"With AlphaFold, molecule generation with MIM, and docking with DiffDock, we can now generate and screen candidate molecules in a matter of minutes."
"It's a very exciting time. The knowledge is exploding, and now that we have computers and bioinformatics and even artificial intelligence, we're only going to get able to do better analysis of things."
"So this was a brief glimpse at what can be done with data-driven bioinformatics approach."
"What's very lucky is that biology is packed with interesting classical algorithms. Like, this is what first brought me to bioinformatics indeed."
"We're going to create what will be the largest bioinformatics databank in the world focused on mental health."
"Profile HMMs are a hidden Markov model that's made based on a multiple alignment of proteins which have a related function or share a common domain."
"WGCNA by default has a much more sophisticated and iterative process for identifying clusters."
"The group with the WGCNA package have done a fantastic job of making it super easy to implement this analysis."
"Module eigengene is a way to summarize the expression patterns across our samples for a given module."
"The WGCNA algorithm includes what we first principal component is what it's calling its module eigengene."
"It reduces that multiple testing because now we're just looking at one module eigen gene against our trait."
"Enrich R is one of my favorites; it looks at over 160 different libraries."
"GPS is the name of this algorithm... it locates proteins on the genome."
"For site map, you can run it on any protein; it will give you an initial idea about where can be a possible binding pocket."
"Based on the d score, if you have d score value more than one, then definitely you need to choose this as a best binding pocket."
"How to identify which protein-protein interaction is the good one is based on the binding free energy between two proteins."
"For an apo enzyme where there are no active sites present and no crystallized ligand, is it possible to get an active site predicted using site map? Yes."
"Heat maps are a great way to visualize gene expression data."
"Volcano plots are useful for identifying genes that are significantly regulated."
"WGCNA is a really good method to start off with when learning about network analyses."
"You need to know how it went from the raw sequence all the way to VCFs."
"They've been described as the LEGOs of computational sequence analysis."
"So the information content of the motif is just 2 minus the entropy of that motif model."
"We're doing de novo motif finding."
"You make a weight matrix model of width, W, from the instances in the other sequences."
"You're going to give it a guess of what the length of the motif is."
"The high information content motif, those are the very strong ones, like that first one. Those are much easier to find."
"A VCF file is the output for a bioinformatics pipeline, storing gene sequence variations."
"Sequence variations like SNPs, insertions, deletions, and structural variants are all recorded in a VCF file."
"The first few lines in a VCF file describe the format and content of a specific VCF file."
"The metadata lines start with two pound symbols and describe the format and content of the VCF file."
"The header section is prefixed by one pound symbol, followed by records which are data lines storing information about the variants."
"Chromosome and position columns hold information on where the variant was found."
"Quality values estimate whether the variant call at that site is due to sequencing error."
"The filter column tells us what filters have been applied to our data set."
"The info column will find information for certain abbreviations for these sites."
"What actually makes scVelo unique is that it solves a couple of issues mainly based on assumptions past programs have made."
"I work in bioinformatics and I'm trying to develop machine learning methods that will help us understand better cardiomyopathies."
"We will use the plotting functions to show some of the most highly expressed genes in our data."
"Uniprot you can use to look for all kinds of information about the protein."
"Bioinformatics has biology in it and you should understand where data comes from."
"The goal for me was to encourage more biologists to get into bioinformatics."
"If you're coming from a CS software background, you might also have some of these great skills that you can use as you're moving into a bioinformatics role."
"Yes, it's absolutely possible for you to come from computer science and software and get into bioinformatics."
"Bioconductor is a very nicely curated open source software repository for bioinformatics packages written in R."
"Bioconductor is only becoming more utilized and more popular."
"There is a huge community of bioinformaticians surrounding Bioconductor that only continues to make it more valuable."
"Those who know bioinformatics will be more effective at their research, they'll be more competitive for jobs and for funding, and they'll be more flexible and adaptable to changes in their field."
"Bioinformatics is the intersection of statistics, computer science, and biology."
"Bioinformatics is using data science techniques to understand things such as RNA and RNA transcription, understanding the genome."
"My research group develops algorithms for processing DNA sequencing data, with a particular focus on de novo genome assembly."
"Genentech invests heavily in applying bioinformatics and machine learning to large transcriptomic, genomic, epigenomic, and proteomic datasets."
"Bioinformatics is used in cancer research to understand how different drugs interact and affect different types of tumors."
"The goal of the omics logic programs is to provide training in bioinformatics, enabling independent research guided by mentors and pure example."
"The important thing is to understand the application like transcriptomics, how to analyze transcriptomic data, genomics, how to analyze genomic data."
"You can probably be part of a lot of teams that do some form of bioinformatics or related work that you can join without having formal biology knowledge."
