Andrea Telatin

About me

I'm a bioinformatician, currently working at BMR Genomics, analyzing data from Next Generation Sequencing projects. I'm a visiting scientist at the University of Padua.

I host my blog.

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Shell tips

Apple Swift under Linux

Following instructions found here (and here) you can install Swift on your Ubuntu machine (precompiled binaries). If you plan to make Swift projects, I wrote a script to easily make empty projects. To install Swift: wget https://swift.org/builds/ubuntu1404/swift-2.2-SNAPSHOT-2015-12-18-a/swift-2.2-SNAPSHOT-2015-12-18-a-ubuntu14.04.tar.gz sudo aptitude update sudo apt-get install git cmake ninja-build clang uuid-dev libicu-dev icu-devtools libbsd-dev libedit-dev libxml2-dev libsqlite3-dev swig […]

Posted on 11 January 2016 | 1:44 am

Bitmap to vector: tracing in Linux

Inkscape gives the possibility to trace a bitmap object to a vector one from the menu Path > Trace Bitmap item, or Shift+Alt+B (see this page). More interesting is the possibility to to the same from the shell, without the need of an interactive program. I loved potrace for this, available from the repository. Its input are BMP […]

Posted on 18 December 2015 | 2:38 am

CMS with Plain Text files

I stumbled upon Grav, a CMS based on flat files that will turn mark-down text into nice websites. What I like about it, in particular, is the fact that can be used to turn your pipelines output into an easily browseable website.

Posted on 6 December 2015 | 2:22 am

Evernote from command line

As mentioned before, you get a productivity boost when you link your mobile life with the terminal, with a program you can pipe, parse, grep… Geeknote (www.geeknote.me) is a command line interface for your Ever Note account. Installation is as easy as: git clone git://github.com/VitaliyRodnenko/geeknote.git cd geeknote sudo python setup.py install geeknote login The latter […]

Posted on 1 December 2015 | 1:54 am

Google Calendar from command line

The connection between my mobile phone and the rest of my IT life (i.e.  the Linux terminal :) ) will likely get a little bit harder, at least this is what if fear. Thankfully there are awesome packages that still seems robust and insanely useful. Gcalcli (https://github.com/insanum/gcalcli), a Python script to manage your Google Calendar via APIs […]

Posted on 26 November 2015 | 1:40 am

PHP: MySQLi procedural tutorial

The deprecated mysql extension can be easily upgraded to the future proof mysqli, that supports both a procedural and an object-oriented syntax (creating some confusion at first when you find either one or the other in public forums…). The procedural syntax is quite similar to the previous one, except for the mandatory “connection” argument. Connection […]

Posted on 22 November 2015 | 11:17 pm

change pidgin status via command line

purple-remote "setstatus?status=away&message=this is the status" and change "away" to "online" if needed :)

Posted on 20 January 2014 | 12:57 am

Disable laptop monitor if external monitor is plugged

At work now I use an old laptop connected to a monitor. With arandr you have a GUI for setting the dual monitors. What I wanted was to switch off the built-in display: EXTERNAL_OUTPUT="VGA" INTERNAL_OUTPUT="LVDS" xrandr |grep $EXTERNAL_OUTPUT | grep " connected " if [ $? -eq 0 ]; then xrandr --output $INTERNAL_OUTPUT --off --output […]

Posted on 13 January 2014 | 5:12 am

An elegant editor

I was looking for a cross platform editor. I never fell in love with a Linux editor, that’s why I usually use Gedit from the default installation. On Mac i love BBedit 10, that I could purchase discounted… I was recently suggested to try Sublime Text. After a few minutes I really liked its powerful […]

Posted on 2 January 2014 | 2:44 am

Digital turnstile with Bluetooth and Linux

Blueproximity is a Linux program that (un)locks your PC detecting the presence/absence of a paired Bluetooth device (i.e. your mobile phone). In its preference pane you can set a command to be executed when detecting the phone. I set it up with “checkmein in” and “checkmein out” commands, where the checkmein scritpt is this simple stuff: […]

Posted on 31 December 2013 | 1:06 am

Papers

Microbial dynamics during shelf-life of industrial Ricotta cheese and identification of a Bacillus strain as a cause of a pink discolouration

Dairy products are perishable and have to be preserved from spoilage during the food chain to achieve the desired shelf-life. Ricotta is a typical Italian soft dairy food produced by heat coagulation of whey proteins and is considered to be a light and healthy product. The shelf-life of Ricotta could be extended, as required by the international food trade market; however, heat resistant microflor...

E. Sattin, N.A. Andreani, L. Carraro, L. Fasolato, S. Balzan, E. Novelli, A. Squartini, A. Telatin, B. Simionati, B. Cardazzo, (2016) Food Microbiology :

Posted on 10 January 2016 | 11:16 pm

SATRAP: SOLiD Assembler TRAnslation Program.

SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space sequences. In fact, the nature of color-space is such that any misinterpreted color leads to a chain of further translation errors, producing total...

Davide Campagna, Fabio Gasparini, Nicola Franchi, Lucia Manni, Andrea Telatin, Nicola Vitulo, Loriano Ballarin, Giorgio Valle (2015) PloS one 10: 9

Posted on 9 December 2015 | 6:18 am

Comprehensive transcript profiling of two grapevine rootstock genotypes contrasting in drought susceptibility links the phenylpropanoid pathway to enhanced tolerance.

In light of ongoing climate changes in wine-growing regions, the selection of drought-tolerant rootstocks is becoming a crucial factor for developing a sustainable viticulture. In this study, M4, a new rootstock genotype that shows tolerance to drought, was compared from a genomic and transcriptomic point of view with the less drought-tolerant genotype 101.14. The root and leaf transcriptome of bo...

