📝 A detailed BLAST exercise with answers
✍️ Level: Introductory
🔹Exercise:
https://teaching.healthtech.dtu.dk/22111/index.php/Exercise:_BLAST
🔸Answers:
https://teaching.healthtech.dtu.dk/22111/index.php/ExBlast-Answers
In this exercise we will be using BLAST (Basic Local Alignment Search Tool) for searching sequence databases such as GenBank (DNA data) and UniProt (protein). When using BLAST for sequence searches it is of utmost importance to be able to critically evaluate the statistical significance of the results returned.
The BLAST software package is free to use (Open Source) and can be installed on any local system — it's originally written for UNIX type Operating Systems. The package contains both programs for performing the actual sequence searches against preexisting databases (e.g. "blastn" for DNA databases and "blastp" for protein databases), as well as a tool for creating new databases from scratch (the "fortmatdb" program).
In this exercise we will be using the Web-interface to BLAST hosted by the NCBI. For our purpose there are several advantages to this approach:
-We don't have to mess around with a UNIX command prompt.
-NCBI offers direct access to preformatted BLAST databases of all the data that they host:
▫️GenBank (+ derivates)
▫️Full Genome database
▫️Protein database (Both from translated GenBank and UniProt)
It should be noted that running BLAST locally (for example at the super-computer cluster at CBS/DTU) offers much more fine-grained control of DATA and workflow (everything can be noscripted/automated) than running BLAST through a web-interface.
📲Channel: @Bioinformatics
✍️ Level: Introductory
🔹Exercise:
https://teaching.healthtech.dtu.dk/22111/index.php/Exercise:_BLAST
🔸Answers:
https://teaching.healthtech.dtu.dk/22111/index.php/ExBlast-Answers
In this exercise we will be using BLAST (Basic Local Alignment Search Tool) for searching sequence databases such as GenBank (DNA data) and UniProt (protein). When using BLAST for sequence searches it is of utmost importance to be able to critically evaluate the statistical significance of the results returned.
The BLAST software package is free to use (Open Source) and can be installed on any local system — it's originally written for UNIX type Operating Systems. The package contains both programs for performing the actual sequence searches against preexisting databases (e.g. "blastn" for DNA databases and "blastp" for protein databases), as well as a tool for creating new databases from scratch (the "fortmatdb" program).
In this exercise we will be using the Web-interface to BLAST hosted by the NCBI. For our purpose there are several advantages to this approach:
-We don't have to mess around with a UNIX command prompt.
-NCBI offers direct access to preformatted BLAST databases of all the data that they host:
▫️GenBank (+ derivates)
▫️Full Genome database
▫️Protein database (Both from translated GenBank and UniProt)
It should be noted that running BLAST locally (for example at the super-computer cluster at CBS/DTU) offers much more fine-grained control of DATA and workflow (everything can be noscripted/automated) than running BLAST through a web-interface.
📲Channel: @Bioinformatics
🧑🏫 Workshop on Advance Bioinformatics - NGS Data Analysis and Proteomics
⏱ Time: 1-5 March 2021 | 6:30 to 8:30 PM IST
📝 Registration link:
https://genespectrum.co.in/bioinformatics-training/ngs-proteomics-workshop/
📞 For more details contact on whatsapp/telegram : +91 7021386045
📲Channel: @Bioinformatics
⏱ Time: 1-5 March 2021 | 6:30 to 8:30 PM IST
📝 Registration link:
https://genespectrum.co.in/bioinformatics-training/ngs-proteomics-workshop/
📞 For more details contact on whatsapp/telegram : +91 7021386045
📲Channel: @Bioinformatics
Study Estimates Two-Thirds of COVID-19 Hospitalizations Due to Four Conditions:
obesity, hypertension, diabetes, and heart failure
✍️ Level: General, Advanced
https://www.ahajournals.org/doi/10.1161/JAHA.120.019259
📲Channel: @Bioinformatics
obesity, hypertension, diabetes, and heart failure
✍️ Level: General, Advanced
https://www.ahajournals.org/doi/10.1161/JAHA.120.019259
📲Channel: @Bioinformatics
⚙️ DEBKS – a tool to detect differentially expressed circular RNA
Circular RNAs (circRNAs) are involved in various biological processes and disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that circRNA is formed from the host gene by back-splicing (BS). To distinguish the expression difference originated from BS or the host gene, Peking University researchers have developed DEBKS, an effective software program to streamline the discovery of differential BS events between two rRNA-depleted RNA sequencing (RNA-seq) sample groups.
