<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/23838?offset=420 https://bioinformaticsonline.com/blog/view/44705/pirna-and-bioinformatics-decoding-the-guardians-of-the-genome Sat, 07 Dec 2024 02:15:11 -0600 https://bioinformaticsonline.com/blog/view/44705/pirna-and-bioinformatics-decoding-the-guardians-of-the-genome <![CDATA[piRNA and Bioinformatics: Decoding the Guardians of the Genome]]> In the symphony of small RNAs, PIWI-interacting RNAs (piRNAs) stand out as the protectors of genomic integrity. These small, non-coding RNAs play critical roles in silencing transposable elements, regulating gene expression, and maintaining germline stability. The rise of bioinformatics has revolutionized our understanding of piRNAs, enabling researchers to decipher their biogenesis, functions, and evolutionary significance.

What Are piRNAs?

piRNAs are the largest class of small non-coding RNAs, typically 24–32 nucleotides in length. Unlike microRNAs (miRNAs) and small interfering RNAs (siRNAs), piRNAs do not rely on Dicer enzymes for maturation. Instead, they are processed from long single-stranded precursors and associate with PIWI proteins, a subclass of the Argonaute protein family.

The primary functions of piRNAs include:

  1. Silencing Transposable Elements: By targeting transposons, piRNAs prevent genomic instability, particularly in germline cells.
  2. Regulating Gene Expression: piRNAs modulate gene expression at transcriptional and post-transcriptional levels.
  3. Epigenetic Modulation: They guide epigenetic modifications, such as DNA methylation, to specific genomic loci.

Challenges in piRNA Research

Studying piRNAs is fraught with challenges, including:

  • Short Length: Their small size complicates sequencing and alignment.
  • Lack of Sequence Conservation: Unlike miRNAs, piRNAs exhibit limited sequence conservation across species.
  • Complex Biogenesis: The intricate pathways of piRNA generation require sophisticated computational tools to unravel.

Bioinformatics: Illuminating the World of piRNAs

Bioinformatics has emerged as an indispensable tool for studying piRNAs, facilitating their discovery, annotation, and functional analysis. Here's how bioinformatics is transforming piRNA research:

1. Identification and Annotation

The discovery of piRNAs relies on next-generation sequencing (NGS) data. Bioinformatics tools such as piRNApredictor and Piano identify piRNA clusters and predict potential targets. Databases like piRBase and piRNAdb curate information about known piRNAs, their sequences, and associated proteins.

2. Mapping and Alignment

piRNAs often originate from repetitive regions, making their alignment challenging. Tools like Bowtie and STAR handle the unique mapping requirements of piRNAs, enabling accurate identification of piRNA clusters in genomes.

3. Functional Analysis

Bioinformatics approaches predict piRNA functions by analyzing their interactions with transposons, genes, and epigenetic marks. Algorithms such as TargetFinder and RIblast explore piRNA-mRNA interactions, shedding light on regulatory networks.

4. Evolutionary Studies

piRNAs are evolutionarily diverse, reflecting their roles in species-specific genomic defense. Comparative genomics tools help trace the evolution of piRNA clusters and their associated PIWI proteins across species.

5. Epigenomic Insights

piRNAs are key players in epigenetic regulation. Bioinformatics pipelines integrate piRNA data with chromatin immunoprecipitation sequencing (ChIP-seq) and DNA methylation data to uncover their role in shaping the epigenome.

Case Study: piRNAs in Germline Integrity

One of the hallmark functions of piRNAs is the suppression of transposable elements in the germline. For example, in Drosophila melanogaster, piRNAs target retrotransposons like gypsy and copia. Bioinformatics analyses revealed that these piRNAs guide PIWI proteins to transposon-derived RNA, ensuring genome stability during gametogenesis.

Clinical Relevance of piRNAs

Recent studies suggest that piRNAs may serve as biomarkers for diseases such as cancer, infertility, and neurodegenerative disorders. For instance:

  • Cancer: Dysregulated piRNA expression has been linked to tumorigenesis, making them potential targets for cancer therapies.
  • Infertility: Aberrant piRNA pathways are implicated in male infertility due to their role in spermatogenesis.
  • Neurodegeneration: piRNAs may regulate neuronal gene expression, highlighting their potential in neurological research.

