Tags
- ABI-SoLID
- color space
- introductory
- bioinformatics
- Other
- de-bruijn
- transcriptome assembly
- genome assembly
- GEO
- R
- K-mer
- hadoop
- computer
- RAM
- maintenance
- oases
- velvet
- Trinity
- SRA
- contrail
- search
- bowtie
- BWT
- BWA
- inchworm
- compression
- humor
- lincRNA
- Roadmap
- metagenome
- Bloom
- FPGA
- Pac Bio
- N50
- SOAPdenovo
- Polymorphic
- Minia
- Bloom filter
- Scaffolding
- Paired end
- immunology
- Pacbio
- RNAseq
- Diginorm
- Phasing
- Rectangular graph
- SPAdes
- move
- Rosalind
- de Bruijn graph
- assembly
- string graph
- NGS
- technology
- video
- social
- philosophy
- algorithm
- bwt
- graph
- epigenetics
- book
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- elhaik
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- suicide
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- genome
ABI-SoLID
- Untangling Genomes from Metagenomes (Attn. SOLiD users) 07 Mar 2012
- Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps 27 Sep 2011
- K-mer Sizes for Genome Assembly 27 Sep 2011
- Do de Bruijn Assemblers Work in Color Space? 09 Sep 2011
- The Mathematics of Color Space Sequencing 15 Feb 2010
color space
- Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps 27 Sep 2011
- K-mer Sizes for Genome Assembly 27 Sep 2011
- Trinity and Contrail for Color Space 18 Sep 2011
- Do de Bruijn Assemblers Work in Color Space? 09 Sep 2011
- The Mathematics of Color Space Sequencing 15 Feb 2010
introductory
- Tutorials - An Absolute Beginner's Guide to Bioinformatics 10 Jun 2019
- (Remotely Taught Module) - Data Visualization in R 04 Apr 2019
- A Bioinformatics Study Guide for the Biologists - (i) 25 Feb 2019
- If You are New Here 22 Nov 2011
- Do not Go for a Swim after Having an Ice Cream 17 Nov 2011
- A Road Map for our Journey through the Transcriptomic Maze 08 Aug 2011
- Comparison of data analysis packages 05 Aug 2011
- Highlights - 7/30/2011 30 Jul 2011
- Highlights - 7/25/2011 25 Jul 2011
- Algorithms for Next-gen Sequence Analysis 25 Jul 2011
- A beginner's guide to bioinformatics - part II 22 Jul 2011
- A beginner's guide to bioinformatics - part I 22 Jul 2011
bioinformatics
- Must-have Tools for a Bioinformatician 19 Sep 2011
- A Road Map for our Journey through the Transcriptomic Maze 08 Aug 2011
- Comparison of data analysis packages 05 Aug 2011
- Algorithms for Next-gen Sequence Analysis 25 Jul 2011
- A beginner's guide to bioinformatics - part II 22 Jul 2011
- A beginner's guide to bioinformatics - part I 22 Jul 2011
Other
de-bruijn
- K-mer Distribution of a Transcriptome 26 Oct 2011
- Output of Oases Transcriptome Assembler 04 Oct 2011
- Explaining Output of Trinity Component - Inchworm 04 Oct 2011
- Partitioning Libraries to Fit Small RAM Size 28 Sep 2011
- Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps 27 Sep 2011
- K-mer Sizes for Genome Assembly 27 Sep 2011
- Watching a de Bruijn Assembler in Action (Contrail) 21 Sep 2011
- Maximizing Utility of Available RAMs in K-mer World 20 Sep 2011
- Trinity and Contrail for Color Space 18 Sep 2011
- Do de Bruijn Assemblers Work in Color Space? 09 Sep 2011
