evolving all we are: computational molecular biology lab

2012年5月1日星期二

computational molecular biology lab

http://cmb.molgen.mpg.de/

Gene Regulation (Martin Vingron)

Evolutionary Genomics (Peter Arndt)

Gene Structure and Array Design (Stefan Haas)

Mechanisms of transcriptional regulation Group (Sebastiaan H. Meijsing)

Long non-coding RNA (Ulf Andersson Ørom)

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我的博客列表

FlowingData

Rise in prison death rates during the pandemic - The Marshall Project highlights research on excess mortality in U.S. prisons: The slowdown… *Tags:* Marshall Project, mortality, pandemic
4 小时前
Discover Blogs

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16 小时前
OUseful.Info, the blog...

Simple Playwright Tests for Jupyter Environments - In passing, I’ve been revising a couple of JupyterLab extensions I’ve cobbled together in the past and started looking at producing some simple Playwright ...
19 小时前
Phylogenetic Tools for Comparative Biology

Pruning a mega-phylogeny to include a list of taxa in which the names don't match exactly - The other day a colleague asked me for advice on getting a reasonable time-calibrated phylogeny for a set of taxa to use for a comparative physiology ex...
20 小时前
Nothing in biology makes sense!

Ile kalorii ma miód? Dowiedz się ile kalorii ma łyżeczka miodu! - Miód – słodki składnik zdrowej diety Miód – ten naturalny słodzik od wieków jest ceniony nie tylko za swoje walory smakowe, ale również za liczne korzyśc...
2 天前
Quantum Forest

A dollop of Spanish - Most of my followers are English speakers (native speakers, second-language, third-language, nth-language speakers) so they could be confused by my occasio...
3 天前
The Molecular Ecologist

Molecular Ecology call for papers: Genomics of Speciation - Molecular Ecology invites papers to be considered for inclusion in a planned Special Issue on the genomics of speciation. The special issue editors are int...
5 天前
iPhylo

Notes on transforming BHL images - How to cite: *Page, R. (2024). Notes on transforming BHL images https://doi.org/10.59350/2gpbb-98a53* I’ve been down this road before, e.g. BHL, DjVu, and ...
5 天前
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4 周前
Shige's Research Blog

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2 个月前
Living in an Ivory Basement

Speeding sourmash the heck up - Faster things are always nice, right?
2 个月前
PubMed New and Noteworthy

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2 个月前
The Tree of Life

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2 个月前
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3 个月前
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3 个月前
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Bye, RStudio/Posit! - Who is down? Me. After more than 10 years at RStudio/Posit, the time has come for me to explore other opportunities. A little over two weeks ago, I was t...
3 个月前
Python for Bioinformatics

Ratio boxes - I worked up a short new chapter for my Geometry book. It's about a device I'm calling ratio boxes, for want of a better word. When we have similar triangle...
5 个月前
theBioBucket*

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Public Rambling

State of the lab 10 and 11 - the first years at ETH Zurich - [image: a lake by a mountain] *Yet another lake by a mountain in Switzerland*This blog post is part of a (nearly) yearly series on running a research grou...
5 个月前
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Time to leave “species richness” behind, as it serves no scientific purpose on x- or y-axis - A guest post by Carsten F. Dormann, University of Freiburg In “biodiversity science”, species richness takes a very prominent role. It is the most analysed...
6 个月前
Gregor Gorjanc

Overload of the term "additive" in quantitative genetics - The following discussion came up on SLiM (https://messerlab.org/slim/) mailing list (https://groups.google.com/g/slim-discuss), which I think is highly ind...
6 个月前
Abhishek Tiwari

Kernel of a good strategy - Why, How and What - In the rapidly changing landscape of business, having a well-defined strategy is crucial for success. A good strategy should address the core problems or...
6 个月前
Econometric Sense

Master of Science in Agriculture (Emphasis in Biometry) - As defined by R.A. Fisher *“Biometry, the active pursuit of biological knowledge by quantitative methods”* is the application of statistical and quantita...
7 个月前
The OpenHelix Blog

Dynamics 365 Finance moderniza las operaciones financieras de tu empresa - Dynamics 365 Finance es un sistema ERP basado en la nube diseñado para optimizar los procesos comerciales. Al ofrecer una plataforma para todas las funci...
7 个月前
Junk Charts

Losing the plot while stacking up the bars - Kaiser looks at an infographic about dirty American cities.
7 个月前
microBEnet: The microbiology of the Built Environment network.