Future Directions

The integration of bioinformatics with emerging technologies offers exciting opportunities for piRNA research:

  • Single-Cell Sequencing: Unveiling cell-specific piRNA expression and function.
  • Machine Learning: Predicting piRNA functions and targets with greater accuracy.
  • CRISPR-Based Tools: Editing piRNA clusters to explore their roles in vivo.

Conclusion

piRNAs are the unsung guardians of the genome, safeguarding genetic material from transposable elements and contributing to gene regulation and epigenetic programming. Bioinformatics has opened the floodgates of discovery, unraveling the complexities of piRNAs and their myriad roles in biology and disease.

As we continue to decode the piRNA landscape, these small RNAs promise to unveil big secrets about genome stability, evolution, and human health, cementing their place as a fascinating frontier in molecular biology.

]]> LEGE https://bioinformaticsonline.com/blog/view/44770/nvidia-and-arc-institute-unveil-evo-2-a-breakthrough-ai-for-dna-design Fri, 21 Feb 2025 10:39:47 -0600 https://bioinformaticsonline.com/blog/view/44770/nvidia-and-arc-institute-unveil-evo-2-a-breakthrough-ai-for-dna-design <![CDATA[NVIDIA and Arc Institute Unveil Evo 2: A Breakthrough AI for DNA Design]]> NVIDIA and the Arc Institute have introduced Evo 2, a groundbreaking AI model designed to understand, predict, and generate DNA sequences. This marks a major advancement in computational biology, offering scientists an unprecedented tool to decode the genetic blueprint of life and even design entirely new biological systems.

The Power of Evo 2: AI Meets DNA

Evo 2 is the largest AI model for biology ever created, trained on an astonishing 9.3 trillion DNA "letters" (nucleotides) carefully selected from genomes spanning the entire tree of life. This massive dataset ensures that Evo 2 can recognize patterns and relationships in genetic sequences at an unparalleled scale.

For the first time, scientists can design DNA with AI, moving beyond simple sequence analysis to active DNA generation. Evo 2 enables researchers to predict, modify, and even create entire genetic sequences, opening new possibilities in medicine, agriculture, and synthetic biology.

Decoding the Dark Genome

One of the biggest challenges in genetics is understanding the non-coding regions of DNA—vast stretches of the genome that do not code for proteins but play crucial roles in regulating gene expression. These regions control when and how genes are activated, influencing everything from development to disease.

Evo 2 is designed to decode these non-coding elements, helping researchers uncover their functions and use this knowledge to develop gene-based therapies, synthetic life forms, and precision agriculture solutions.

From Reading DNA to Writing It

To put Evo 2’s impact into perspective:

  • Previous AI models could "read" DNA like a book, analyzing genetic sequences and identifying patterns.
  • Evo 2 can "write" entirely new DNA, designing functional genes, chromosomes, and even full genomes from scratch.

This means scientists can now engineer biological systems with AI, designing new proteins, metabolic pathways, and genetic circuits to address real-world challenges.

A Step Toward Generative Biology

The Arc Institute describes Evo 2 as a major step toward "generative biology"—a revolutionary approach where AI is used to create novel biological structures rather than just analyzing existing ones. This could lead to breakthroughs such as:

  • New medicines: AI-generated enzymes and proteins tailored for targeted therapies.
  • Disease-resistant crops: Genetically optimized plants for higher yield and climate resilience.
  • Synthetic organisms: Custom-designed microbes for bioremediation, biofuel production, and industrial applications.

An Open-Source Revolution

Unlike many proprietary AI models, Evo 2 is open source, making its capabilities accessible to researchers worldwide. This democratization of AI-driven biology means that scientists from different disciplines can collaborate, experiment, and innovate, accelerating discoveries in genetic engineering and synthetic biology.

With Evo 2, the boundaries of what’s possible in DNA design, genetic engineering, and biological innovation are being redrawn. The future of life sciences is no longer just about understanding life’s code—it’s about writing it.

