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Papers

Biocontrol traits of Bacillus licheniformis GL174, a culturable endophyte of Vitis vinifera cv. Glera.

Bacillus licheniformis GL174 is a culturable endophytic strain isolated from Vitis vinifera cultivar Glera, the grapevine mainly cultivated for the Prosecco wine production. This strain was previously demonstrated to possess some specific plant growth promoting traits but its endophytic attitude and its role in biocontrol was only partially explored. In this study, the potential biocontrol action ...

Sebastiano Nigris, Enrico Baldan, Alessandra Tondello, Filippo Zanella, Nicola Vitulo, Gabriella Favaro, Valerio Guidolin, Nicola Bordin, Andrea Telatin, Elisabetta Barizza, Stefania Marcato, Michela Zottini, Andrea Squartini, Giorgio Valle, Barbara Baldan (2018) BMC microbiology 18: 1

Posted on 23 November 2018 | 8:15 am

A targeted next-generation gene panel reveals a novel heterozygous nonsense variant in TP63 gene in Arrhythmogenic Cardiomyopathy patients.

Arrhythmogenic Cardiomyopathy (ACM) is associated with arrhythmias and risk of sudden death. Mutations in genes encoding proteins of cardiac intercalated discs account for about 60% of ACM cases, but the remaining 40% is still genetically elusive.

Giulia Poloni, Martina Calore, Ilaria Rigato, Elena Marras, Giovanni Minervini, Elisa Mazzotti, Alessandra Lorenzon, Ilena Egle Astrid Li Mura, Andrea Telatin, Ivano Zara, Barbara Simionati, Martina Perazzolo Marra, Jessica Ponti, Gianluca Occhi, Libero Vitiello, Luciano Daliento, Gaetano Thiene, Cristina Basso, Domenico Corrado, Silvio Tosatto, Barbara Bauce, Alessandra Rampazzo, Marzia De Bortoli (2018) Heart rhythm :

Posted on 23 November 2018 | 8:15 am

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


Latest tweets

@telatin: On my way home after a seminar in @SapienzaRoma #rome on #microbiome analysis — intense day with Matteo Pallocca

@telatin: What a day in Rome, at the CNR headquarters! 🌞

@telatin: @yaasircheema @HendersonLab @ChrisIckeMicro @jameshaycocks @mjpallen @TheQuadram @UoBbiosciences Kudos 😎

@telatin: RT @StevenSalzberg1: Our new human gene database, CHESS, is published! Over 100,000 novel gene isoforms (splice variants), many new noncodi…

@telatin: RT @EricTopol: For decades, we believed "mitochondrial DNA (mtDNA) is inherited solely from the mother."—@Wikipedia Today, @PNASNews we lea…

@telatin: @pathogenomenick Let’s sequence the mammalians living in the ISS. They could have Neanderthal ancestry and a remark… https://t.co/J5NupLcQqM

@telatin: RT @hall_lab: Introducing the FLORINASH study - and highlighting importance of carefully planning these types of clinical studies - get you…

@telatin: @disinformatico @terminologia #parlacomeBEVI

@telatin: @manudispe @PossoAnche @RosannaRuscito @LorenzoGhezzi2 @VagnarelliSira E chi parla di Gesù? Io parlo della religion… https://t.co/r25cfnzju2

@telatin: @PossoAnche @Freegracielou @RosannaRuscito @LorenzoGhezzi2 @VagnarelliSira C’entra qualcosa con il thread? Ovviamen… https://t.co/ouUcTMGELo

@telatin: @PossoAnche @RosannaRuscito @LorenzoGhezzi2 @VagnarelliSira Neanche il cattolicesimo ha la separazione. È lo stato… https://t.co/SEwDvra7vO

@telatin: @RosannaRuscito @LorenzoGhezzi2 @VagnarelliSira Se lo dice lei... i miei amici musulmani qui in UK mi paiono di div… https://t.co/A4IjGYahvR

@telatin: @strnr Specific the title, yes. not so true about the content :)

@telatin: @LorenzoGhezzi2 @VagnarelliSira @RosannaRuscito Anche la Bibbia contiene cazzate, ma quasi nessuno la osserva tutta… https://t.co/VsQBhM38kt


Linux and Programming posts

efetch failed

efetch installed via conda, this time failed in one of the VM i use. Trying to manually install LWP::protocol::https result in further errors, arriving to complain for lacking a C compiler… Bash went to the rescue: curl -s https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?id=LT906492.1\&db=nuccore\&rettype=fasta Advertisements

Posted on 27 November 2018 | 6:29 am

Dump html content with lynx

Lynx is an incredibly useful text-only browser, that you can use to read webpages (interactively) from the command line. I used it sometimes to access websites restricted to some areas where I could access a server, for example. It can be used to output the webpage (non interactively) to the standard output, both the HTML … Continue reading Dump html content with lynx

Posted on 23 November 2018 | 3:02 am

Upload file FTP via curl

curl -T my-local-file.txt ftp://ftp.example.com --user user:secre From here

Posted on 9 August 2018 | 8:28 am

Test cron scripts

From a question in Ask Ubuntu, i found this useful way to test the behaviour of a script that one wants to run as a cron job: /bin/sh -c "(export PATH=/usr/bin:/bin; /path_to_script/script.php </dev/null)"

Posted on 18 April 2018 | 4:11 am

a nice tmux look configuration

The default satus bar of tmux looks poor and can be improved. A possible source: https://github.com/gpakosz/.tmux cd git clone https://github.com/gpakosz/.tmux.git ln -s -f .tmux/.tmux.conf cp .tmux/.tmux.conf.local .

Posted on 6 March 2018 | 5:25 am

~/.screenrc

The common and widespread status bar for screen, plus minor tweaks for the GNU screen configuration file (.screenrc). Copy from below or download it from here. # Bind F11 and F12 (NOT F1 and F2) to previous and next screen window bindkey -k F1 prev bindkey -k F2 next startup_message off # Window list at … Continue reading ~/.screenrc

Posted on 21 November 2017 | 9:21 am

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


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