DEBKS is available at https://github.com/yangence/DEBKS as open-source software.
🗒 Study more about the research here:
https://www.sciencedirect.com/science/article/pii/S1672022921000292?via%3Dihub
📲Channel: @Bioinformatics
Circular RNAs (circRNAs) are involved in various biological processes and disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that circRNA is formed from the host gene by back-splicing (BS). To distinguish the expression difference originated from BS or the host gene, Peking University researchers have developed DEBKS, an effective software program to streamline the discovery of differential BS events between two rRNA-depleted RNA sequencing (RNA-seq) sample groups.
DEBKS is available at https://github.com/yangence/DEBKS as open-source software.
🗒 Study more about the research here:
https://www.sciencedirect.com/science/article/pii/S1672022921000292?via%3Dihub
📲Channel: @Bioinformatics
👍1
📹 How to Share Text Mining Results in Biology
https://www.youtube.com/watch?v=tvKtOgl-Tlc
⏰ Duration: 00:18:51
This webinar is aimed at individuals who wish to learn more about sharing and reusing results of biomedical text-mining. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.
📲Channel: @Bioinformatics
https://www.youtube.com/watch?v=tvKtOgl-Tlc
⏰ Duration: 00:18:51
This webinar is aimed at individuals who wish to learn more about sharing and reusing results of biomedical text-mining. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.
📲Channel: @Bioinformatics
YouTube
How to Share Text Mining Results in Biology
Though text mining becomes more widespread in biology, an average researcher can rarely use it to their advantage. In this video Europe PMC (https://europepmc.org/) presents a tool to easily share annotated bioentities and relations with the research community.…
🔬 Exploring the computational methods for protein-ligand binding site prediction
✍️ Level: Advanced
Identifying the residues participating in these interactions not only provides biological insights for protein function studies but also has great significance for drug discoveries. In this review, authors introduce the research background of predicting protein–ligand binding sites and then classify the methods into four categories, namely, 3D structure-based, template similarity-based, traditional machine learning-based and deep learning-based methods.
https://www.sciencedirect.com/science/article/pii/S2001037019304465
📲Channel: @Bioinformatics
✍️ Level: Advanced
Identifying the residues participating in these interactions not only provides biological insights for protein function studies but also has great significance for drug discoveries. In this review, authors introduce the research background of predicting protein–ligand binding sites and then classify the methods into four categories, namely, 3D structure-based, template similarity-based, traditional machine learning-based and deep learning-based methods.
https://www.sciencedirect.com/science/article/pii/S2001037019304465
📲Channel: @Bioinformatics
👦 Using machine learning to identify blood biomarkers for early diagnosis of autism
✍️ Level: Advanced
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246581
The more significantly affected the child is, the higher or lower than normal the blood biomarker is. Ideally, there will be a day when a child is identified using blood biomarkers as being at risk for developing ASD and therapies can be started immediately. That would help the child develop skills to optimize their communication and learning.
📲Channel: @Bioinformatics
✍️ Level: Advanced
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246581
The more significantly affected the child is, the higher or lower than normal the blood biomarker is. Ideally, there will be a day when a child is identified using blood biomarkers as being at risk for developing ASD and therapies can be started immediately. That would help the child develop skills to optimize their communication and learning.
📲Channel: @Bioinformatics
journals.plos.org
Blood biomarker discovery for autism spectrum disorder: A proteomic analysis
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication and social interaction and restricted, repetitive patterns of behavior, interests, or activities. Given the lack of specific pharmacological…
💊 A new survey research of computational methods for drug-target interaction (DTI) prediction and related datasets
✍️ Level: Advanced
https://academic.oup.com/bib/article/22/1/247/5681786
The task of predicting the interactions between drugs and targets plays a key role in the process of drug discovery. In this article, authors describe the data required for the task of DTI prediction followed by a comprehensive catalog consisting of machine learning methods and databases, proposed and utilized to predict DTIs. The advantages and disadvantages of each set of methods are also discussed. Lastly, the challenges in prediction of DTI using machine learning approaches are highlighted and they conclude by shedding some lights on important future research directions.