]]> BioStar https://bioinformaticsonline.com/news/view/2645/dna-bending-propensity-in-the-presence-of-base-mismatches-implications-for-dna-repair Mon, 19 Aug 2013 16:01:44 -0500 https://bioinformaticsonline.com/news/view/2645/dna-bending-propensity-in-the-presence-of-base-mismatches-implications-for-dna-repair <![CDATA[DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair]]> Understanding how the human body recognizes damaged DNA and initiates repair fascinates Michael Feig, professor of biochemistry and molecular biology at Michigan State University. Feig studies the proteins MutS and MSH2-MSH6, which recognize defective DNA and initiate DNA repair. Natural DNA repair occurs when proteins like MutS (the primary protein responsible for recognizing a variety of DNA mismatches) scan the DNA, identify a defect, and recruit other enzymes to carry out the actual repair.

Results from computer simulations show that it is energetically less expensive to bend mismatch-containing, defective DNA (G:T, C:C, C:T, G:A, G:G, T:T, A:A, A+:C) vs. non-defective DNA (containing A:T or G:C base pairs). DNA repair mechanisms likely take advantage of this feature to detect defective DNA based on an increased bending propensity.

http://www.tacc.utexas.edu/news/feature-stories/2013/how-dna-repair-helps-prevent-cancer

http://pubs.acs.org/doi/abs/10.1021/jp403127a

]]> Jitendra Narayan https://bioinformaticsonline.com/researchlabs/view/4656/pandey-lab Fri, 20 Sep 2013 13:19:18 -0500 <![CDATA[Pandey Lab]]> The Pandey Lab at Johns Hopkins University is a Systems Biology lab that combines molecular biology, analytical chemistry and computational biology with various "Omics" technologies including genomics and proteomics to understand signaling pathways and to identify therapeutic targets and biomarkers in a number of cancers.

More at http://pandeylab.igm.jhmi.edu/

http://scholar.google.com/citations?user=OhuG0FcAAAAJ&hl=en

]]> https://bioinformaticsonline.com/opportunity/view/13338/protein-function-annotation-and-machine-learning-upmc-paris-france Sat, 02 Aug 2014 01:22:52 -0500 <![CDATA[Protein function annotation and machine learning - UPMC - Paris, France]]> Protein function annotation and machine learning - UPMC - Paris, France

Job Description: We are interested in finding an excellent postdoc with interests in protein functional annotation, machine learning and computer grids. The position is open for 3.5 years at the Université Pierre et Marie Curie, in the heart of paris.

Research topic: Protein function annotation, multiple probabilistic models, domain architecture, machine learning, combinatorial optimization, computer grid.

Title: A novel integrative platform for large scale protein annotation that exploits a multitude of diversified probabilistic models in several protein signature databases.

We propose a novel integrated approach for large scale protein annotation that will exploit an unprecedented amount of genomic data as well as sophisticated machine learning techniques and combinatorial optimization approaches taking advantages of High Performance Computing (HPC) environments. The idea is to uncover as much as possible the evolutionary processes of protein sequences that took place throughout the whole tree of life and that affected the evolution of a protein family. We have already demonstrated in a previous work that the problem of functional annotation is inherent to the ability of uncovering such paths. Now, we shall extend this approach to large scale genome annotation by considering 11 different protein databases, constituted by about 10^9 protein sequences, and by producing a large pool of diversified probabilistic models coding for about 10^7 evolutionary protein pathways. Such models will be used to search for specific domains in genomes to be annotated. Our previous methodology needs to be fundamentally improved to deal with this large amount of biological data. In this project, we shall work on the algorithms to reduce the space of models and the search complexity, and we shall implement some important algorithmic changes towards the realization of a powerful integrated annotation tool.

Where: This project is run on the Laboratoire de Biologie Computationnelle et Quantitative UMR7238 CNRS-UPMC – Analytical Genomics team, headed by A.Carbone. It is co-advised with Pierre-Henri Wuillemin, Laboratoire d’Informatique de Paris 6 – Equipe DECISION.

Start date: September 1st, 2014
Contact Person: Alessandra Carbone
Contact: alessandra.carbone@lip6.fr

]]> https://bioinformaticsonline.com/pages/view/18749/list-of-biotechnology-research-laboratory-university-and-centre-in-india Thu, 30 Oct 2014 12:34:34 -0500 https://bioinformaticsonline.com/pages/view/18749/list-of-biotechnology-research-laboratory-university-and-centre-in-india <![CDATA[List of Biotechnology Research Laboratory, University, and Centre in India]]> DEPARTMENT OF BIOTECHNOLOGY

INDIAN COUNCIL OF MEDICAL RESEARCH (ICMR)

COUNCIL OF SCIENTIFIC & INDUSTRIAL RESEARCH (CSIR)

 

CITYWISE

City Wise Llist of Govt. and Non Govt. Research institutions in India -

Ahmedabad

Allahabad

Bangalore

Barrackpore (W. B.)