- Contrail - A de Bruijn Genome Assembler that uses Hadoop 08 Sep 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – IV 25 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – III 23 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. - II 22 Aug 2011
- Using Mate Pair Information in de Bruijn Graphs 17 Aug 2011
- De Novo Transcriptome Assemblers - Oases, Trinity, etc. 15 Aug 2011
- A Drawback of de Bruijn Graph Approach 11 Aug 2011
- De Bruijn Graphs for Alternative Splicing and Repetitive Regions 09 Aug 2011
- How do sequencing errors affect de Bruijn graphs? 01 Aug 2011
- De Bruijn Graphs - III 31 Jul 2011
- De Bruijn graphs - II 29 Jul 2011
- De Bruijn graphs - I 28 Jul 2011
transcriptome assembly
- Oases Transcriptome Assembler 07 Aug 2012
- K-mer Distribution of a Transcriptome 26 Oct 2011
- Output of Oases Transcriptome Assembler 04 Oct 2011
- Explaining Output of Trinity Component - Inchworm 04 Oct 2011
- Partitioning Libraries to Fit Small RAM Size 28 Sep 2011
- Maximizing Utility of Available RAMs in K-mer World 20 Sep 2011
- Trinity and Contrail for Color Space 18 Sep 2011
- Do de Bruijn Assemblers Work in Color Space? 09 Sep 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – IV 25 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – III 23 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. - II 22 Aug 2011
- De Novo Transcriptome Assemblers - Oases, Trinity, etc. 15 Aug 2011
- De Bruijn Graphs for Alternative Splicing and Repetitive Regions 09 Aug 2011
- How do sequencing errors affect de Bruijn graphs? 01 Aug 2011
- De Bruijn Graphs - III 31 Jul 2011
- De Bruijn graphs - II 29 Jul 2011
- De Bruijn graphs - I 28 Jul 2011
genome assembly
- Can Trinity be Used for Genome Assembly? 29 Mar 2012
- Untangling Genomes from Metagenomes (Attn. SOLiD users) 07 Mar 2012
- Partitioning Libraries to Fit Small RAM Size 28 Sep 2011
- K-mer Sizes for Genome Assembly 27 Sep 2011
- Watching a de Bruijn Assembler in Action (Contrail) 21 Sep 2011
- Maximizing Utility of Available RAMs in K-mer World 20 Sep 2011
- Trinity and Contrail for Color Space 18 Sep 2011
- Do de Bruijn Assemblers Work in Color Space? 09 Sep 2011
- Contrail - A de Bruijn Genome Assembler that uses Hadoop 08 Sep 2011
- Using Mate Pair Information in de Bruijn Graphs 17 Aug 2011
- A Drawback of de Bruijn Graph Approach 11 Aug 2011
- De Bruijn Graphs for Alternative Splicing and Repetitive Regions 09 Aug 2011
- How do sequencing errors affect de Bruijn graphs? 01 Aug 2011
- De Bruijn Graphs - III 31 Jul 2011
- De Bruijn graphs - II 29 Jul 2011
- De Bruijn graphs - I 28 Jul 2011
GEO
- GEO and SRA - Quarterly Growth in Transcriptomic Research 28 Aug 2011
- Where are the global hotbeds of transcriptomic research? 23 Aug 2011
- A Bird's Eye View of NCBI GEO Database - II 17 Aug 2011
- A Bird's Eye View of NCBI GEO Database 03 Aug 2011
R
- RNAseq Questions - How to Load and Combine Salmon Data in R? 25 Sep 2019
- RNAseq Questions - Loading Many Kallisto Count Files in R 24 Sep 2019
- RNAseq Questions - How to Combine Gene Annotations (gff/gtf) with Kallisto Counts? 24 Sep 2019
- RNAseq Questions - How to Load and Combine Kallisto Counts in R? 23 Sep 2019
- Tryst between Marilyn Monroe and Albert Einstein 20 Sep 2019
- A Minimalist R Cheatsheet for NGS Biology 20 Sep 2019
