protocols.io
The Spectroscope
protocols.io
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The difficulties of executing simple algorithms: Why brains make mistakes computers don't.
Nov 18, 2013 By Gary Lupyan Is 798 an even number?Essay on paper The difficulties of executing simple algorithms: why brains make mistakes computers don't.
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My Break-up Nature Paper
Jun 27, 2013 By Meleah Hickman Some [papers] are simply the result of hard work, persistence and follow-through and as such, eventually fade into the background. But others become so intertwined with the entirety of your life that they become fixed points in your timeline.Essay on paper The 'obligate diploid' Candida albicans forms mating-competent haploids.
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The job's not over till the paperwork is done
Jul 09, 2013 By Jasper Rine Here I am baring my soul, so be sure to keep this to yourself and your closest friends. I have a remarkable lack of interest in anything I did in the past, and reserve most of my passion and interest for what is going on now or will be going on in the future. Hence, once the work was done and the mutants sent to anyone who wanted them, I just lacked the juice to get the damn thing written.Essay on paper Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae.
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It’s great when experts disagree.
Nov 06, 2013 By Lenny Teytelman ...I needed to pause my main project and quickly publish a paper on the artifact, to alert the community. I presented this to a number of labs and the contradictory advice that I got from brilliant researchers made me dizzy.Essay on paper Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins.
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Dr. Strangelove, or: How I stopped worrying and learned to love a brain parasite.
Oct 09, 2013 By Wendy Ingram ...research suggested that the tiny single-celled parasite had evolved a way to specifically alter the innate hard-wired aversion that rodents had to cats for its own benefit. I honestly couldn’t believe it. While the studies seemed to be designed well and the results looked pretty solid, there were a lot of questions left unanswered. My curiosity got the best of me and I designed a thesis project to answer the question, ‘If this parasite causes loss of aversion to cats in mice, what is the mechanism by which it accomplishes this?Essay on paper Mice infected with low-virulence strains of Toxoplasma gondii lose their innate aversion to cat urine, even after extensive parasite clearance.
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The gift that keeps on giving
Dec 16, 2013 By Ravi Sachidanandam The problem of biases in small RNA deep-sequencing is so interesting and important that journals will let researchers repeatedly publish the same results and conclusions provided they claim originality and cite the literature.Essay on paper Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.
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The Awesome Power of Preprint in Genetics
Aug 26, 2013 By Peter Combs My PI, Mike Eisen, is famous for his outspoken views on Open Access—including his willingness to put his money where his mouth is: he co-founded PLoS and the lab only publishes in OA journals. In addition to believing that the current system doesn't let enough people read the literature, Mike has long felt that the rate of science publishing is too slow, meaning that interesting results don't appear in print until months, or sometimes years, after the work has been done.Essay on paper Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.
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That's not supposed to happen, or is it?
Jul 17, 2013 By Christine Chaffer I see now that even for the most accomplished and confident post-docs, the first six months in a new lab are challenging. I still remain cautious, but now of the science rather than of myself.Essay on paper Poised chromatin at the ZEB1 promoter enables breast cancer cell plasticity and enhances tumorigenicity.
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The ripples produced by my love of small waves
Jan 27, 2014 By Erin McKiernan This is a story about an article roughly four years in the making; about my fascination with how a tiny animal moves; and about the experimentation that was necessary before I could answer the questions that first piqued my interest.Essay on paper Effects of manipulating slowpoke calcium-dependent potassium channel expression on rhythmic locomotor activity in Drosophila larvae.
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My HeLa Story
Sep 04, 2013 By Andrew Adey Way back when I was just a fledgling graduate student, even before the NYT bestseller The Immortal Life of Henrietta Lacks by Rebecca Skloot, I proposed to my PI the idea of sequencing the genome of HeLa cells. At the time all I knew was that they were ubiquitous, fast growing and robust enough that a post doc in my undergraduate lab taught cell culture techniques to me with them, stating “don’t worry – you can’t screw up with HeLa”. Years later I can say with confidence that I am no longer that fledEssay on paper The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line.
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The power of n=1
Jul 02, 2013 By Arjun Raj Sure, it was just one cell, could have been a fluke, could have been any number of technical artifacts. Whatever. I knew we were on to something!Essay on paper Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation.
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The story behind the story of my new #PLoSOne paper on "Stalking the fourth domain of life" #metagenomics #fb
Nov 01, 2013 By Jonathan Eisen …We are not doing a press release for the paper, for a few reasons. But one of them is that, well, I am starting to hate press releases. So I guess this is kind of my press release.Essay on paper Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.
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A Wonderful Christmas with Mysterious Oscillations
Sep 26, 2013 By Nikolai Slavov ...Doing the sampling was time-consuming and demanding in the extreme, but I was so eager to know what was happening that I spent Christmas Day of 2010 collecting samples, the ones that ultimate were used for our article. It is still the longest, the happiest and the most exciting Christmas Day I have had in my life.Essay on paper Metabolic cycling without cell division cycling in respiring yeast.
