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A Multi-Omics Approach to Evaluate the Quality of Milk Whey Used in Ricotta Cheese Production

In the past, milk whey was only a by-product of cheese production, but currently, it has a high commercial value for use in the food industries. However, the regulation of whey management (i.e., storage and hygienic properties) has not been updated, and as a consequence, its microbiological quality is very challenging for food safety. The Next Generation Sequencing (NGS) technique was applied to s...

E Sattin, NA Andreani, L Carraro, R Lucchini, L Fasolato, A Telatin, S Balzan, E Novelli, B Simionati and B Cardazzo (2016) Frontiers in Microbiology :

Posted on 17 August 2016 | 3:06 am

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

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Linux and Programming posts

Extract text from PDF, from the command line

pdftotext is a command line tool for converting PDF files to plain text. Included by default with many Linux distributions. $ pdftotext file.pdf The gs (Ghostscript) program can also handle the process: $ gs -sDEVICE=txtwrite -o extractedText.txt input.pdf

Posted on 14 February 2017 | 1:10 am

Terminal session to animated GIF

A tutorial on How_to_make_an_animated_GIF_of_a_terminal_session by blogobramje:

Posted on 13 February 2017 | 5:24 am

Bash if

if [ $value -eq 1 ] then echo "Good job" elif [ $value -gt 1 ] then echo "Excellent job" else echo "Nothing happened" fi  

Posted on 9 February 2017 | 1:15 am

Test .htaccess rules

The online tool htaccess.mwl.be allows to easily debug HTACCESS redirects, and already saved me some headaches 🙂

Posted on 2 February 2017 | 2:50 am

Twig PHP templating system

Twig is a popular templating system, from the creators of the Symphony framework. Here I describe a minimal startup guide for those preferring a manual installation (i.e. no composer). <? require_once 'lib/Twig/Autoloader.php'; Twig_Autoloader::register(); $loader = new Twig_Loader_Filesystem('templates/'); $twig = new Twig_Environment( $loader, array( 'cache' => 'cache/') ); $twig = new Twig_Environment($loader); echo $twig->render('index.template', array('name' => […]

Posted on 22 December 2016 | 6:54 am

Salting passwords with PHP

As nobody would store plain password in a database, I’d like to write a short memo on how to encrypt passwords to be safely store them in our databases. The first concept is hashing. In brief we use a function that takes a string as input (i.e. our plain text password) and produces an output […]

Posted on 20 November 2016 | 8:01 am

Mounting an FTP directory. No need to have an FTP editor then

Using FUSE to mount remote directories (when the more secure SSH connection is not available), with a program like curlftps, it’s possible to mount any remote directory like: curlftpfs -o user=user:pass ftp.server.com /my/mount/point This means that after any standard editor will become an FTP enabled editor.

Posted on 14 November 2016 | 5:01 am

ImageMagick: watermark logo

composite logo.png photo.jpeg -dissolve 90% -gravity NorthEast test.jpg To tile the watermark: composite logo.pngphoto.jpeg -dissolve 55% -tile  test.jpg

Posted on 1 October 2016 | 3:50 am

ImageMagick: remove background color (make transparent background)

convert input.png -transparent white -fuzz 90% output.png Replace “white” with the color you want to replace, or “rgba(0,0,0,0)” to set it to a custom value. “Fuzz” is the tolerance.

Posted on 28 September 2016 | 3:45 am

some HTML5 learning resources

HTML5 for Webdesigners (PDF format) Dive into HTML5 (online) Course specification (PDF) Cheat sheet (PDF)

Posted on 23 September 2016 | 7:12 am

Apple and OS X stuff

Affinity found!

My first graphic design program has been CorelDraw 4.0, bundled with my inkjet printer I think, for Windows 3.1. It featured fake gradients (let’s say, 10 colors from yellow to red, typically) and a general lack of complexity that was perfect for beginners. I upgraded to CorelDraw 5 and several things became day by day … Continue reading Affinity found!

Posted on 6 October 2016 | 3:38 am

Fine tune volume (and brightness)

Apple computers have dedicated keyboard buttons for volume and display brightness adjustment. If you also press Shift+Option (alt) you’ll be able to fine tune both as shown in the video below.

Posted on 8 March 2016 | 3:44 am

Spotify and kernel panic

Last week I had a kernel panic. The only time I had it before was (on 2012!) using my 27″ iMac that had a defective motherboard and thus… I was scared to have an hardware problem in the quite new retina MacBook pro… Today I had a second kernel panic, and I could connect the dots… … Continue reading Spotify and kernel panic

Posted on 28 February 2016 | 10:57 am

Power up the terminal

OhMyZSH is a gorgeus enhancement to the standard shell, with better tab-completion and visual feedback. Installing the vanilla version is as easy as: sh -c "$(curl -fsSL https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh)"

Posted on 16 February 2016 | 6:32 am

Max OS X, change directory where screenshots are saved

First you can create a new directory, then to change the system setting: defaults write com.apple.screencapture location /path/to/screenshots/ Finally to make the change immediately available: killall SystemUIServer The picture below is an example.

Posted on 11 February 2016 | 7:02 am

Syntax highlight in Keynote presentations

When preparing slides with a lot of code inside having a proper syntax highlighter is mandatory, and hacks like taking screenshots don’t work both for the useless amount of bytes wasted and for the inability to correct mistakes later on. You can install highlight via Brew: brew install highlight then simply: highlight -O rtf input_file.php … Continue reading Syntax highlight in Keynote presentations

Posted on 10 February 2016 | 9:38 am

Prevent the Mac falling asleep

The famous app “Caffeine” now has its command line hack. Since Lion there’s the command: caffeinate -t 600 to do this. With several switces like “-d” to keep the display active, “-s” to keep the system running (only on AC power). See man caffeinate for more.

Posted on 29 January 2016 | 1:55 am

Colors in Objective-C

With this post I start annotating some basic tips on Apple programming, as most newbies do. We want to change the text and color of a label: Thanks to Stack Overflow I stumbled upon a macro: To be used like: Using like: [attributedString addAttribute:NSForegroundColorAttributeName value:RGB(66, 79, 91) range:NSMakeRange(0, attributedString.length)]; Again via Stack Overflow (what else?) there’s … Continue reading Colors in Objective-C

Posted on 12 January 2016 | 2:05 am

OS X “Can’t connect to wifi” because of USB 3.0 HD

With a 2015 MacBook retina I was experiencing a frustrating issue with home WiFi: it couldn’t join any router. I was transferring data from one external drive to another, and both of them were USB 3.0… so after a while I realized that I didn’t burn the Airport card, but rather experienced the known issue … Continue reading OS X “Can’t connect to wifi” because of USB 3.0 HD

Posted on 10 January 2016 | 11:38 pm

Hide and show desktop icons with a Perl script (MacOS)

There are many utilities in the App Store that easily allow hide all the desktop stuff, and they are useful when going to plug a projector to our Mac Book… But there is an easy way, a simple Perl script that when launched hides (or shows if already hidden) icons from our Desktop.  #!/usr/bin/env perl … Continue reading Hide and show desktop icons with a Perl script (MacOS)

Posted on 6 June 2013 | 5:16 am