- Git Tricks to be Dangerous 01 Aug 2019
- Please Join Our Expert Membership Section 26 Jul 2019
- The Hardest Easy Problem in Bioinformatics 10 Jul 2019
- R is the Most Powerful Language, but not for Bioinformatics 01 Jul 2019
- (Remotely Taught Module) - Data Visualization in R 04 Apr 2019
- A Bioinformatics Study Guide for the Biologists - (i) 25 Feb 2019
- Unpacking S4 Objects in R 22 Feb 2019
- Here is How RNAseq.work Works 20 Feb 2019
- R Code for Adding Isoform Data in RNAseq 19 Feb 2019
- Formula Syntax in RNAseq Packages like DESeq2 or edgeR 10 Dec 2018
- Rnaseq.work - Current APIs and Design Decisions 09 Dec 2018
- Rnaseq.work - Plotting Functions in RNAseq-related Packages 05 Dec 2018
- Rnaseq.work - A Package with Clean APIs for Statistical Analysis of RNAseq Data 04 Dec 2018
- Live Online Class - RNAseq Data Analysis using R 27 Nov 2018
- R / Bioconductor (limma) 22 Nov 2011
- Comparison of data analysis packages 05 Aug 2011
- Using R for Transcriptome Analysis - I 04 Aug 2011
K-mer
- An Intuitive Explanation for Running Velvet with Varying K-mer Sizes 17 Jun 2012
- Efficient Methods for Counting K-mers 28 Mar 2012
- K-mer Distribution of a Transcriptome 26 Oct 2011
- Partitioning Libraries to Fit Small RAM Size 28 Sep 2011
- K-mer Sizes for Genome Assembly 27 Sep 2011
- Maximizing Utility of Available RAMs in K-mer World 20 Sep 2011
- Hadoop Example - FAQ 05 Sep 2011
- Using Hadoop for Transcriptomics - An Example to Get Started 31 Aug 2011
- Using Hadoop for Transcriptomics 08 Aug 2011
hadoop
- Watching a de Bruijn Assembler in Action (Contrail) 21 Sep 2011
- Trinity and Contrail for Color Space 18 Sep 2011
- Contrail - A de Bruijn Genome Assembler that uses Hadoop 08 Sep 2011
- Hadoop Example - FAQ 05 Sep 2011
- Using Hadoop for Transcriptomics - An Example to Get Started 31 Aug 2011
- Using Hadoop for Transcriptomics 08 Aug 2011
computer
RAM
maintenance
- If You are New Here 22 Nov 2011
- The Report of our Death was an Exaggeration 16 Nov 2011
- Few Small Updates with the Website 26 Oct 2011
- Wordpress Comment Section is Open 20 Sep 2011
- We are on Twitter 17 Aug 2011
- Why no comments section? 10 Aug 2011
oases
- Oases Transcriptome Assembler 07 Aug 2012
- Output of Oases Transcriptome Assembler 04 Oct 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – IV 25 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – III 23 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. - II 22 Aug 2011
- De Novo Transcriptome Assemblers - Oases, Trinity, etc. 15 Aug 2011
velvet
- More Details on Velvet Roadmaps File Based on Reader's Question 27 Dec 2012
- Oases Transcriptome Assembler 07 Aug 2012
- An Intuitive Explanation for Running Velvet with Varying K-mer Sizes 17 Jun 2012
- An Explanation of Velvet Parameter exp_cov 08 Jun 2012
- Velvet Optimizer and MetaVelvet 06 Dec 2011
- Format of Velvet Output File 'Roadmaps' 06 Dec 2011
- Two Simple Rules 24 Oct 2011
- Output of Oases Transcriptome Assembler 04 Oct 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – III 23 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. - II 22 Aug 2011
- De Novo Transcriptome Assemblers - Oases, Trinity, etc. 15 Aug 2011