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9 个月前
JAGS News

JAGS 4.3.2 is released - This is another patch release from the 4.3.x series. This one is required to keep up with the evolving C++ standard. Previous JAGS releases contained some ...
1 年前
ENMTools

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1 年前
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1 年前
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1 年前
Fabio Marroni’s Blog

An R function to compute Tumor Mutational Burden (TMB) - Tumor mutational (or mutation) burden, TMB, is considered a useful estimation of tumor neoantigenic load (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336...
1 年前
Cartesian Faith

Wallets as a reward and penalty mechanism for online behavior - I’m creating an AI moderator for social media using reinforcement learning (RL). My goal is to reduce toxicity/outrage and increase … Continue reading →
1 年前
The EEB & flow

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1 年前
the mind wobbles

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1 年前
One Tip Per Day

some Vi shortcuts - Copy and paste one line With the cursor at your desired line press yy. Press p wherever you like and the line will be pasted below the line you are on. ...
1 年前
The Genome Factory

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1 年前
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2 年前
My Biased Coin

Postdoc call for FODSI - As a member of FODSI (Foundations of Data Science Institute -- an NSF funded institute with the aim of advancing theoretical foundations for data science...
2 年前
My Weblog on Bioinformatics, Genome Science, Next Generation Sequencing

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2 年前
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3 年前
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3 年前
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3 年前
Genomes Unzipped

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3 年前
MYRMECOS

The 9th Annual Holiday Print Sale - I am excited to announce the return of the Holiday Insect Print Sale, now in its 9th year! I have selected 35-ish photographs that will be available at 70%...
3 年前
Linux Commando

Useful command-line date utilities - My earlier post, Fun with Date Arithmetic shows how to use the *date* command to compute a future or past date that is a certain number of days ahead or ...
3 年前
The UNIX School

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3 年前
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4 年前
Yixf's blog

无题 - 无题万言不入秦王耳，南花魂游丞相园。六月雪飞君莫笑，一秋更比一秋寒。
4 年前
geolabs

Map of an meadow orchard (Streuobst) - A few months ago I rented a meadow with orchards (ca. 8000m²). Some of the 70 trees (mainly cherry trees) are over 40 years old. The age, however, has no i...
4 年前
HubLog

Converting PDF to PNG or JPEG - What are the best tools or services for converting a page of a PDF file to an image? The first thing that usually shows up for converting PDF to PNG or J...
4 年前
Biospherica

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4 年前
Vijay Barve

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5 年前
Next-Gen Sequencing

Some tips to optimize bacterial genome assembly - I just finished a revised genome assembly for a collaborating lab. We do de novo sequencing of bacterial genomes all the time, sometimes in batches of 50 ...
5 年前
nzprimarysectortrade

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5 年前
Keep on Fighting!

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5 年前
Sharp Statistics

EasyER Version 1.2 - Version 1.2 of EasyER has now been released. The main change is the addition of a chart builder interface for interactively creating charts. The chart bu...
5 年前
Mailund on the Internet

Lecture notes on Computational Thinking - I am working on some lecture notes that should become a book at some point. It is for a class on “Computational Thinking”, which I guess is just a fancy te...
5 年前
The MolBio Hut

A “bottoms-up” approach to scientific publishing - A few days ago, a piece was posted at ASAPbio which reminded me of an idea I had a long time ago about a new model for publishing and peer review. I descri...
6 年前
Sam Harris: Author, neuroscientist, philosopher.

#113 — Consciousness and the Self - In this episode of the Waking Up podcast, Sam Harris speaks with Anil Seth about the scientific study of consciousness, where consciousness emerges in natu...
6 年前
i'm a chordata! urochordata!