📲Channel: @Bioinformatics
✍️ Level: Advanced
https://academic.oup.com/bib/article/22/1/247/5681786
The task of predicting the interactions between drugs and targets plays a key role in the process of drug discovery. In this article, authors describe the data required for the task of DTI prediction followed by a comprehensive catalog consisting of machine learning methods and databases, proposed and utilized to predict DTIs. The advantages and disadvantages of each set of methods are also discussed. Lastly, the challenges in prediction of DTI using machine learning approaches are highlighted and they conclude by shedding some lights on important future research directions.
📲Channel: @Bioinformatics
👨💻 Getting Started in Gene Expression Microarray Analysis
✍️ Level: Intermediate
Gene expression microarrays provide a snapshot of all the trannoscriptional activity in a biological sample. Unlike most traditional molecular biology tools, microarrays facilitate the discovery of totally novel and unexpected functional roles of genes. The power of these tools has been applied to a range of applications, including discovering novel disease subtypes, developing new diagnostic tools, and identifying underlying mechanisms of disease or drug response. However, this technology necessarily produces a large amount of data, challenging us to interpret it by exploiting modern computational and statistical tools. In this brief review, we aim to indicate the major issues involved in microarray analysis and provide a useful starting point for new microarray users.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000543
📲Channel: @Bioinformatics
✍️ Level: Intermediate
Gene expression microarrays provide a snapshot of all the trannoscriptional activity in a biological sample. Unlike most traditional molecular biology tools, microarrays facilitate the discovery of totally novel and unexpected functional roles of genes. The power of these tools has been applied to a range of applications, including discovering novel disease subtypes, developing new diagnostic tools, and identifying underlying mechanisms of disease or drug response. However, this technology necessarily produces a large amount of data, challenging us to interpret it by exploiting modern computational and statistical tools. In this brief review, we aim to indicate the major issues involved in microarray analysis and provide a useful starting point for new microarray users.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000543
📲Channel: @Bioinformatics
💪 Computational Biology Boundaries
https://www.youtube.com/watch?v=eyFGZjiqLGg
📲Channel: @Bioinformatics
https://www.youtube.com/watch?v=eyFGZjiqLGg
📲Channel: @Bioinformatics
YouTube
Is Computational Biology an answer to our health problems | Neelanjana Sengupta | TEDxHITKolkata
Can difficult diseases have a cure, is computational biology the answer to this problem?
Neelanjana Sengupta, a computational biologist almost by accident. She had been a curious child who felt bothered unless she was able to grasp, at least conceptually…
Neelanjana Sengupta, a computational biologist almost by accident. She had been a curious child who felt bothered unless she was able to grasp, at least conceptually…
🧬 Sequencing Key Molecules in Just Minutes Instead of Years
https://scitechdaily.com/sequencing-key-molecules-in-just-minutes-instead-of-years/
📲Channel: @Bioinformatics
https://scitechdaily.com/sequencing-key-molecules-in-just-minutes-instead-of-years/
📲Channel: @Bioinformatics
SciTechDaily
Sequencing Key Molecules in Just Minutes Instead of Years
Research demonstrates potential for rapid, accurate glycan sequencing. Using a nanopore, researchers have demonstrated the potential to reduce the time required for sequencing a glycosaminoglycan — a class of long chain-linked sugar molecules as important…
⚙ Nvidia and Harvard develop AI tool that speeds up genome analysis
https://venturebeat.com/2021/03/08/nvidia-and-harvard-develop-ai-tool-that-speeds-up-genome-analysis/
📲Channel: @Bioinformatics
https://venturebeat.com/2021/03/08/nvidia-and-harvard-develop-ai-tool-that-speeds-up-genome-analysis/
📲Channel: @Bioinformatics
VentureBeat
Nvidia and Harvard develop AI tool that speeds up genome analysis
Nvidia and Harvard researchers say they've developed an AI tool that can dramatically speed up genome analysis.