Trinity
- Can Trinity be Used for Genome Assembly? 29 Mar 2012
- Explaining Output of Trinity Component - Inchworm 04 Oct 2011
- Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps 27 Sep 2011
- Trinity and Contrail for Color Space 18 Sep 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – IV 25 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. – III 23 Aug 2011
- De Novo Transcriptome Assemblers – Oases, Trinity, etc. - II 22 Aug 2011
- De Novo Transcriptome Assemblers - Oases, Trinity, etc. 15 Aug 2011
SRA
contrail
- Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps 27 Sep 2011
- Watching a de Bruijn Assembler in Action (Contrail) 21 Sep 2011
- Trinity and Contrail for Color Space 18 Sep 2011
- Contrail - A de Bruijn Genome Assembler that uses Hadoop 08 Sep 2011
search
- Data Compression Algorithms 21 Oct 2011
- Finding us in homolog.us III (Search Algorithm and Indexing) 17 Oct 2011
- Finding us in homolog.us - part II 05 Oct 2011
- Finding us in homolog.us 03 Oct 2011
bowtie
- Suffix Arrays 22 Nov 2011
- Data Compression Algorithms 21 Oct 2011
- Burrows Wheeler transform, Suffix Arrays and FM Index 20 Oct 2011
- Finding us in homolog.us III (Search Algorithm and Indexing) 17 Oct 2011
- Finding us in homolog.us - part II 05 Oct 2011
- Finding us in homolog.us 03 Oct 2011
BWT
- Suffix Arrays 22 Nov 2011
- Data Compression Algorithms 21 Oct 2011
- Burrows Wheeler transform, Suffix Arrays and FM Index 20 Oct 2011
- Finding us in homolog.us III (Search Algorithm and Indexing) 17 Oct 2011
- Finding us in homolog.us - part II 05 Oct 2011
- Finding us in homolog.us 03 Oct 2011
BWA
- Suffix Arrays 22 Nov 2011
- Data Compression Algorithms 21 Oct 2011
- Burrows Wheeler transform, Suffix Arrays and FM Index 20 Oct 2011
- Finding us in homolog.us III (Search Algorithm and Indexing) 17 Oct 2011
- Finding us in homolog.us - part II 05 Oct 2011
- Finding us in homolog.us 03 Oct 2011
inchworm
compression
- Compression of Next-generation Sequencing Reads Aided by Highly Efficient de novo Assembly 22 Aug 2012
- Data Compression Algorithms 21 Oct 2011
- Burrows Wheeler transform, Suffix Arrays and FM Index 20 Oct 2011
humor
lincRNA
Roadmap
- More Details on Velvet Roadmaps File Based on Reader's Question 27 Dec 2012
- Format of Velvet Output File 'Roadmaps' 06 Dec 2011
metagenome
- Quip, Minia, SlimGene and Titus Brown's paper on Scaling Metagenome 19 Jul 2012
- Untangling Genomes from Metagenomes (Attn. SOLiD users) 07 Mar 2012
- Velvet Optimizer and MetaVelvet 06 Dec 2011
Bloom
FPGA
Pac Bio
N50
- What is Wrong with N50? How can we make it better? 26 Jun 2012
- What is Wrong with N50? How can we make it better? - part II 26 Jun 2012
SOAPdenovo
- Testing SOAPdenovo2 Prerelease – V (map and scaff) 10 Jul 2012
- Testing SOAPdenovo2 Prerelease - IV (building contigs) 05 Jul 2012
- Testing SOAPdenovo2 Prelease Version - III 05 Jul 2012
- Testing SOAPdenovo2 Pre-release Version - II (pregraph_sparse) 04 Jul 2012
- Testing SOAPdenovo2 Pre-release Version 27 Jun 2012
Polymorphic
- How Do Haplotype Differences Appear to de Bruijn Assemblers ? 29 Aug 2012
- HaploMerger: A Software Tool for Assembling Highly Polymorphic Genomes 11 Jul 2012
Minia