Bayesian SEM with BRMS - Note: for the most up to date version of this, see this post on rpubs Background So, it looks like brms version 2.0 implements multivariate responses – and...
6 年前
Tr8dr

Blog Moved - After a long hiatus, have started writing again., however have moved the blog to GitHub. The new URL is: https://tr8dr.github.io Advertisements
6 年前
The Spittoon

23andMe Adds New Genetic Health Risk Reports - 23andMe released two new genetic health risk reports for customers for Age-Related Macular Degeneration and Hereditary Hemochromatosis. The post 23andMe ...
6 年前
Research tips

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7 年前
Timely Portfolio

Picking the Top - In Shorting With Reckless Abandon I expressed my views. I have now started documenting my journey at Picking The Top for anyone who wants to see my foolish...
7 年前
Getting Genetics Done

Staying Current in Bioinformatics & Genomics: 2017 Edition - A while back I wrote this post about how I stay current in bioinformatics & genomics. That was *nearly five years ago*. A lot has changed since then. A few...
7 年前
CoreGenomics

CoreGenomics has moved - *Follow this link to Enseqlopedia/coregenomics...* "CoreGenomics is dead...long live CoreGenomics"...the CoreGenomics blog has moved to its new home: http...
7 年前
YOKOFAKUN

Creating a custom GATK Walker (GATK 3.6) : my notebook - This is my notebook for creating a custom engine in GATK. Description I want to read a VCF file and to get a table of category/count. Something like this: ...
7 年前
Portfolio Probe

US market portrait 2016 final - US large cap market returns. Fine print The data are from Yahoo The S&P 500 stocks are used (as implied by Wikipedia on 2016 January 16) that still survive...
7 年前
Ewan's Blog; bioinformatician at large

My blog has moved! - As you may already be aware, I have moved my blog over to WordPress for practical reasons. I've enjoyed Blogger for its simplicity, but the experience on ...
7 年前
Quantitative Ecology

Recursively search for text in R scripts. - Often I find myself needing to search for .R or or .Rmd files in which I have used a specific function. There are a variety of searches that you can do; ho...
7 年前
The Praise of Insects

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7 年前
librestats

Comparing Symmetric Eigenvalue Performance - Lazy reader’s guide: skip to the pretty pictures, skim the conclusions section, ignore the rest. Background I think a lot about eigenvalue and singular ...
7 年前
EvoPhylo

Software and real carpentry - I like Software Carpentry, a non-profit organization teaching basic computing skills to researchers. But if I had one little criticism it would be that the...
7 年前
Graph of the Week

And Yet It Moves: Gravitational Waves - "The moment he was set at liberty, he looked up to the sky and down to the ground, and, stamping with his foot, in a contemplative mood, said, *Eppur si mu...
7 年前
数据科学与R语言

艺术风格的神经网络算法实验 - 2015年九月的时候出现了一篇很趣的论文《A Neural Algorithm of Artistic Style》。论文中提出了一种算法，可以将一张普通的图片，转换成具有某种艺术家的风格。用语言来描述计算流程如下： 1、首先用一个给定参数的卷积神经网络（VGG网络），将原始的内容图片和风格图片进行函数映射...
7 年前
Blog | Wainwright Lab | University of California, Davis

Hello world! - Welcome to Faculty Network Sites. This is your first post. Edit or delete it, then start blogging!
7 年前
bioCS

My knitr LaTeX template: manuscript and supplement interleaved in one source file - Most of the time between starting manuscript and having it accepted after peer-review is spent writing, re-writing and re-arranging content. In Word, keepi...
7 年前
Treevolution: Biology through the evolutionary lens

Response to Late Mitochondrial Origin is Pure Artefact - We recently published a study showing that protobacterial derived proteins in the Last Eukaryotic Common Ancestor (LECA) show a tendency to have shorter...
7 年前
Genome Toolbox

R Function to Calculate Confidence Interval from Odds Ratio and P-value - Every once in a while I need a confidence interval from a published estimate that only reports the estimated odds ratio and respective p-value. With a litt...
8 年前
Haldane's Sieve

Positive selection on a regulatory insertion-deletion polymorphism in FADS2 influences apparent endogenous synthesis of arachidonic acid - Positive selection on a regulatory insertion-deletion polymorphism in FADS2 influences apparent endogenous synthesis of arachidonic acid Kumar S.D. Kothapa...
8 年前
me nugget

RSpectra::svds function now default method for sinkr::dineof - The summary blog post describing the RSpectra (formerly rARPACK) package made a convincing case for the improved decomposition speed of the "svds" function...
8 年前
Bigcomputing

Setting up the Twitter R package for text analytics - The Twitter R package by Jeff Gentry is a great way to get started in Text Analytics. This tutorial is about how to get setup to pull twitter data into R s...
8 年前
IDV User Experience

