCounts: For quantifying gene expression.
• DESeq2/EdgeR: For differential expression analysis.

2. Transcriptome Assembly and Annotation

For analyzing transcriptomes from non-model organisms or assembling novel transcripts:

• Trinity: For de novo transcriptome assembly.
• StringTie: For transcript assembly and quantification from RNA-seq alignments.
• TransDecoder: To predict coding regions within assembled transcripts.
• TAU: Tools for annotating non-coding and coding RNAs.

3. Exploring Non-Coding RNA (ncRNA)

Non-coding RNAs play critical regulatory roles. Dedicated tools for studying them include:

• Infernal: For identifying ncRNA sequences based on covariance models.
• Rfam: Database and tools for ncRNA families.
• miRDeep: For identifying microRNAs in RNA-seq datasets.

4. RNA Structure and Motif Analysis

Structural biology of RNA helps in understanding its function:

• RNAfold (ViennaRNA): Predicts secondary structures from RNA sequences.
• RNAstructure: Tools for RNA secondary structure prediction and analysis.
• MEME Suite: For identifying motifs in RNA sequences.
• IntaRNA: For RNA-RNA interaction prediction.

5. RNA Editing and Modifications

Epitranscriptomics is a growing field focusing on RNA modifications:

• REDItools: For RNA editing analysis.
• m6Aboost: For identifying m6A modifications in RNA.

6. Long-Read RNA Sequencing Analysis

Long-read technologies like Nanopore and PacBio are transforming RNA research:

• FLAIR: For isoform-level analysis of long-read RNA-seq data.
• NanoMod: For detecting modifications in RNA from Nanopore sequencing.

7. RNA-Protein Interactions

To study RNA-protein interactions and complexes:

• RBPmap: For identifying RNA-binding protein motifs.
• PARalyzer: For analyzing PAR-CLIP data.

8. Functional Enrichment Analysis

Understanding biological functions and pathways from RNA-seq data:

• getENRICH: A tool designed for pathway enrichment analysis of non-model organisms (hypergeometric P-value calculation with FDR correction).
• ClusterProfiler: For GO and KEGG pathway enrichment analysis.

9. Visualization and Data Sharing

Presenting and sharing RNA sequence analysis results effectively:

• IGV: Genome browser for visualizing RNA-seq alignments.
• Circos: Circular visualization of RNA-seq data.
• DashBio: A Python library for creating bioinformatics visualizations.

Conclusion

The bioinformatics landscape for RNA sequence analysis is vast, with tools catering to specific needs. Whether you’re studying coding RNAs, non-coding RNAs, or exploring RNA-protein interactions, the right tools can transform your data into biological insights.

The genomics platform uses cancer genome sequencing and other high-throughput techniques to identify genes critical to the development of cancer and anomalies in the genomic profile of the tumours.

For more info visit : http://oicr.on.ca/

While the expectations are not entirely off base, the reality of life as a bioinformatician is a mix of exciting discoveries, troubleshooting, and, let’s admit it, a fair amount of frustration. Here’s what it’s really like:

1. Expectation: Seamlessly Working with Perfect Datasets

Reality: You often receive messy, incomplete, or poorly annotated datasets. Hours are spent cleaning, normalizing, and validating data before you even begin your analysis. "Garbage in, garbage out" is a constant reminder in your workflow. Tools designed to handle these problems exist, but they require significant customization, which adds another layer of complexity.

2. Expectation: Effortless Multidisciplinary Integration

Reality: Bridging biology and computational science is far from straightforward. You need to be proficient in both domains while keeping up with advancements in genomics, machine learning, and statistics. Additionally, collaborating with biologists who might not be fluent in computational jargon requires patience and effective communication skills.

3. Expectation: Rapid, Groundbreaking Results

Reality: Analysis often involves waiting—waiting for scripts to run, pipelines to complete, or software to install. Bioinformatics projects are iterative; you analyze, debug, and refine repeatedly. A single project might take months to complete due to unforeseen challenges, like computational bottlenecks or the need for additional experiments.

4. Expectation: Beautiful Visualizations with a Click

Reality: While tools like R, Python, and specialized software can create stunning plots, generating a publication-ready visualization requires significant effort. You’ll spend hours tweaking axes, labels, and color palettes, ensuring clarity and accuracy.

5. Expectation: All Work, No Bugs

Reality: Debugging is an integral part of the job. Whether it’s a misconfigured server, a script throwing unexpected errors, or a pipeline breaking due to an update, you’ll develop a knack for problem-solving under pressure.

6. Expectation: Ample Time for Skill Development

Reality: Bioinformatics moves fast. Juggling ongoing projects, tight deadlines, and the constant stream of new tools and algorithms leaves little time for leisurely learning. Staying updated requires proactive effort—evenings, weekends, or dedicated study breaks.

7. Expectation: Publishing Papers Regularly

Reality: Publishing in bioinformatics is a marathon, not a sprint. Your analysis needs to be thorough, reproducible, and supported by strong biological insights. Reviewers often demand additional experiments or clarifications, stretching the timeline even further.

8. Expectation: A Clear Career Path

Reality: Bioinformatics offers diverse career paths, from academia and industry to healthcare and government. However, the choice can be daunting, with each path requiring unique skill sets and presenting different challenges. Navigating these options takes time, research, and sometimes trial and error.

Finding Joy in the Chaos

Despite these challenges, being a bioinformatician is immensely rewarding. You are at the forefront of science, enabling discoveries that impact medicine, agriculture, and the environment. The thrill of uncovering insights hidden in complex datasets and the satisfaction of solving biological puzzles make the hard work worthwhile.

Advice for Aspiring Bioinformaticians

• Embrace Learning: The field is ever-evolving. Stay curious and adaptable.
• Develop Communication Skills: Bridging the gap between biology and computation is as much about explaining your methods as it is about applying them.
• Find a Community: Collaborate with peers, join forums, and attend conferences to stay inspired and updated.
• Celebrate Small Wins: Every cleaned dataset, successful script, or informative plot is a step forward.

Bioinformatics is a blend of science, technology, and artistry. While the reality might not match the polished expectations, the journey is nothing short of exhilarating. If you’re ready to embrace the chaos and keep learning, the field of bioinformatics will never cease to amaze you.