Bloom filter
- Probabilistic Data Structures - an Excellent Introduction 27 Aug 2012
- Quip, Minia, SlimGene and Titus Brown's paper on Scaling Metagenome 19 Jul 2012
Scaffolding
- From de Bruijn Graphs to Rectangle Graphs for Genome Assembly 12 Sep 2012
- An Efficient Preprocessing Module for Joining Paired end Reads before Assembly 30 Jul 2012
Paired end
immunology
Pacbio
- Finding SNPs from Long Noisy Reads 18 Jul 2018
- Mixing Illumina and PacBio Data for Genome Finishing 02 Aug 2012
RNAseq
- Live Online Class - RNAseq Data Analysis using R 27 Nov 2018
- Salmonberry Genomics by High-school Students 18 Apr 2018
- Oases Transcriptome Assembler 07 Aug 2012
Diginorm
Phasing
Rectangular graph
SPAdes
move
- New Species of "Walking" Shark Found in Indonesia 31 Aug 2013
- Surprise of the Day - Zebrafish Genome 'Published' 30 Apr 2013
- Genome of a 'Living Fossil' 19 Apr 2013
- Lamprey Genome Shows When Humans Evolved Jaws, Matching Arms, Legs and More 27 Feb 2013
- Challenges in Assembling Fish Genomes 12 Dec 2012
Rosalind
de Bruijn graph
- Practical Dynamic de Bruijn Graphs 20 Jul 2018
- Integration of String and de Bruijn Graphs for Genome Assembly 18 Jan 2016
assembly
- Hybrid Metagenomic Assembler OPERA-MS 30 Jul 2019
- Please Join Our Expert Membership Section 26 Jul 2019
- Genome Assembly is a Nearly Solved Problem with Long Reads 26 Jul 2019
- Campbell Biology is a Horrendously Expensive Worthless Book 26 Jul 2019
- Pay Attention to These Three New and Impressive Genome Assemblers 29 May 2019
- Genome assembly algorithms through jigsaw puzzles - III 01 Mar 2017
- Genome assembly algorithms through jigsaw puzzles - II 21 Feb 2017
- KMC tools tutorial - II 16 Feb 2017
- A tutorial on KMC tools 15 Feb 2017
- Genome assembly algorithms through jigsaw puzzles 14 Feb 2017
- Integration of String and de Bruijn Graphs for Genome Assembly 18 Jan 2016
string graph
NGS
technology
video
social
- Transistors, Translation and tRNAs 10 May 2016
- Geopolitics - Several New Developments Will Define the World in the Coming 01 May 2016
- Freedom of Speech 01 May 2016
philosophy
- Transistors, Translation and tRNAs 10 May 2016
- Geopolitics - Several New Developments Will Define the World in the Coming 01 May 2016
algorithm
bwt
graph
- GRASS for Rapid Reannotation of RNAseq Data 16 Dec 2016
- A Graph Extension of the Positional Burrows-Wheeler Transform and its Applications 02 May 2016
epigenetics
book
jewish
- Is '23 and Me' Misleading its Jewish Customers on Ancestry? 30 Oct 2017
- Population Genetics of Ancient Jewish Population in India 11 May 2016
- Jewish Genetics - Forward Magazine Makes Elhaik's Work Go Viral 06 May 2016
elhaik
job
- Postdoctoral Scholar Position in Comparative Plant Genomics and Bioinformatics 12 Oct 2016
- Job Opening - Postdoctoral Scholar: Forest Genomics Database and Software Developer 06 May 2016
university
human health
- Suicide Epidemic: Since NIH-funded Clowns Do Not Want to Discuss It, We Will 12 May 2016
- Organoids and the Coming Medical Revolution - (ii) 10 May 2016
- Transfer RNAs and Neurodegenerative Disorders 09 May 2016
- Organoids and the Coming Medical Revolution - (i) 09 May 2016
- The Wall Will be Built and Mexico Will Pay for It 06 May 2016