🧑🏫 New research trends for metabolic network reconstruction
⏱ Time: 14-Mar-2021 / 19:00
🕸https://vc.sharif.edu/ch/soal
📲Channel: @Bioinformatics
⏱ Time: 14-Mar-2021 / 19:00
🕸https://vc.sharif.edu/ch/soal
📲Channel: @Bioinformatics
🧑⚕️ Whole genome sequencing shows promise in routine treatment of blood cancers
A study by university doctors found that sequencing the genome of people with blood cancers is often better and even quicker than conventional tests and costs about the same. The study was published Wednesday in the New England Journal of Medicine, one of the most prestigious peer-reviewed medical journals.
“What we showed is that genome sequencing has reached a point that it is now practical, fast, economical, clinically feasible and accessible for the routine testing of patients,” said Dr. David Spencer, medical director of Washington University’s McDonnell Genome Institute Clinical Sequencing Lab.
https://medicine.wustl.edu/news/for-blood-cancers-whole-genome-sequencing-may-be-able-to-replace-standard-genetic-tests-that-guide-therapy/?_ga=2.42947427.71587469.1615559294-1696562336.1615559294
📲Channel: @Bioinformatics
A study by university doctors found that sequencing the genome of people with blood cancers is often better and even quicker than conventional tests and costs about the same. The study was published Wednesday in the New England Journal of Medicine, one of the most prestigious peer-reviewed medical journals.
“What we showed is that genome sequencing has reached a point that it is now practical, fast, economical, clinically feasible and accessible for the routine testing of patients,” said Dr. David Spencer, medical director of Washington University’s McDonnell Genome Institute Clinical Sequencing Lab.
https://medicine.wustl.edu/news/for-blood-cancers-whole-genome-sequencing-may-be-able-to-replace-standard-genetic-tests-that-guide-therapy/?_ga=2.42947427.71587469.1615559294-1696562336.1615559294
📲Channel: @Bioinformatics
Washington University School of Medicine in St. Louis
Promising role for whole genome sequencing in guiding blood cancer treatment | Washington University School of Medicine in St.…
Sequencing results returned in a few days; costs similar to conventional testing
🧑🏫 Workshop on Genome Annotation using Ensembl Genome Browser
⏱ 23, 24 and 25 March 2021 | 6:00 to 9:00 PM IST (+5:30 GMT)
📝 Register Here:
https://genespectrum.co.in/bioinformatics-training/ensembl_workshop/
📞 For more details contact on whatsapp/telegram : +91 7021386045
📲Channel: @Bioinformatics
⏱ 23, 24 and 25 March 2021 | 6:00 to 9:00 PM IST (+5:30 GMT)
📝 Register Here:
https://genespectrum.co.in/bioinformatics-training/ensembl_workshop/
📞 For more details contact on whatsapp/telegram : +91 7021386045
📲Channel: @Bioinformatics
👁 Researchers identify 50 additional genes for eye color
An international team of scientists has identified 50 more genes for eye color. “We knew of all these people whether they had brown, blue or any other color eyes. Computers searched their DNA for areas that have something to do with eye color. In this way, we found 61 genes associated with eye color, 50 of which were still unknown,” Dr. Manfred Kayser of the Erasmus University Medical Center Rotterdam, said in an article on the university’s website. Study the paper here:
https://advances.sciencemag.org/content/7/11/eabd1239
📲Channel: @Bioinformatics
An international team of scientists has identified 50 more genes for eye color. “We knew of all these people whether they had brown, blue or any other color eyes. Computers searched their DNA for areas that have something to do with eye color. In this way, we found 61 genes associated with eye color, 50 of which were still unknown,” Dr. Manfred Kayser of the Erasmus University Medical Center Rotterdam, said in an article on the university’s website. Study the paper here:
https://advances.sciencemag.org/content/7/11/eabd1239
📲Channel: @Bioinformatics
Science
Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color
Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We…
📹 64 Short lecture videos on bioinformatics
from the Center for Computational Biology and bioinformatics
at Indiana University School of Medicine