· Central Inland Capture Fisheries Research Institute

Bhopal

Bhubaneswar

Calcutta

Chandigarh

Chennai (Madras)

Delhi

Dehradun

Dirang (Arunachal Pradesh)

Durgapur

Eluru (A. P.)

Gandhi Nagar

Goa

Hyderabad

Indore

Jammu

Jhansi (U. P)

Jodhpur (Rajasthan)

Kanpur

Kasaragod

Kharagpur

Kochi

Lucknow

Mathura

Mumbai (Bombay)

Palakkad

Palampur (H.P.)

Peechi

Pilani

Puttur (Karnataka)

Pune

Roorkie (U. P.)

Trivandrum (Thiruvananthapuram)

Varanasi (U. P.)

· Indian Institute of Vegetable Research

 

UNIVERSITIES/COLLEGES UNDER UGC

DST

•  Agharkar Research Institute, Pune

•  Birbal Sahni Institute of Palaeobotany, Lucknow

•  Bose Institute, Kolkata

•  Indian Association for the Cultivation of Science, Kolkata

•  International Advanced Research Centre for Powder Metallurgy and New Materials,
...esr ...Hyderabad

•  Indian Institute of Astrophysics, Bangalore

•  Indian Institute of Geomagnetism, Mumbai

•  Indian Institute of Tropical Meteorology, Pune

•  Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore

•  National Accreditation Board for Testing & Calibration Laboratories, New Delhi

•  Raman Research Institute, Bangalore

•  S.N. Bose National Centre for Basic Sciences, Kolkata

•  Sreechitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram

•  Technology Information, Forecasting & Assessment Council (TIFAC), New Delhi

•  Vigyan Prasar, New Delhi

 

Indian Council of Agricultural Research

  • National Bureaue of Soil Survey & Land Use Planning (NBSSLUP)
  • Central Research Institute for Jute & Allied Fibres (CRIJAF)
  • National Bureaue of Agriculturally Important Micro-Organisms (NBAIMO
  • Central Research Institute for Dryland Agriculture
]]> Jit https://bioinformaticsonline.com/opportunity/view/23122/candidates-required-in-bioinformatics-and-genomics-uk-only Fri, 03 Jul 2015 08:22:41 -0500 <![CDATA[Candidates required in Bioinformatics and Genomics UK ONLY]]> I have various permanent positions available based in London, Manchester, Herftfordshire, Oxford and Belfast, as well as other areas throughout the UK.

If you are looking for a new opportunity and have skills within any sector of Bioinformatics with an IT skill then I would love to hear from you. I have various exciting opportunities from programmers to researchers to scientists.

Call me now on 01772 278050 or email me your cv and requirements and I will call you back dareen.evans@itworkshealth.co.uk

]]> https://bioinformaticsonline.com/researchlabs/view/26828/bioinfolab Fri, 25 Mar 2016 11:05:35 -0500 <![CDATA[BioinfoLab]]> Laboratory of Statistics and Computational tools for Bioinformatics

The Laboratory of Statistics and Computational tools for Bioinformatics (BioinfoLab) is hosted at the Istituto per le Applicazioni del Calcolo "Mauro Picone" - CNR . The laboratory has been officially opened in 2012 with the support of Programma Operativo Nazionale "Ricerca e Competitività" 2007-2013 (PON "R&C"), and it incorporates several expertise and research activities started since 2007, and supported by several CNR projects. Main interest of BioinfoLab is to develop novel statistical methods and computational tools for the analysis of high dimensional data arising from "Multi-omics" applications. In particular, current activities involve the analysis of ChIP-seq and RNA-seq experiments.

More at http://bioinfo.na.iac.cnr.it/BioinfoLab/index.html

]]> https://bioinformaticsonline.com/opportunity/view/29998/csir-nehru-science-postdoctoral-research-fellowship Tue, 29 Nov 2016 12:34:59 -0600 <![CDATA[CSIR Nehru Science Postdoctoral Research Fellowship]]> CSIR Nehru Science Postdoctoral Research Fellowship

About Fellowship:
CSIR Nehru Science Postdoctoral Research Fellowship Scheme is an Research Fellowship awarded/given by HRD Ministry, Govt. of India every year to more than 100 fellows.

