Bio-Bio-1

05/03/2026

https://thedailycampus.com/mukto-column/244585

বাংলাদেশ আজ এক সন্ধিক্ষণে দাঁড়িয়ে। একদিকে জলবায়ু পরিবর্তনের অভিঘাত, খাদ্যনিরাপত্তার চাপ, বৈশ্বিক প্রযুক্তিগত প...

01/03/2023

FYI post
Dear colleagues, teachers, and friends
We're looking for Bioinformaticians to join our research team at Peking University, Institute of Advanced Agricultural Sciences as post-doctoral fellows/assistant research fellows/associate research fellows. He or she requires a PhD and a solid foundation in plant bioinformatics. He or she should be well-versed in Python or C++. Please email your resume to [email protected] if you are interested.
Note: I'm disseminating this on my boss's behalf. I will obtain the applicants' resumes, but my supervisor will make the final selection.

26/02/2023

একুশের ভাষা শহীদদের এই মাসে মায়ের ভাষায় আধুনিক বিজ্ঞানের সর্বশেষ যুগান্তকারী আবিষ্কার নিয়ে লিখা বাংলা বই "জিনোম এডিটিং" লিখেছেন বিশিষ্ট বিজ্ঞানী, বাংলাদেশ বিজ্ঞান একাডেমী ফেলো, অধ্যাপক ড. তোফাজ্জল ইসলাম স্যার।

27/06/2021

Bio-Bio-1 Summer seminar series #2
Our next guest is Prof. Ruhul H. Kuddus from Utah Valley University, USA.

You can join seminar using the zoom link: https://cua.zoom.us/j/89243516289
Or, you can watch live from Bio-Bio-1 page (https://www.facebook.com/biobio.one/).

01/04/2021

New findings shed light on mechanisms controlling the most basic processes of life. Five years ago, scientists created a single-celled synthetic organism that, with only 473 genes, was the simplest living cell ever known. However, this bacteria-like organism behaved strangely when growing and div

03/03/2021

The genetic algorithm is a stochastic global optimization algorithm. It may be one of the most popular and widely known biologically inspired algorithms, along with artificial neural networks. The algorithm is a type of evolutionary algorithm and performs an optimization procedure inspired by the bi...

05/02/2021

Research and Life in Science, Seminar #9, Winter 2020-21

This winter, Bio-Bio-1 is arranging a seminar series on bioscience research to share cut-edge progress in science among Bioinformatics enthusiastic and practitioners in Bangladesh.

This Saturday, February 06, 2021, our guest will be Sabrina M Elias, Ph.D., Assistant professor, Department of Life Sciences, Independent University, Bangladesh (IUB).

You can join the seminar using Zoom.
The meeting link: https://ucr.zoom.us/j/98411827396
There will be no live casting on social platforms.

Title: Exploring the hidden gems for salt tolerance determinants using omics tools.

Abstract: Climate change and resulting soil salinity rising have been limiting rice production in the coastal region of Bangladesh. We need tolerant plants that gives sufficient yield to feed our large population. The aim of the work was to understand the tolerance mechanism as well as the selection of tolerant donor plants through a breeding program with tolerant plant Horkuch and high yielding IR29. Horkuch is a local landrace found in the coastal region of Bangladesh and we are trying to find the specific treasures hidden in our own germplasms. We have identified regions in the genome of Horkuch and IR29 which are responsible for their differential tolerance and selected promising tolerant plants with good yield. For this, sequence based genotyping, RNAseq based expression analysis, phenomics, QTL and eQTL analysis was performed. These plants are now being used in a Marker-assisted backcrossing program in collaboration with BRRI for variety release to farmers, funded by the World Bank. Also CRISPR and molecular cloning techniques are being used to observe the gain/loss of function of these genes. This extensive study has the potential to narrow down significant genes to support the future breeding programs of improved, salt tolerant and high yielding rice.