https://www.youtube.com/playlist?list=PLusPIkuVew_75IRojlv8uOhoxI89CFbKD
📲Channel: @Bioinformatics
from the Center for Computational Biology and bioinformatics
at Indiana University School of Medicine
https://www.youtube.com/playlist?list=PLusPIkuVew_75IRojlv8uOhoxI89CFbKD
📲Channel: @Bioinformatics
👷♂️ Full-time fully virtual Co-Op position
2021 Computational Biology, Bioinformatics
https://jobs.merck.com/us/en/job/MERCUSR105237ENUS/2021-Computational-Biology-Bioinformatics-Co-Op?utm_source=linkedin&utm_medium=phenom-feeds
📲Channel: @Bioinformatics
2021 Computational Biology, Bioinformatics
https://jobs.merck.com/us/en/job/MERCUSR105237ENUS/2021-Computational-Biology-Bioinformatics-Co-Op?utm_source=linkedin&utm_medium=phenom-feeds
📲Channel: @Bioinformatics
🧑🏫 Workshop from McGill University on Introduction to single cell analysis concepts
This workshop intends to introduce the basic concepts underlying single-cell data generation, processing, and analysis. We will introduce the current state-of-the-art technologies for molecular profiling at the single cell level. The goal is to help participants get familiar with existing tools and understand the differences between them. The main focus of the hands-on section will be an example of the typical analysis workflow of single-cell RNA sequencing data. It is strongly recommended to have previous coding experience and a basic understanding of bulk genomic analyses. See more details here:
https://www.mcgill.ca/channels/channels/event/introduction-single-cell-analysis-concepts-329688
⏱ March 29, 2021 | 1 PM- 5 PM
📝 Register here:
https://mcgill.zoom.us/meeting/register/tZUvfumsqTgpG9w0bZmqEcEWCm1CMi2CfrvD
📲Channel: @Bioinformatics
This workshop intends to introduce the basic concepts underlying single-cell data generation, processing, and analysis. We will introduce the current state-of-the-art technologies for molecular profiling at the single cell level. The goal is to help participants get familiar with existing tools and understand the differences between them. The main focus of the hands-on section will be an example of the typical analysis workflow of single-cell RNA sequencing data. It is strongly recommended to have previous coding experience and a basic understanding of bulk genomic analyses. See more details here:
https://www.mcgill.ca/channels/channels/event/introduction-single-cell-analysis-concepts-329688
⏱ March 29, 2021 | 1 PM- 5 PM
📝 Register here:
https://mcgill.zoom.us/meeting/register/tZUvfumsqTgpG9w0bZmqEcEWCm1CMi2CfrvD
📲Channel: @Bioinformatics
📉 Workflow overview of pathway analysis protocol for RNA-seq data
Input data of normalized differentially expressed genes lists for samples (Top) is subjected to Data Processing and Pathway Analysis steps to generate both ranked lists and nodal network maps of biological functions and pathways of interest (Bottom).
🗒Source Paper:
https://www.mdpi.com/2409-9279/4/1/21/htm
📲Channel: @Bioinformatics
Input data of normalized differentially expressed genes lists for samples (Top) is subjected to Data Processing and Pathway Analysis steps to generate both ranked lists and nodal network maps of biological functions and pathways of interest (Bottom).
🗒Source Paper:
https://www.mdpi.com/2409-9279/4/1/21/htm
📲Channel: @Bioinformatics
🎞 NCBI Mastery: A Beginner's Guide to Bioinformatics
A complete and Up to Date NCBI Video Guide
🗒 Including tons of tools and databases of NCBI like:
mRNA Sequence Retrieval and Analysis, Gene Database, FASTA Format, Genbank Format, Genbank Database, RefSeq Database, ORF Finder, Genome Database, Genome Data Viewer, Genome Assembly, SNP Database (dbSNP), ...
📝 More information details:
https://www.udemy.com/course/ncbi-mastery-beginners-guide-to-bioinformatics
⏱ Lifetime Time Access
📲Channel: @Bioinformatics
A complete and Up to Date NCBI Video Guide
🗒 Including tons of tools and databases of NCBI like:
mRNA Sequence Retrieval and Analysis, Gene Database, FASTA Format, Genbank Format, Genbank Database, RefSeq Database, ORF Finder, Genome Database, Genome Data Viewer, Genome Assembly, SNP Database (dbSNP), ...
📝 More information details:
https://www.udemy.com/course/ncbi-mastery-beginners-guide-to-bioinformatics
⏱ Lifetime Time Access
📲Channel: @Bioinformatics