organoid
- Organoids and the Coming Medical Revolution - (ii) 10 May 2016
- Organoids and the Coming Medical Revolution - (i) 09 May 2016
tRNA
population genetics
NIH failure
suicide
alignment
- SibeliaZ - An Extremely Fast Aligner for Multiple Genomes 24 Feb 2019
- Qudaich - a Smart Sequence Aligner 13 Sep 2016
protein
suffix array
pacbio
- Illumina Offers to Donate Pacbio Patents, But Will That Save Oxford Nanopore? 18 Nov 2019
- Woodford's WEIF Dead, Oxford Nanopore IPO Doubtful 15 Oct 2019
- Pacbio Releases HiFi Data on Drosophila, Rice and Those Pesky Little Creatures (aka Humans) 10 Oct 2019
- All Against All Fight Breaks Out among the Sequencing Businesses 10 Oct 2019
- Hybrid Metagenomic Assembler OPERA-MS 30 Jul 2019
- Genome Assembly is a Nearly Solved Problem with Long Reads 26 Jul 2019
- Uncertainty over Pacbio-Illumina Deal May Spill over to Oxford Nanopore 12 Jul 2019
- I Wish Ryan Wick Does not "Publish" his Long Read Assembler Comparison 10 Jul 2019
- Scrubbing Tools for Long Noisy Reads from Rayan Chikhi and Collaborators 24 Jun 2019
- Pay Attention to These Three New and Impressive Genome Assemblers 29 May 2019
- Illumina Buys Pacbio, What Are the Implications? 02 Nov 2018
- Roche Dumps Pacbio 16 Dec 2016
- Ongoing Pacbio bioinformatics meeting (#SMRTBFX) 14 Sep 2016
long reads
- Pacbio Releases HiFi Data on Drosophila, Rice and Those Pesky Little Creatures (aka Humans) 10 Oct 2019
- Ongoing Pacbio bioinformatics meeting (#SMRTBFX) 14 Sep 2016
gene myers
kallisto
- Debugging RNAseq - (iv) Effective Length and TPM 04 Oct 2019
- Debugging RNAseq - (iii) Expectation Maximization Hands on 03 Oct 2019
- Debugging RNAseq - (ii) Core Concept - Expectation Maximization 03 Oct 2019
- Debugging RNAseq Analysis - (i) 02 Oct 2019
- Lior Pachter's Zika Paper 14 Sep 2016
sleuth
ruby
jekyll
protein folding
LISP
visualization
- Zipper plot for visualizing transcriptional activity of genomic regions 02 Oct 2016
- SuperTranscript - a reference for analysis and visualization of the transcriptome 02 Oct 2016
rna-seq
- Please Join Our Expert Membership Section 26 Jul 2019
- Mantis and the Counting Quotient Filter 14 Jul 2018
- Using Multidimensional Bloom filters to Search RNAseq Libraries - (i) 13 Dec 2016
bloom filter
- Practical Dynamic de Bruijn Graphs 20 Jul 2018
- Mantis and the Counting Quotient Filter 14 Jul 2018
- Using Multidimensional Bloom filters to Search RNAseq Libraries - (i) 13 Dec 2016
annotation
nanopore
- Oxford Nanopore IPO Takes Place on the Same Day UK Runs out of Petrol 08 Oct 2021
- Illumina Offers to Donate Pacbio Patents, But Will That Save Oxford Nanopore? 18 Nov 2019
- Woodford's WEIF Dead, Oxford Nanopore IPO Doubtful 15 Oct 2019
- All Against All Fight Breaks Out among the Sequencing Businesses 10 Oct 2019
- Hybrid Metagenomic Assembler OPERA-MS 30 Jul 2019
- Uncertainty over Pacbio-Illumina Deal May Spill over to Oxford Nanopore 12 Jul 2019
- Scrubbing Tools for Long Noisy Reads from Rayan Chikhi and Collaborators 24 Jun 2019
- Will Companies Like Oxford Nanopore be at the Epicenter of the Next Financial Crisis? 12 Jun 2019
- Pay Attention to These Three New and Impressive Genome Assemblers 29 May 2019