"This program is just an introduction to bioinformatics, where we will cover different types of analyses and project examples."
"Scoring system should favor matching identical or related amino acids, penalize poor matches and for gaps."
"Bioinformatics is an interdisciplinary field that involves the application of computational and statistical methods to comb through biological data."
"As bioinformaticians, we develop and work with computational tools designed for studying biological systems."
"Bioinformatics could be used in Marine Biology to study the DNA of marine species in order to map the abundance and distribution of marine species in the ocean."
"The programming languages most used in the field of bioinformatics are Python, R, Perl, and Java."
"Bioinformaticians and data scientists differ not only in their primary focus but also in their domain expertise, applications, and the actual tools and techniques that they use."
"Bioinformaticians are looking to advance biological understanding and data scientists are looking to drive insights and help with decision-making across a range of different fields."
"Be proactive in seeking opportunities, building a diverse skill set, and staying engaged and up-to-date with the ever-evolving landscape of bioinformatics."
"Bioinformatics is one of those cool emerging fields of science for anyone looking for a career involving computers."
"So, what we would like to do then, is to take this kind of information and automatically learn, or automatically annotate the genome as to its functional elements."
"The TCGA Biolinks package not only allows us to perform data retrieval but also allows us to build a query and integrate different data types."
"So essentially the whole point of doing this exercise is to show you how convenient TCGA Biolinks package makes it for us."
"GenBank is human readable, it has a header, it has a sequence annotation, and the sequence itself."
"FASTA, basically a universal format for sequence analysis programs."
"It lets you get the sequences directly with batch access without a web browser and most importantly there is no scripting required."
"This has a greater look back time. It tells you more about the structure function of a protein than ordinary BLAST."
"BLAST stands for Basic Local Alignment Search Tool."
"It's probably the most widely used sequence similarity search tool, especially when you're talking about large database searches."
"What BLAST really tells you is about non-chance similarities between biological sequences."
"The important statistic that you get from BLAST is something called the Expect Value or the E-value."
"The protein scoring system is more sophisticated."
"These kinds of scoring systems give much more accurate alignments and they are more sensitive at identifying distant homologies."
"COBALT stands for Constraint Based Alignment Tool."
"It uses conserved domains to guide the alignment."
"Primer-Blast is another BLAST variant."
"It combines with BLAST so that it can do a specificity check."
"MOLE-BLAST is very useful for identifying 16S and other kinds of targeted sequences."
"It also has a feature of being able to tie these things back to sequences from type material so you can get accurate identification."
"If bioinformatics is successful and things are working the way we want to, we will get scientific publications, we will help people that need help in terms of being sick and need to find cures, and we'd also make environmental discoveries."
"Bioinformatics is the process through which the interpretation of billions of sequence observations yields a distillate of actionable findings."
"Mega-BLAST is faster than blastn."
"It's going to be a nice little case study of how to do a small bioinformatics project."
"Python is probably one of the best programming languages that you could use for bioinformatics."
"Bioinformatics is like computer science and biology."
"The idea behind cbio portal was really to address some of the challenges of cancer omics."
"R has an active community that constantly develops codes and packages for bioinformatics analysis."
"Bioconductor repository is very bioinformatics-centric, meant to hold packages to allow for open source software to be accessible to all bioinformaticians."
"I hope this is helpful for anyone who is looking to start out in bioinformatics."
"We have a tool called BioMart for data export."
"This is the age of bioinformatics where we really can start to look at virtually every database available to us."
"Magic-BLAST can work with RNA-seq and DNA-seq and it can align RNA-seq to a genome reference or to a transcript reference."
"Magic-BLAST is NCBI's next-gen read alignment program."
"So we are going to focus, here, on, really, the computational biology, bioinformatics content."
"So after we have done the FASTQC reports, we can go ahead and start on the next step which is going to be HISAT2."
"With one little click here on this filter button, you can actually exclude all mutations and copy number alterations of unknown significance from the counts and from the visualizations."
"This compression so this convert file format conversion from Sam to Bam is lossless so all of the information that was in the Sam file is also in the BAM file."
"Gene set enrichment analysis is initially developed to do something like this."
"If you look at programs called Rosetta and ITASSER, they are program packages that are a proper culmination of domain modeling, ab initio, fold recognition, as well as energy minimization, statistical analysis."
"All right, so this is another in the set of bite-size bioinformatics talks."
"The gene ontology is a computable lexicon of controlled structured vocabulary for describing the attributes of genes and gene products in a species-neutral way."
"Guilt by association is very useful for gene function prediction."
"Bioinformatics is basically defined as the application of computer and computational sciences to the field of molecular biology."
"The sequencing gets cheaper and better, the bottleneck is the bioinformatics."