University of Peradeniya : Computational Biology Research Group

Department of Computer Engineering, Faculty of Engineering, University of Peradeniya, Peradeniya, Sri Lanka.

As much as there is a universe as we look up, there is a universe to explore within ourselves, at the micro level. The computational biology research lab at the Department of Computer Engineering, University of Peradeniya focuses on exploring the use of Computer science and Engineering to elucidate the biological systems around us and using that knowledge in various applications.

News

2024 Our work, titled "Enhancing Long-read Metagenomic Binning with Read-overlap Graphs Across Microbial Kingdoms," has been accepted for an oral presentation at the IESL YMS Technical Conference 2024. This marks a significant milestone for our group as it contributes to the broader understanding of microbial communities.
2024 The department is set to offer a new technical elective, Computational BioEngineering, featuring contributions from members of our research group. This course will focus on the intersection of computational methods and bioengineering, equipping students with skills essential for modern biological data analysis.
2024 Our research group recently presented a poster demonstrating our long reads binning tool at the MARC Display. The tool focuses on improving the accuracy and efficiency of long-read binning in metagenomic data analysis. The poster generated significant interest, highlighting the tool's potential applications in microbial research.
2023 Dr. Damayanthi recently delivered a seminar at the prestigious Academia Sinica in Taiwan. Her presentation focused on the latest advancements in computational biology, with an emphasis on long-read sequencing technologies. The seminar was well-received, strengthening our academic ties with one of Asia's leading research institutes.
2021 Our work on Accurate plant disease classification with transfer learning based on leaf images has been accepted for the 16th IEEE conference on Industrial and Automation Systems (ICIIS 2021)
2021 Our group members will be conducting a workshop on Explainable Machine Learning at ICIIS 2021.
2021 Our group members will be inovled in a workshop on Feature Engineering in Machine Learning at ICIET 2021.
2021 Our work on Machine Learning for detecting alzhemizers disease using Next Generation Sequencing Data has been accepted for the IEEE International Conference on Industrial and Financial Automation Systems (ICIAFS ) 2021.
2021 We have been awarded a University of Peradeniya Researh Grant to work further on the project "Counting the uncountable : Estimating species richness from metavirome data".
2021 Our systematic review titled "Machine learning for plant microRNA prediction: A systematic review" is now available as a preprint.
2021 Our work miRNAFinder: A Comprehensive Web Resource for Plant Pre-microRNA Classification is now available as a preprint.
2021 Our work on Crop disease detection with Deep learning has been accepted for an oral presentation at iPURSE 2021. Further work on the project is up at https://damayanthiherath.github.io/leaf-disease-classification/ We will be organizing a special session on data engineering for biology and medicine at ICIAFS conference 2021.

Publications

  • DeepSelectNet: deep neural network based selective sequencing for Oxford Nanopore sequencing

    Senanayake, A., Gamaarachchi, H., Herath, D., Ragel, R.

    BMC Bioinformatics, 24(1), 31

  • Machine learning for plant microRNA prediction: A systematic review

    Author 1, Author 2, Author 3

    Journal Name, Volume, Issue, Pages

  • Counting the Uncountable: Estimating Species Diversity measures of communities of viruses

    Herath, D.

    Hantana Vision Magazine, 7(1)

  • Mirnafinder: A comprehensive web resource for plant mirna classification

    Author 1, Author 2, Author 3

    BioSystems Journal

    Submitted

  • Revealing MicroRNA Biomarkers for Alzheimer's Disease Using Next Generation Sequencing Data

    Author 1, Author 2, Author 3

    ICIAFS 2021-Special Session on Data Engineering for Biology

  • miRNAFinder: A pre-microRNA classifier for plants and analysis of feature impact

    P Ihalagedara, S Lokuge, S Jayasundara, D Herath, I Kahanda

    2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)

  • Detection of Novel Biomarker Genes of Alzheimer's Disease Using Gene Expression Data

    Perera, S., Hewage, K., Gunarathne, C., Navarathna, R., Herath, D., Ragel, R.G.

    2020 Moratuwa Engineering Research Conference (MERCon), 1-6

  • CoMet: A workflow using contig coverage and composition for binning a metagenomic sample with high precision

    Herath, D., Tang, S.L., Tandon, K., Ackland, D., Halgamuge, S.K.

    BMC bioinformatics

  • CoMet: A workflow using contig coverage and composition for binning a metagenomic sample with high precision

    Herath, D., Tang, S.L., Tandon, K., Ackland, D., Halgamuge, S.K.

    BMC Bioinformatics, 18, 161-172

  • Assessing species diversity using metavirome data: methods and challenges

    Herath, D., Jayasundara, D., Ackland, D., Saeed, I., Tang, S.L., Halgamuge, S.

    Computational and Structural Biotechnology Journal, 15, 447-455

Presentations/Talks

MiraNET: Accurate plant pre-microRNA classification

Presenter: Sandali Devni Lokuge

University of Peradeniya

July 30, 2023

Watch on YouTube

SigNet: A Python-based Web Application for Gene Expression Analysis

Presenter: Lakshitha Gunasekara

University of Peradeniya, Sri Lanka

July 21, 2023

Watch on YouTube

People

Academic Staff


External Collaborators


Students / Past Students

  • Nethmi Sudeni
  • Sathsarani Atthanayake
  • Jayathri Ranasinghe
  • Thanujan Tharmapalan
  • Nishankar
  • Sasini Arachchige
  • L.A.C. Deshan
  • Hans Thisanke
  • Shyaman Jayasundara
  • Sandali Dewni Lokuge
  • Puwasuru Ihaladegara
  • Kaveesha Dilshani
  • Chamara Gunarathne
  • Shehan Perera
  • Geeth Priyanka
  • Kasun Vimukthi
  • Prabhath Bandara
  • Vidwa Sripadi
  • Hasini Thilakarathna
  • Imalsha Dinuwanthi

Join us

How to Join?

Send Us an Email: If you are interested in joining our group, please send an email to Dr. Damayanthi Herath at damayanthiherath@eng.pdn.ac.lk.

Webmaster

This website is maintained by Chiran Devinda [Department of Computer Engineering, Univeristy of Peradeniya]

Last Update : 19-09-2024