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The Longest Quick Experiment of my Life
Mar 25, 2014 By Lenny Teytelman On the fourth page of this article is a sentence – “Hence, we replaced the HMR-E variant (AAACCCATAAC) with the genome-wide consensus sequence for the Rap1 protein (ACACCCATACATT).” This sentence is three years of my life.Essay on paper The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer.
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The Search for a White Worm
Aug 07, 2013 By James Sikes I chatted with my new PI about potential research projects and chose what I thought was a novel and innovative project. At the same time, I was training to run a marathon. I probably should have realized what to expect over the next three years when he told me, “Training for this marathon is going to be so easy compared to the project you’ve undertaken.”Essay on paper Restoration of anterior regeneration in a planarian with limited regenerative ability.
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Reflections on a scientific project 10 years on: the winding path to cryptic transcription in yeast
Aug 21, 2013 By Craig Kaplan One aspect of working in molecular biology is that all discoveries in the end are probably inevitable. Someone will figure it out eventually. There are too many smart or lucky people thinking lots of different ways for this not to be the case.Essay on paper Transcription elongation factors repress transcription initiation from cryptic sites.
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MacGyver, Dinosaurs and Viruses
Aug 13, 2014 By Michael Lee Why would someone who usually works on fossil reptiles delve into molecular evolution of viruses? It turns out the two fields have a lot in common.Essay on paper Dinosaur evolution. Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds.
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An "overnight" success
Aug 13, 2013 By Arjun Raj It was a really cool moment, because it was one of those rare instances when you have an idea and you just know it will work deep down in your gut. It was also a really special moment for me as a PI, because it was Marshall's idea, and I was so very proud of him for coming up with it.Essay on paper Visualizing SNVs to quantify allele-specific expression in single cells.
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Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution
Nov 01, 2013 By Jonathan Eisen ...A paper on which I am the senior author is being published in Nature... Today in this blog I am going to do my best to tell the story behind the paper - about the people and the process and a little bit about the science.Essay on paper A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
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Some hypotheses you cannot plan
Dec 31, 2013 By Kristen DeAngelis As I was preparing for my big leap from the relative safety of postdochood into assistant professorship, I'd worked to construct myself some safety lines.Essay on paper Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1.
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Caffeine regulates serendipity in the Corridors of ENS
Jul 23, 2013 By Xavier Darzacq This finding started with the collision of a physicist and a biologist in the corridors of the École Normale Supérieure. While this event looked random at the time, I feel now that the weight of several generations of our peers had a lot to do with placing us in those corridors and creating the necessary conditions for the fruitful result of those seemingly random collisions.Essay on paper Real-time dynamics of RNA polymerase II clustering in live human cells.
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How I found the silver lining in my cloud.
Dec 13, 2013 By Bilge Ozaydin It was just a routine experiment where I was checking the binding of silencing proteins at the silent loci in a number of yeast mutants...Essay on paper Expanded roles of the origin recognition complex in the architecture and function of silenced chromatin in Saccharomyces cerevisiae.
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Discovery of a new protein... now what?
Sep 19, 2013 By Ericca Stamper … I was determined to learn something about the regulation of meiotic double-strand break formation by studying DSB-1. Even after my thesis committee suggested that maybe I should consider pursuing another project, I still couldn’t give it up. DSB-1 was, after all, my scientific baby.Essay on paper Identification of DSB-1, a protein required for initiation of meiotic recombination in Caenorhabditis elegans, illuminates a crossover assurance checkpoint.
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My first PLoS One paper .... yay: automated phylogenetic tree based rRNA analysis
Oct 31, 2013 By Jonathan Eisen Well, I have truly entered the modern world. My first PLoS One paper has just come out. It is entitled "An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)" and well, it describes automated software for analyzing rRNA sequences that are generated as part of microbial diversity studies. The main goal behind this was to keep up with the massive amounts of rRNA sequences we and others could generate in the lab and to develop a tool that would remove the need for "manual" work in analyzing rRNAs.Essay on paper An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
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Show me the data - but in a clear and understandable way
Jul 30, 2013 By Karin Voordeckers As scientists, most of us are focused on carrying out experiments and gathering data – but working on this manuscript really showed all of us just how important it is to spend just as much time on thinking about exactly how to depict all this data.Essay on paper Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication.
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The story behind our new paper in PeerJ
Oct 14, 2013 By Todd Vision ...Publishing this paper with PeerJ has been a fun ride, both because the staff have been so responsive and the platform is so well-designed, but also because we have had a chance to test-drive new features as they are introduced. Our unreviewed manuscript was the first PeerJ PrePrint, and now that it has been published, we have already started interacting with readers via PeerJ’s innovative new Q&A; feature.Essay on paper Data reuse and the open data citation advantage.
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From discovery to technology: a mucus story.
Sep 17, 2013 By Thomas Crouzier This paper is about how mucins, a family of glycoproteins that composes our mucus, can be used as a cell-repellent coating for cell patterning. But this is also a story about how perseverance, good communication and a bit of luck are key in research.Essay on paper Cell patterning with mucin biopolymers.
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To measure or not to measure or how to measure
Jun 03, 2014 By Nikolai Slavov Easier and indirect measurements that appear to save time and money often take longer and end up being more expensive than the best measurement one can do.Essay on paper Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis.
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