- A Decision Point Arrives for Oxford Nanopore 22 May 2019
- A New Nemesis for Nanopore 30 Jan 2018
- Business analysis - Oxford Nanopore 16 Dec 2016
human
rosalind
- Annual Bioinformatics Contest from the Rosalind Team 18 Jan 2019
- Bioinformatics Contest - 2018 31 Jan 2018
- Online Bioinformatics Contest from Stepik/Rosalind 13 Jan 2017
contest
- Annual Bioinformatics Contest from the Rosalind Team 18 Jan 2019
- Bioinformatics Contest - 2018 31 Jan 2018
- Online Bioinformatics Contest from Stepik/Rosalind 13 Jan 2017
review
- The Best of 2021 31 Dec 2021
- Tuesday Review - SAVE your day for CRISPR, Nature Fake News and Other Stories 28 Feb 2017
- Monday review - Myers' dBG Paper, Pacbio's Multiplexing and Bioinformaticians' Foray into Escapism 20 Feb 2017
- Monday review - KMC3 and other seXY topics 13 Feb 2017
kmer
- Counting Quotient Filter and SeqOthello 02 Oct 2019
- KMC tools tutorial - II 16 Feb 2017
- A tutorial on KMC tools 15 Feb 2017
online courses
- Another Tutorial - This Time on Pevzner's Videos 04 Mar 2017
- A Tutorial with Ben Langmead's Bioinformatics Videos 03 Mar 2017
molecular biology, autobiography
NIH
- Time to Shrink the National Institute of Health (NIH)? 22 Mar 2017
- Is Google Tweaking Search Results to Block Our Posts Critical of NIH Director? 21 Mar 2017
life expectancy
fake science
minimizer
dock
tutorial
ancestry
- DIY Ancestry Analysis using the GPS Algorithm 13 Dec 2017
- The Diversity of REcent and Ancient huMan (DREAM) 12 Dec 2017
- Is '23 and Me' Misleading its Jewish Customers on Ancestry? 30 Oct 2017
GPS
- DIY Ancestry Analysis using the GPS Algorithm 13 Dec 2017
- The Diversity of REcent and Ancient huMan (DREAM) 12 Dec 2017
- Is '23 and Me' Misleading its Jewish Customers on Ancestry? 30 Oct 2017
open-source
china
hardware
multi-core
autoconf
code
crowdfunding
aligners
post-doc
Nanopore
SNP
graur
- Dan Graur's Excellent Book Sold Only One Copy so Far 26 Jul 2019
- Genomfart 27 Jun 2019
- Puzzling observations from various eukaryotic genomes (part III) 27 Sep 2018
- How do the eukaryotic genomes evolve? (part II) 25 Sep 2018
- How do the eukaryotic genomes evolve? (part I) 24 Sep 2018
- Molecular and Genome Evolution by Dan Graur 19 Sep 2018
genome evolution
- Please Join Our Expert Membership Section 26 Jul 2019
- Dan Graur's Excellent Book Sold Only One Copy so Far 26 Jul 2019
- Campbell Biology is a Horrendously Expensive Worthless Book 26 Jul 2019
- Genomfart 27 Jun 2019
- Weird Patterns in Japanese Genome Evolution Explained by Garbage-in Garbage-out Effect 07 May 2019
- Puzzling observations from various eukaryotic genomes (part III) 27 Sep 2018
- How do the eukaryotic genomes evolve? (part II) 25 Sep 2018
- How do the eukaryotic genomes evolve? (part I) 24 Sep 2018
- Molecular and Genome Evolution by Dan Graur 19 Sep 2018
sequencing
illumina
- Illumina Offers to Donate Pacbio Patents, But Will That Save Oxford Nanopore? 18 Nov 2019
- Woodford's WEIF Dead, Oxford Nanopore IPO Doubtful 15 Oct 2019
- All Against All Fight Breaks Out among the Sequencing Businesses 10 Oct 2019
- Uncertainty over Pacbio-Illumina Deal May Spill over to Oxford Nanopore 12 Jul 2019