Massimiliano Corso, Alessandro Vannozzi, Elie Maza, Nicola Vitulo, Franco Meggio, Andrea Pitacco, Andrea Telatin, Michela D'Angelo, Erika Feltrin, Alfredo Simone Negri, Bhakti Prinsi, Giorgio Valle, Angelo Ramina, Mondher Bouzayen, Claudio Bonghi, Margherita Lucchin (2015) Journal of experimental botany 66: 19 5739-5752

Posted on 9 December 2015 | 6:18 am

A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype

Background Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes. Results We used the RNAseq data to upd...

N Vitulo, C Forcato, E Corteggiani Carpinelli, A Telatin, D Campagna, M D'Angelo, R Zimbello, M Corso, A Vannozzi, C Bonghi, M Lucchin, G Valle (2014) BMC Plant Biology 14: 99

Posted on 24 April 2014 | 6:53 am

Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion

Nannochloropsis is rapidly emerging as a model organism for the study of biofuel production in microalgae. Here we report a high quality genomic assembly of Nannochloropsis gaditana, consisting of large contigs, up to 500 kbp long, and scaffolds that in most cases span the entire length of chromosomes. We identified 10,646 complete genes and characterized possible alternative transcripts. The a...

Corteggiani Carpinelli E, Telatin A, Vitulo N, Forcato C, D'Angelo M, Schiavon S, Vezzi A, Morosinotto T, Giacometti G M, Valle G (2013) Molecular Plant :

Posted on 25 August 2013 | 3:28 am

PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads

The sequencing of bisulfite-treated DNA (Bi-Seq) is becoming a gold standard for methylation studies. The mapping of Bi-Seq reads is complex and requires special alignment algorithms. This problem is particularly relevant for SOLiD color space, where the bisulfite conversion C/T changes two adjacent colors into 16 possible combinations. Here, we present an algorithm that efficiently aligns Bi-Seq ...

D Campagna, A Telatin, C Forcato, N Vitulo, G Valle (2012) Bioinformatics 29: 2 268-270

Posted on 21 February 2013 | 2:23 am

The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in toxR mutant and its parental strain.

BACKGROUND: The deep-sea bacterium Photobacterium profundum is an established model for studying high pressure adaptation. In this paper we analyse the parental strain DB110 and the toxR mutant TW30 by massively parallel cDNA sequencing (RNA-seq). ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae, where it regulates a considerable number of genes involved in environme...

S Campanaro, F De Pascale, A Telatin, R Schiavon, DH Bartlett, G Valle (2012) BMC Genomics 13: 567

Posted on 10 November 2012 | 10:40 am

Design and implementation of novel algorithms to integrate different DNA sequencing technologies for de novo genome assembly: Nannochloropsis as a test case

The advent of next generation sequencing technologies marked the beginning of a new era in the production of genomic data; nonetheless it also offered novel challenges to the bioinformatics community. While re- sequencing of genomes was made relatively easy and cheap, de novo assembly of eukaryotic genomes still presents significant hurdles. In this thesis we attempted the application of a mixed-...

A Telatin (2012)

Posted on 30 March 2012 | 2:51 pm

Investigating high-pressure adaptation of Photobacterium profundum SS9 by means of custom microarray

The deep sea is the most common habitat of the biosphere, as most Earth’s surface is covered by water with an average depth around 3000 meters. Photobacterium profundum, viable both at high (28 MPa) and atmospheric (0.1 MPa) pressure, is the model organism for high pressure adaptation. Its transmembrane transcription factor ToxR is a pressure sensing transductor. To better understand the role ...

Andrea Telatin (2007)

Posted on 8 July 2008 | 6:39 am

Twitter

@telatin: At the science museum in #London remember @ECorteggiani?

@telatin: Barbara Simionati (AD di #BMR Genomics) intervistata da "L'Italia che va" (al minuto 6:00): https://t.co/8ALvYe34nH

@telatin: The building next to the #ComputerLab in #Cambridge looks cool, huh? #svegliatitalia

@telatin: RT @digitalsci: "Your manuscript is your first priority, but everyone else’s last priority." https://t.co/bA0ZcGIs37 #coffeetimescience

@telatin: @CLaddomada ciao! scrivevi libri su Delphi?

@telatin: RT @tim_brannigan: Ha. The way we live now. via @thepoke

@telatin: RT @wef: In which country is your boss more likely to be a woman? https://t.co/uigZtg2abB #work #gender

@telatin: RT @lexnederbragt: DeNovoMAGIC - The Ultimate Genome Assembler. A reference genome using only 180X in short (100 – 250 bp) reads. https://thttps://t.co/UdPuvNgsSs

@telatin: RT @JohnCleese: I would like 2016 to be the year when people remembered that science is a method of investigation,and NOT a belief system

@telatin: @DarioBressanini fatto l'ultimo dell'anno, grazie!

@telatin: RT @l_haddad: "Unprecedented!" "Amazing!" "Novel!": the rise of hype in scientific journals https://t.co/ETl4tZ4mY2 via @voxdotcom

@telatin: Proud to be the 5,016th backer on @BackerKit for Micro Drone 3.0: Flight in th... | Thx @extreme_fliers! https://t.co/aaGwiMD049

@telatin: Moved to #Fastweb - Speedtest result by @Ookla https://t.co/f9uL9q2hTn #speedtest

@telatin: RT @WebDevHumour: I've been using Vim now for around 3 years, mainly due to the fact I still can't figure out how to save and exit.