That's All - I started blogging at IDV in April of 2007. Over the years it has become a terribly important venue for me, where I've shared surprisingly personal events ...
8 年前
Oscillatory Thoughts

New Voytek Lab paper by Richard Gao! - Voytek Lab Cognitive Science PhD student, Richard Gao, wrote a detailed piece about his new paper, "Interpreting the Electrophysiological Power Spectrum,” ...
8 年前
Stochastic Nonsense

Splitting Audio with ffmpeg - Here’s a quick utility to use a set list and ffmpeg to split single audio files into multiple tracks. It splits audio files via a setlist then sets the s...
8 年前
Jeffrey Horner

This is one of my favorite ggplot2 plots I’ve ever made, but it... - This is one of my favorite ggplot2 plots I’ve ever made, but it makes me sad. Can you deduce what this plot conveys? Explain the sporadically dashed colo...
8 年前
Omnia sunt Communia!

Sistemas Fotovoltaicos en Redes de Distribución - Hace un par de meses conseguí una plaza de Profesor Contratado Doctor en la Escuela Técnica Superior de Ingeniería y Diseño … Sigue leyendo →
8 年前
We think therefore we R

The curious case of ARIMA modelling using R - I recently made an interesting observation that I thought is worth sharing. During a data expedition process while trying to fit an ARIMA (auto-regressi...
9 年前
Biochemistry, Molecular, Cellular & Developmental Biology

Night Vision Without the Goggles - The human eye consists of focusing elements and photoreceptors. Images are formed when light is projected onto the retina, which houses photoreceptors call...
9 年前
Systematic Investor

New Home of Systematic Investor Blog - Please visit the New Home of Systematic Investor Blog at SystematicInvestor.GitHub.io
9 年前
Left Censored

R and MPI on Ohio Supercomputer Center’s Oakley cluster - A few years ago, I wrote a short guide to Using R and snow on the Ohio Supercomputer Center’s Glenn cluster. Several things have changed in the world of R ...
9 年前
Statistic on aiR

Adjustment for Multiple Comparison Tests with R: Resources on the web - *1. Bonferroni correction* p.adjust(p, method = "bonferroni") Read: http://en.wikipedia.org/wiki/ *2. Sidak (Dunn-Sidak) correction* Read: http://en.wiki...
9 年前
Carnival of Evolution

Carnival of Evolution #78 - the Short-Arse edition - Finally, the 78rd edition is up. Not too much has happened in the evolution blogosphere to my knowledge, so this edition is really short but good. Like sho...
9 年前
MycorWeb Fungal Genomics

1000 Fungal Genome (1KFG) project: Graduate Student-Postdoc Challenge (2014) - The 1000 Fungal Genome (1KFG) project is a large-scale community sequencing project supported by the Joint Genome Institute (JGI). The goal of 1KFG is to ...
9 年前
Matt's Stats n stuff

Shading between two lines – ggplot - First one to say geom_ribbon loses. I was plotting some data for a colleague, had two lines (repeated experiment) per person (time on the x axis) facetted ...
9 年前
Bioinformatics Tutorials

Comments on “Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines” - I recently co-authored a paper in Genome Biology entitled “Clinical drug response can be predicted using baseline gene expression levels and in vitro drug ...
10 年前
The Ubuntu R Blog

c2d4u and RRutter Ubuntu PPA Updates - On January 27, 2014 Raring Ringtail (13.04) reached end of life. I have been slowly removing the Raring repositories from the RRutter PPA, c2d4u PPA, and...
10 年前
ExploringDataBlog

A question of model uncertainty - It has been several months since my last post on classification tree models, because two things have been consuming all of my spare time. The first is th...
10 年前
PremierSoccerStats

Craig Bellamy – quite dplyr - This weekend brought a couple of firsts in Cardiff’s winner against Norwich After a wretched time at Manchester United, Wilfried Zaha recorded his first Pr...
10 年前
The Atavism

A Very Special edition of Sunday Spinelessness - Wow, it's been a long time since I wrote something here. Let's see if I can remember how this goes: I find a weird-looking bug and take some photos. Then ...
10 年前
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Database Reflection using dplyr - At work I write a ton of SQL, and I do most of my querying using R. The workflow goes: Create a string with the SQL in R Plug the string into fetchQuery (...
10 年前
Jack Zhu's Bioinfo

userstyles.org - Dictionary.com - permanent IPA pronounciation - Dictionary.com - permanent IPA pronounciation - Themes and Skins for Reference - userstyles.org
10 年前
Sacha Epskamp