It was started to identify promising and young researchers with novel ideas and provide them research opportunities in the areas of basic science, engineering, medicine & agriculture.

The fellowship aims at facilitating their transition from mentored to independent research career.

In addition, check these ICTS Research Fellowships:
1.) Max-Planck Partner Group Fellowships 2017-18
2.) ICTS-Simons Postdoctoral Fellowships 2017
3.) ICTS Post Doctoral Fellowships 2017
4.) Airbus Prize Postdoctoral Fellowship 2017-18

Eligibility: To be eligible for this fellowship, you:
1.) PhD degree (within 3 years of award of PhD degree), OR
2.) Those who have submitted PhD theses.
3.) Applicants should have research publications in good impact factor SCI journals.
4.) Indian nationals, Persons of Indian Origin (PIO) & Overseas Citizen of India (OCI), a can also apply.
5.) Maximum Age Limit: 32 years.

Duration:
– 2 Years.
– extendable for a maximum of 1 more year based on performance.

Remuneration:
– Rs. 50,000/- per month plus House Rent Allowance (HRA)
– A contingency grant of Rs. 3.0 lakh per annum.
– 25% of the contingency grant can be used for domestic and international travel.

Mode of Selection: You can apply throughout the year, but selection will be made twice a year, in June and December.

How to Apply:
– Read the instructions, given at Annexure-I in this PDF file.
– And, application form is given as, Annexure-II.
– Fill the form & send it to the given address in the PDF file.

Deadline: Rolling Deadline (Applications accepted throughout the year)

Also See: Research Internship/ Fellowship in India:
1.) IIT Bombay Research Internship Awards Programme 2016-17
2.) IIT Delhi Internship Program 2016-17
3.) DAAD WISE – International Internship in Germany
4.) Summer Research Fellowship Programme| JNCASR Bangalore
5.) Indian Academy of Sciences Summer Internships 2017
6.) Winter Internship – IIT Bombay NPDE-TCA
7.) Viterbi – India Program 2017 | Research Internship in US
8.) Internship – Centre for Stem Cell Research, Vellore

Accommodation & other benefits:
– Accommodation may be provided by CSIR, if available.
– Medical benefits as per CSIR norms.

For more details:
– Check this PDF Notification of Fellowship.
– List of CSIR Labs & their work/activities can be seen at www.csir.res.in.

]]> https://bioinformaticsonline.com/opportunity/view/32822/phd-positions-in-genova-at-dibris-univ-of-genoa-italy Thu, 18 May 2017 00:04:07 -0500 <![CDATA[PhD positions in Genova at DIBRIS - Univ. of Genoa, Italy]]> PhD positions in Genova at DIBRIS - Univ. of Genoa (Italy)

http://www.disi.unige.it/person/MasulliF/ricerca/PhDinGenova2017.html

The call for some funded positions for the 3 years PhD studies at the Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS) in Genova is available at

http://www.studenti.unige.it/postlaurea/dottorati/XXXIII/ENG/

The deadline for applications is June13, 2017 and the PhD courses and fellowships should start on Nov 2017.

Details for the application to the PhD Program in Computer Science and Systems Engineering (CODICE 6608) are at http://phd.dibris.unige.it/csse/index.php/how-to-apply

The research activity of my research group is focused on Computational Intelligence, Machine Learning, Bioinformatics, Systems Biology, and Positive Technology as described at http://www.disi.unige.it/person/MasulliF/ricerca/index.html

The research themes proposed by me and Prof. Stefano Rovetta are:

- Computational Intelligence and Machine Learning (see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T1.html)

- Computational Intelligence and Health and Wellbeing Support( see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T3.html)

You can also propose a different research theme belonging to the research activity of my group.

Looking for self-motivated PhD candidates, interested to the mathematical aspects of their research and to the development of new algorithms for intelligent data analysis, and skilled in programming and in thorough experimental data analysis. They will be part of my research group and will collaborate to our research projects and publications.

Italian and international students interested to work are invited to send their cv and the name/email-addresses of 3 referees to my email address francesco.masulli@unige.it A.S.A.P.

]]>