The Computational Biology Research Center

The Computational Biology Research Center (CBRC) was founded in 2011 by Dr. Fatemeh Zare-Mirakabad , a faculty member of the Amirkabir University of Technology. The purpose of this center is to be a place for students and professors who are interested in computational topics of bioinformatics field to come together. This center Has played a significant role in promoting the scientific level of students and researchers by creating a relaxed and ambient environment. In this center, there are 14 bachelor students, 55 master students, 11 Ph.D. students and 4 researchers gathered to work and exchange up-to-date ideas in bioinformatics field.

Ongoing events


Weekly Seminars 2021

Weekly Seminars

Online - Weekly Seminars - Autumn & Winter 2021

Time:
Wednesdays at 18:00 (GMT +3:30)

Topics:

  • RNA
  • Cancer
  • Protein
  • Drug Design
  • Biological Network
  • Reads Mapping
  • Machine Learning in Bioinformatics
More Info

Next Event starting Dec 01( )

Research areas

Coronavirus disease

Structural bioinformatics

Drug

Sequence in bioinformatics

Biological network

Tutorials

ClustalW & BLAST

BLAST is a powerful tool to find sequences in a database. ClustalW is a general-purpose multiple-sequence alignment program for DNA or protein sequences.

SVM Application in Gene expression

We can use Support Vector Machine models to examine whether the new sample has cancer or not by using gene expression of genes involved in the disease

SVM Application in Protein

We can use Support Vector Machine models in protein problems like Secondary structure prediction, Fold recognition, Cleavage site identification, and RNA-binding proteins.

Publications

Protein sequence profile prediction using ProtAlbert transformer

Armin Behjati, Fatemeh Zare-Mirakabad, Seyed Shahriar Arab, et al.
bioRxiv
21 September 2021

The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains

Najmeh Salehi, Bahareh Attaran, Fatemeh Zare-Mirakabad, et al.
Helicobacter on Wiley Online Library
14 August 2020

Softwares

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ADRP-ML-NMF

Identifying and controlling adverse drug reactions is a complex problem in the pharmacological field. Despite the studies done in different laboratory stages, some adverse drug reactions are recognized after being released, such as Rosiglitazone. Due to such experiences, pharmacists are now more interested in using computational methods to predict adverse drug reactions.

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DRP-VEM

Traditional drug discovery methods are costly and time-consuming. The use of the existing approved drugs for treating another disease is called drug repositioning, a common strategy to overcome traditional drug discovery issues.

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TranDTA

TranDTA is the first method that applies transformers to extract feature of protein sequence and uses transformer representations in drug target binding affinity (DTBA) prediction.

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CNDP_PPI_networks

The data set used in the paper contains the PPI networks of E. coli and S. cerevisiae which are extracted from the Database of Interacting Proteins (DIP). To label the proteins as essential/non-essential, the essential genes data of these species are collected from DEG database.