A general Shiny app for reading data - A general Shiny app for reading data A general Shiny app for reading data I have been playing around a lot with making web-applications using shiny. What...
10 年前
mintgene

Reconstructing Principal Component Analysis Matrix - Edit: I’ve updated afterPCA function to work with input of any dimensions. Previously it only generated correct output for square matrices. PCA is widely u...
11 年前
Modern Toolmaking

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11 年前
Dodecad Ancestry Project

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11 年前
Simply Statistics

We've Moved! - Simply Statistics has moved to a new platform and so if you’ve been following our blog on Tumblr, you’ll have to update your links/RSS feeds to the new w...
11 年前
genomeboy

Closing time - A note from PLOS Blogs Community Manager Victoria Costello: We’re sad to see Misha Angrist leave our blog roster but we’ve been honored to host the last tw...
11 年前
Quantitative Ecology

Blog Moving - Thanks to everyone who's visited this blog and provided encouragement and suggestions. My blog is moving to http://danieljhocking.wordpress.com/quantitativ...
11 年前
EvolvingSpaces

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11 年前
Coffee and Econometrics in the Morning

Using apply() to create a unique id - Suppose you have a data set with two identifiers. For example, maybe you're studying the relationships among firms in an industry and you have a way to lin...
12 年前
Talk To Myself

多重PCR引物设计 (2) ——平衡反应体系 - 文 / 屈武斌 (quwubin@gmail.com) 多重PCR的一个关键点在于反应体系的平衡。即使多重PCR体系内每对引物的特异性都很好，在单重PCR测试中扩增效果也非常好，但到了多重体系中却经常出现某些目标产物扩增不出来的现象。原因就在于反应体系的不平衡，这种不平衡导致在前期的几轮反应中某些优势引物...
12 年前
Consistently Infrequent

R: A Quick Scrape of Top Grossing Films from boxofficemojo.com - Introduction I was looking at a list of the top grossing films of all time (available from boxofficemojo.com) and was wondering what kind of graphs I wou...
12 年前
Recology

Recology has moved - Recology has moved to Github, using Jekyll. I just finished moving the Recology blog content, etc. to Github. This move is intended to make it easy to do...
12 年前
Adventures in Statistical Computing

Portfolio Optimization in R, Part 4 Redeux - So where did we mess up? In the calculation of returns for the market cap weighted portfolio and the portfolio optimization portfolio, we simply took the...
12 年前
BMB's commonplace

Google Scholar (still) sucks - (This is a follow-up to my previous post on the topic.) I was encouraged by the appearance of *two* R-based Scholar-scrapers, within a week of each other. ...
12 年前
The Plant Informatics

Rod Page’s VIZBI 2011 annotated links - iPhylo is hands-down my favorite blog, whose author is Rod Page. In the blog post “Some VIZBI 2011 links”, Rod grabbed a list of visualization softwa...
12 年前
dechronization

- Applications for our r-workshop are still being accepted - please apply by June 15! We are pleased to announce an intensive short course on using R to per...
12 年前
joint posterior

compiler and runiregGibbs (bayesm) - So everyone's excited about the new R 2.13 release because of the compiler package. Apparently it is easy to get a 3x speed increase by simply compiling a ...
13 年前
The Prince of Slides

Introduction to The Prince of Slides - In my everlasting search for the answer to every sports (among other topics) question imaginable, I decided to create this blog. While there are a number o...
14 年前
alexfarquhar's posterous

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FinchTalk

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Biology-blog.com: The place for biology

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Data Jujitsu

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Jinlong Zhang's Homepage - Main

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From the bottom of the heap

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Back Side Smack

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猴子的博客

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Carl Boettiger

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Zero Intelligence Agents

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Edwin Chen's Blog

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怡然轩 | Yixuan's Blog

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格物堂

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All Things Tagxedo

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PolStat Blog

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AnthroGenetics' Blog

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Pathogens: Genes and Genomes

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Programming for Scientists

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Genome Engineering | Site Wide Activity

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NYGC Blog | New York Genome Center

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Tore Opsahl

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O|B|F News

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Hottest Questions - BioStar

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Bio and Geo Informatics

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Suprageography

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Jason Bryer

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