Andrea Telatin

Ceci n'est pas un blog

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

Instagram, latest shots

I host my blog here, and archive memos on Macs and Linux on hosted sites.


Shell tips

PHP: UserAgent

$userAgent = getBrowser(); echo $userAgent['name']; See full snippet here: http://pastie.org/10908239

Posted on 18 July 2016 | 2:45 am

PHP video streaming

Excellent tutorial online introducing the “VideoStream” PHP class: http://codesamplez.com/programming/php-html5-video-streaming-tutorial Then use HTML5 video tag as shown in here, <video width="100%"> <source src="/player.php" type="video/mp4"> Your browser does not support the video tag. </video>

Posted on 28 June 2016 | 2:53 am

HTML Editors for your textarea

Several years ago I used FCKEditor. I was quite satisfied and to be honest my needs were really basics. A thing I noted scanning my 404 logs was a noticeable over-representation of /cgi-bin/fckeditor/editor/ requests, and I suppose this means it had a lot of tasty flaws. Now I wanted something new and possibly even simpler. Maybe better […]

Posted on 27 June 2016 | 1:08 am

PHP redirect

header("location: /newLocation.php"); of course before having printed any HTML (i.e. before setting headers).

Posted on 20 June 2016 | 12:55 am

Google reCaptha: we’re all human beings

To implement the simple (for the user) captcha provided by Google one have to get an API key from Google to use it. Then the mechanism is quite simple: the Captcha code is an input of the form that will submit a value. The program receiving the form data will validate the captcha with a request […]

Posted on 16 June 2016 | 1:00 am

From gedit to IDE with plugins

I love and use many text editors, from Sublime Text (being cross-platform) to BBEdit under macOS. Recently I started using more and more gEdit 2, because it’s universally available in most Linux distributions I happen to use. With some tricks, it’s possible to boost productivity. Default gEdit plugins – From the preferences, it’s possible to activate useful […]

Posted on 14 June 2016 | 4:05 am

Bootstrap: colum offset

As mentioned before with Bootstrap it’s possible to combine multiple classes to design a responsive website. We can decide to use six columns on large screen and reduce the number of columns as we reduce the available screen size. <section class="col-sm-6 col-md-4  col-lg-2"></section> This means that on small screens the section will span 6 columns. […]

Posted on 13 June 2016 | 1:02 pm

SQLite and PHP primer

SQLite (3.6+) is a database supporting a SQL-compatible syntax and does not rely on a server, rather it stores data on files. Here we’ll prime how to use SQLite from command line and how to integrate it with PHP (5.3+). Command line operations Invoking “sqlite3 databasefilename” will fire up SQLite, and create the file if […]

Posted on 10 June 2016 | 1:21 pm

PHP ternary operator

$displayname = ($user['Name']) ? $user['Name'] : 'Guest'; See examples: https://davidwalsh.name/php-ternary-examples

Posted on 10 June 2016 | 4:03 am

Bootstrap 3 micro-introduction

Bootstrap is a framework to design mobile friendly websites. Using modern technologies and battle tested is a good start also for small sites. Being a framework you have to write/design the page in a specific way, with the benefits of having pre-built CSS and some JavaScript components (popups, tabs…) ready to use. It’s good for prototyping, to quickly deliver small […]

Posted on 9 June 2016 | 10:46 am

Papers

Multi-omic bioinformatics and adaptive landscapes to extreme environments: an integrative approach

Biological systems show impressive adaptations at extreme environments. In extreme environments, directional selection pressure mechanisms acting upon mutational events often produce functional and structural innovations. Examples are the antifreeze proteins in Antarctic fish and their lack of hemoglobin, and the thermostable properties of TAQ polymerase from thermophilic organisms. During the pa...

C Angione, P Lio, S Pucciarelli, B Can, M Lotti, A Mancini, A Telatin (2016) Lecture Notes in Bioinformatics :

Posted on 10 June 2016 | 7:56 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 10 January 2016 | 11:20 pm

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 10 January 2016 | 11:18 pm

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

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

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: RT @hadleywickham: The 1st part of R for data science (explore) is now complete: https://t.co/T1CKf2EvSJ 🎉 I'd love your comments, question…

@telatin: RT @atulbutte: Comparing tissue RNA/protein expression #opendata @msirota84 @iditkosti @dvir_a @najain1 https://t.co/bY73LxqIsu https://t.c

@telatin: @dhstatus can't access to a mail address even via the webmail (Squirrell). Still issues with mail servers or is it just me?

@telatin: RT @23andMe: News this morning, 23andMe launches new genotyping services for research https://t.co/dYHRAG97kY

@telatin: RT @RichardDawkins: England (not Britain: Scots had more sense) is now the laughing-stock of the world.

@telatin: Saracinesca aperta per l'ultima volta. #despar #Marchioretto #sangiorgiodiperlena @ San Giorgio… https://t.co/yBjCeL8BOd

@telatin: Welcome #macOS #sierra, and auto unlock

@telatin: RT @vickyyyf: Result if balcony of royals were to be put through a flow cytometer. #GFPpositiveQueen #Queenat488nm

@telatin: RT @AppleSupport: Did you know that you can sign and return email attachments directly from your iPhone?

@telatin: @Kunerango hi! i'm trying to sign-up with the form in the landing page but nothing happens (Mint 17, Firefox and Chrome).

@telatin: RT @AcademiaObscura: Nobody reads footnotes. Or introductions. |https://t.co/Ce650sDvsW

@telatin: RT @DarioBressanini: Ma i magistrati prima o poi indagheranno anche quelli che dicevano che #Xylella non esisteva, che era una truffa, che…

@telatin: It's a cool image, seeing a DNA sequencer attached to an iPhone. And it's name is so British-cool! https://t.co/6Vf08676eG

@telatin: RT @BioinfoRRmatics: Whole-Genome Sequencing Has Better Dx Rate Than Exome at Similar Cost, Australian Team Finds https://t.co/EFvopvWU26 h