Speaker's Biography:
Sabrina M Elias is currently working as an Assistant Professor in the Independent University, Bangladesh (IUB) in the Department of life Sciences, School of Environment and Life Sciences. Previously she worked in the Jute genome project, Plant Biotechnology Laboratory of University of Dhaka and in the computational proteomics section of Australian National University. She completed her PhD from University of Dhaka in 2018 under supervision of Dr. Zeba I Seraj, in collaboration with University of Nebraska Lincoln, University of Texas at Austin and International Rice Research Institute. The PhD work was focused on Rice genomics and phenomics study under salt stress. She completed BSc and MS from University of Dhaka in Biochemistry and Molecular Biology. Her PhD fellowship was from Beachelle Borlaug International Scholar Program from Bayer corp. She worked as a post-doctoral fellow in the same project and was chosen for the BBIS impact award in 2020. Her works are mostly focused on omics study of rice plant under salt stress. She has got supportive fund for conducting research from TWAS and is currently focusing on the functional genomics of salt stressed rice plants and quality enhancement, at the same time also collaborating with other institutes. Apart from this she is focusing some bioinformatics works on microbial genomics. She takes computer fundamental classes as a guest faculty in DU and is associated with cBLAST as a lecture contributor, an online platform for bioinformatics learning in Bangla. She is an Executive committee member of Global Network of Bangladeshi Biotechnologists (GNOBB) and working as the acting secretary of National Young Academy of Bangladesh (NYAB).

02/02/2021

“Today, every single publication in experimental biology contains a combination of new experimental data and inferences drawn from comparisons with other data made available in a public database, an approach that Dayhoff started half a century ago,”

The pioneer of bioinformatics modeled Earth’s primordial atmosphere with Carl Sagan and made a vast protein database still used today

29/01/2021

Research and Life in Science, Seminar #8, Winter 2020-21

This winter, Bio-Bio-1 is arranging a seminar series on bioscience research to share cut-edge progress in science among Bioinformatics enthusiastic and practitioners in Bangladesh.

This Saturday, January 30, 2021, our guest will be Md. Tofazzal Islam, Ph.D., Professor, Director of IBGE, BSMRAU.

You can join the seminar using Zoom.
The meeting link: https://ucr.zoom.us/j/98411827396
There will be no live casting on social platforms.

Title: Wheat blast: an emerging threat to global food security

Abstract: Wheat blast is a worrisome plant disease which is caused by a filamentous fungus, Magnaporthe oryzae Triticum pathotype. Originated in Brazil in 1985, it rapidly spread to several neighboring countries in South America such as Argentina, Bolivia and Paraguay. The recent outbreaks of wheat blast in Bangladesh (Asia) and Zambia (Africa) pose a new serious threat to the global food and nutritional security. Using the field pathogenomics, open data sharing, open science and international collaboration, we determined the genetic identity and origin of wheat blast in Bangladesh as a lineage of South American M. oryzae. However, the origin of Zambian wheat blast is still illusive. Genetic resources for breeding durable blast resistant wheat are limited and fungicide application for controlling this wheat head infecting fungus seem unreliable. We developed a rapid and convenient kit using gRNA and CRISPR-Cas12a for the precise diagnosis of wheat blast. Collaborating with Prof. Sophien and Prof. Nick Talbot, we edited 10 S-genes in wheat genome using CRISPR-Cas technology to develop a blast resistant wheat variety. The edited lines are now under screening for blast resistance. Other novel approaches that we have been applying are biocontrol of wheat blast by seed endophytic bacilli, nanomaterials, introgression of resistant genes in the local elite cultivars and mutation breeding using ion beam, gamma ray and X-ray. In this talk, I shall share the progresses in research for mitigation of the fearsome wheat blast, and discuss novel strategies that should be applied to address any new plant health emergencies.

Speaker's Biography:
Professor Tofazzal Islam is an internationally reputed researcher in molecular plant-microbe interactions and agricultural biotechnology. His team uses both classical and frontier research methods for dissecting molecular cross-talks between plant and associated microorganisms. He obtained B.Sc.Ag. (Hons.) and M.Sc.(Ag.) degrees from Bangladesh Agricultural University securing first position in the first class in both the cases. He did MS and PhD at Hokkaido University, Japan. Dr Islam conducted postdoctoral research at Hokkaido University, University of Goettingen (Germany), University of Nottingham (UK) and West Virginia University (USA) under the fellowships of JSPS, Alexander von Humboldt, Commonwealth and Fulbright, respectively.