- Illumina Buys Pacbio, What Are the Implications? 02 Nov 2018
live online class
rnaseq.work
- Formula Syntax in RNAseq Packages like DESeq2 or edgeR 10 Dec 2018
- Rnaseq.work - Current APIs and Design Decisions 09 Dec 2018
- Rnaseq.work - Plotting Functions in RNAseq-related Packages 05 Dec 2018
- Rnaseq.work - A Package with Clean APIs for Statistical Analysis of RNAseq Data 04 Dec 2018
plot
- Rnaseq.work - Current APIs and Design Decisions 09 Dec 2018
- Rnaseq.work - Plotting Functions in RNAseq-related Packages 05 Dec 2018
isoform
expression
- RNAseq Questions - How to Load and Combine Salmon Data in R? 25 Sep 2019
- RNAseq Questions - Loading Many Kallisto Count Files in R 24 Sep 2019
- RNAseq Questions - How to Combine Gene Annotations (gff/gtf) with Kallisto Counts? 24 Sep 2019
- RNAseq Questions - How to Load and Combine Kallisto Counts in R? 23 Sep 2019
- Here is How RNAseq.work Works 20 Feb 2019
tutorials
class
languages
multi-genome
dplyr
ggplot
contanimation
Python
Bioconductor
- R is the Most Powerful Language, but not for Bioinformatics 01 Jul 2019
- Python Sandbox and Other Helpful Resources for Biology/Bioinformatics 21 May 2019
long-reads
- Scrubbing Tools for Long Noisy Reads from Rayan Chikhi and Collaborators 24 Jun 2019
- Pay Attention to These Three New and Impressive Genome Assemblers 29 May 2019
blog
functional programming
synteny
long read
Biopython
open source
python
hybrid
git
biopython
server
hashing
salmon
- Debugging RNAseq - (iv) Effective Length and TPM 04 Oct 2019
- Debugging RNAseq - (iii) Expectation Maximization Hands on 03 Oct 2019
- Debugging RNAseq - (ii) Core Concept - Expectation Maximization 03 Oct 2019
- Debugging RNAseq Analysis - (i) 02 Oct 2019
DEseq2
DESeq2
TPM
bgi
- Illumina Offers to Donate Pacbio Patents, But Will That Save Oxford Nanopore? 18 Nov 2019
- Woodford's WEIF Dead, Oxford Nanopore IPO Doubtful 15 Oct 2019
- All Against All Fight Breaks Out among the Sequencing Businesses 10 Oct 2019
coronavirus
- Devastating Impact of Climate Change Around the World 17 Dec 2021
- Did They Fake Their Entire NGS Experiment? 15 Dec 2021
- Another Unusual Connection Between Covid and AIDS 09 Dec 2021
- A Disturbing Rise in Heart Attacks Explained 09 Dec 2021
- Leaky Vaccines, Freaky Mutants and Viral Quasiparticle Swarms 08 Dec 2021
- Dishonest Trevor Bedford Wins Howard Hughes and MacArthur Awards 04 Oct 2021
- Is It Time to Retract All Papers from Zhengli Shi and Peter Daszak? 24 Sep 2021
- This DEFUSE Grant Proposal is the Scariest Document I Have Ever Read 22 Sep 2021
- Three Major Breakthroughs on the Origin of Covid 21 Sep 2021
- Biologists Want Any Criticism of Them Legally Labeled as "Hate Crime" 05 Aug 2021
- BMJ Criticizes "Sir" Jeremy Farrar in Scathing Articles 14 Jul 2021
- Genome Assembly Experts - Was RaTG13 Fraudulently Constructed? 09 Jul 2021
- Covid Coverup Party (CCP) Invades Zenodo 09 Jul 2021
- Important Covid-related Datasets Disappeared from NCBI SRA 30 Jun 2021
- Discover Novel Viruses Without Leaving Your Couch 29 Jun 2021
- Pangolin - Guilty or Not Guilty? 18 May 2020
- Did SARS-1.0 Come from Bats through Civets? 02 May 2020
- Strains of SARS-CoV-2 28 Mar 2020
- Is Wuhan Coronavirus a Bioweapon? 26 Mar 2020
