Analysis of 243 Genomes – My First Report [Nov. 2016]

analysis-of-243-genomes-my-first-report-nov-2016-1

About two weeks ago I learned about this website OpenSNP where people can share their genetic information and not only. It is similar to 1000genomes, but I think it is much more interesting to work with because aside of genetic information (SNP sequencing, exome, etc.) most users also share phenotype data; data is not anonymized. This is what sparked my interest.

With phenotype data and user’s genetic mutations – SNPs – (or other relevant genetic information), I could run analyses and find possible correlations. This is applied big data.

In this post, I’ll explain how I conducted my first analysis. I want to provide an outline with enough relevant details so I can have a reference point to make things easier in future analyses. Of course, I could simply do this in private but I’d rather post it on the blog so that others who are interested to run similar analyses can have starting point.

This involves: knowledge of genomics, genomics related software and raw data formats, programming, and a lot of patience.

30 Health and Fitness Books – Free Bundle

30-health-and-fitness-books-free-bundle

You have to subscribe to Buckbooks’ email list (not mine)! The promo is on for 3 more days (ends circa Nov. 10, 2016).

If you’re on my email list, you already know about this promo as I broadcasted a message immediately it became available. If you’re not on my list and didn’t know about this, listen up.

I joined forces with a dozen plus authors and we give our books for free – 30 in number. This bundle is available via Buckbooks who made this possible. To get the bundle you have to sign-up (for free) to their list. Once that’s done, wait for the email. Here are a few titles from the bundle:

My Encounter with Curiosity, the Mars Rover

As I came out of the number 1 subway station in Lower Manhattan on Wednesday evening I encountered a scene that was different to what I was used to.

i-met-curiosity-the-mars-rover-1

Instinct had me enter, but I couldn’t stay long because I was already late for an evening lecture at the genome center right across the street. So I rushed asking for details and deciding I was going to come back another day.

After-thoughts of a 44-hour fast – Just completed [Oct. 2016]

my-recent-44-hour-fasting-experiment

I took a trip to DC earlier this week and I decided to take a break from eating for the whole duration – until returning to NYC.

Radiotolerance Lessons from the Tardigrades

radiotolerance-lessons-from-the-tardigrades

Image: female tardigrade containing eggs.

Hashimoto and colleagues (2016) published an article in Nature recently:

Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein

Tardigrades, a.k.a. water bears, are some of the most extreme organisms, capable of surviving in the most un-habitable environments and being exposed to insults that would kill other living beings. Examples include: very high and very low temperatures, high doses of radiation, high pressure, outer space, and others.

Here are some of the particularities (in terms of gene expression) of tardigrades:

The Hallmarks of Cancers #1 – Deregulating Cellular Energetics

the-hallmarks-of-cancers-1-deregulating-cellular-energetics

I wrote a moderate-length review of Hanahan and Weinberg’s papers a few months ago.

In their papers, they discuss the most common similarities among cancers and they base their writing on ~5 decades of research in this field.

While each cancer is unique, especially if we view it from a genetics standpoint, Hanahan and Weinberg discuss 8 hallmarks they found to be common in cancers.

How Steemit Social Platform Rewards its Users – My Quick Intro

How Steemit Social Platform Rewards its Users - My Quick Intro - 1

Introduction

A few weeks ago I decided to join Steemit. This is a social platform where users are rewarded for posting content, for commenting, for voting and for curating the content made by other users.

The first time I heard about the platform was in early July, when two online friends (Leah – stellabelle – and Razvan – razvanelulmarin) kept mentioning it on one of our groups.

Blood Work #5 – August 2016 – [Consistency]

Blood Work #5 - August 2016 - [Consistency]

Introduction

The last time I posted about my blood work was in March 2016. Here is my August 2016 update:

What I’ve Been Reading Recently – My Bookshelf #10

Reading a book at the beach

Intro

I read more than 70 books this year (as of August 2016). I don’t speed read. I allocate sufficient time every day to ‘parse’ books. I mostly read non-fiction. Some of the books are in audio format. Obviously I do not listen to textbooks and programming books. I choose the audio format for the non-technical and more practical ones.

My current interests: genomics, bioinformatics, machine learning, and human irrationality.

Additionally, for knowledge acquisition, I also:

– read research studies
– listen to interviews
– watch lectures and seminars
– take online courses

You can find all past book/reading related posts: #1 #2 #3 #4 #5 #6 #7 #8 and #9

Current philosophy:

The more I read, the more I realize the little I know.
Reading is not a hobby; it is part of my daily routine.
I avoid being superficial. I don’t want to skim through the books I read.
I read 7-10 books at a time.
I think that with practice I’ve been able to develop the skill of reading faster (!=speed reading).

Data from David Blaine’s 44-day Fast – [Metabolic and Physiologic]

David Blaine - Macro and micronutrient looses Study - 1

Introduction

David Blaine has subjected himself to a prolonged fasting experiment lasting between Sept. 5 and Oct. 19, 2003.

“A 30-year-old male, weight 96 kg, height 1.84 m, entered a transparent Perspex box on the banks of the river Thames in London and was suspended in the air from a crane for 44 days. During this period, he took only water to drink.” [2]

At the end of the fast, Blaine had lost 24.5 kg and ~8 BMI points (29 => 21.6). Though his BMI was not life-threatening, he was admitted to the hospital for intensive and careful refeeding, as some of his biomarkers were out of normal limits. [1]

Several research studies have been published based on Blaine’s self experiment. Let’s see some data…

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