Prof. Islam discovered a large number of bioactive secondary metabolites from the host and non-host organisms that are involved in chemotaxis, motility behavior, differentiation, and biorational management of economically important oomycete phytopathogens (e.g., Phytophthora, Aphanomyces, Plasmopara). Another important area of his research accomplishment is the discovery of probiotic bacteria and their applications in sustainable agriculture and industry. He has been leading a large group of national and international researchers for the mitigation of worrisome wheat blast disease caused by Magnaporthe oryzae Trticum since its first epidemic outbreak in Bangladesh in 2016 using genomics, genome editing and other advanced molecular approaches. He collaborated Prof. Sophien Kamoun, FRS and led many international scientists to rapidly determine the origin of wheat blast and develop a convenient method for the diagnosis of wheat blast using Cas12a and gRNA. He advocates and practices open data sharing, open science and international collaborative approaches for tackling the plant health emergencies (such as wheat blast) associated with global food security. He is the Editor-in-Chief of two series books, Bacilli and Agrobiotechnology, and CRISPR-Cas Methods that publish by Springer Nature. An elected Fellow of Bangladesh Academy of Sciences (FBAS), Prof. Islam received by many awards, prizes and medals for his outstanding academic and research accomplishments. He published more than 200 articles in international journals and books with 3639 citations (h-index 33, i10-index 86; and RG Score 42.66).

07/01/2021

Research and Life in Science Seminar #5, Winter 2020-21

This winter, Bio-Bio-1 is arranging a seminar series on bioscience research to share cut-edge progress in science among Bioinformatics enthusiastic and practitioners in Bangladesh.

This Saturday, January 09, 2021, our guest will be Dipan Shaw.

You can join the seminar using Zoom.
The meeting link: https://ucr.zoom.us/j/98411827396
Also, you can scan the QR code too.
There will be no live casting on social platforms.

Topic: Prediction of isoform functions via deep learning.

Abstract: Alternative splicing generates multiple isoforms from a single gene. This process increases the diversity of isoform functions. Although gene functions and interactions have been studied extensively, little is known about isoform functions. Here, we talk about the isoforms function prediction problem. Our first method is a novel deep learning method, DeepIsoFun, that combines multiple-instance learning with domain adaptation. The latter technique helps to transfer the knowledge of gene functions to the prediction of isoform functions and provides additional labeled training data. Our model is trained on a deep neural network architecture so that it can adapt to different expression distributions associated with different gene ontology terms. Our second method, DIFFUSE, increases the performance of isoforms function prediction by integrating data from different sources including sequence, protein domain, and expression. Here we adopt a hybrid framework by first using a deep neural network to predict the functions of isoforms from their genomic sequences and then refining the prediction using a conditional random field based on co-expression relationship. To overcome the lack of isoform-level training labels, we propose an iterative semi-supervised training algorithm based on the multiple-instance learning framework. We test our methods on different organisms including human, mouse, arabidopsis, and fruit-fly. Our methods perform significantly better than the existing methods in terms of cross-validation and de novo prediction. The experimental results demonstrate that our methods are effective in identifying the diverse functions of isoforms.

Speaker's Bio: Dipan Shaw completed his Ph.D. in Computer Science from the University of California, Riverside. His research interest includes machine learning and bioinformatics. His main expertise is to conduct large-scale sequencing data analysis projects.

He completed his master's and bachelor's degrees from the Computer Science department of Bangladesh University of Engineering and Technology. As a software engineer, he worked in Samsung and Western Digital. In his teaching carrier, he served his alma-mater (BUET) and BRAC University as a lecturer.
Website: https://www.cs.ucr.edu/~dshaw003/
LinkedIn: https://www.linkedin.com/in/dipanshaw/