Nettab2011 – Network Tools and Applications in Biology, 12-14 ottobre 2011, Pavia – Nettab 2011

Ritorna come ogni anno l’importantissima conferenza internazionale Nettab –Network Tools and Applications in Biology, organizzata dal professor Paolo Romano dell’Ist di Genova. Quest’anno si terra’ a Pavia in Lombardia, il 12, 13, 14 ottobre 2011.

Ecco l’annuncio di sottomissione dei contributi.

NETTAB 2011 on
“Clinical Bioinformatics”
October 12-14, 2011
Collegio Ghislieri, Pavia, Italy

NETTAB 2011 is the eleventh in a series of international workshops on Network Tools and Applications in Biology.
These workshops are aimed at presenting and discussing emerging ICT technologies whose adoption in support of biology could be of particular interest.

This year, NETTAB is focused on Clinical Bioinformatics and it is aimed at presenting the methods, tools and infrastructures that are nowadays available.
It will also show some of the most interesting applications in this field.

Invited Speakers
Yves A. Lussier, Institute for Translational Medicine, University of Chicago, USA
Thomas Illig, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
Jan-Eric Litton, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
Isacc S. Kohane, Harvard Medical School, Boston, USA

Tutorials given by:
Carlo Combi, Department of Computer Science, University of Verona, Verona, Italy
Pierre Zweigenbaum, LIMSI – CNRS, Orsay, France
Marco Masseroli (to be confirmed), Dipartimento di Elettronica e Informazione, Politecnico di Milano, Milan, Italy
Amnon Shabo, IBM REserach Lab, Haifa, Israel

Call for Papers
Submitted contributions should address one or more of the following topics:
– Methods and Technologies:
Data warehouse – Natural Language Processing – Data Mining – Ontologies, Interoperability, Standardisation – Search Computing – Decision Support
– Tools:
ICT architectures to support – Clinical research – BioBanks – Software for next generation sequencing – Data management and storage
– Applications:
Risk assessment – Diagnosis – Therapy planning- Drug Design

Type of contributions: Oral communications – Posters – Software demoes
Contributions length:
– oral communications: between 3 and 5 pages
– posters and demoes: no more than 3 pages

· July 15, 2011: Oral communications submission
· September 5, 2011: Posters and demoes submission

Submit your contribution through the EasyChair system at

All contributions submitted to NETTAB 2011 will be invited to a restricted Call for full research papers to be published in a Supplement of BMC Bioinformatics.

You can register to the NETTAB 2011 workshop by using the form at
Early registration ends within September 30, 2011.

Visit the website

Contact the organization by sending an email message to nettab(AT)

Corso di dottorato “Current Challenges in Bioinformatics” (PoliMi & UniPv)

Ho il piacere di segnalare a tutti i lettori di questo blog, e specialmente agli studenti di dottorato d’un corso d’Ingegneria o Scienze Mfn di qualsiasi universita’, un interessantissimo corso dal titolo Current Challenges in Bioinformatics, organizzato dal Politecnico di Milano e dall’Universita’ di Pavia, che si terra’ nei prossimi mesi tra Pavia e Milano.

Il corso, come avrete capito, e’ dedicato alla bioinformatica, coinvolge importanti docenti a livello internazionale, e si divide in 3 parti, ognuna di due giorni:

  • lunedi’ 11, martedi’ 12 lugio 2011al Dipartimento di Informatica e Sistemistica dell’Universita’ di Pavia:

-omics data integration for molecular medicine” di Neil SarkarUniversity of Vermont, Vermont, Usa

  • lunedi’ 12, martedi’ 13 settembre 2011al Dipartimento di Informatica e Sistemistica dell’Universita’ di Pavia:

Advanced methods for data analysis and predictive models for Genome Wide Association Studies” di Paola SebastianiBoston University, Boston, Massachusetts, Usa

  • lunedi’ 17 ottobre 2011 al Dipartimento di Elettronica e Informazione del Politecnico di Milano

Bioinformatics for personalized medicine and current challenges in the protein universe” di Alfonso ValenciaSpanish National Cancer Research Center, Spagna, Unione Europea

Course Description:

The course provides an overview of the main current problems, methods and experiences in some fundamental areas of bioinformatics, including: integration of -omics data for molecular medicine, advanced methods for data analysis and predictive models for Genome Wide Association Studies, bioinformatics for personalize medicine, and challenges in the protein universe. Within these topics, current major bioinformatics aspects, from Next Generation Sequencing, to drug-protein interaction, to text mining related aspects, will be covered with emphasis on the challenges they pose and the methodological approach they require to be tackled.

The 24 hour course is organized in collaboration with the University of Pavia within the BIO & ICT Ph.D. Internationalization Project funded by the Fondazione CARIPLO. It consists of three 8 hour seminars, each held in two subsequent days at Politecnico di Milano or at Università di Pavia. Each seminar will be given by an invited well known foreign scientist on a current major bioinformatics topic.

During the course students will be challenged with interesting biological problems that are still open in the field of bioinformatics data integration and analysis.

Sito web del corso (Current Challenges in Bioinformatics)


La partecipazione e’ gratuita, chi volesse prenderne parte puo’ scrivermi una mail a davide.chicco(AT) Enzimi “risorti” grazie alla bioinformatica

Segnalo questo interessante articolo pubblicato oggi su, riguardo ad uno studio effettuato da alcuni scienziati ad Atlanta, Usa.

Le molecole che fummo

I nostri più antichi antenati vivevano in acque calde e acide: lo dimostrano i loro enzimi,“risorti” grazie alla bioinformatica
n un laboratorio ad Atlanta degli scienziati stanno studiando delle molecole batteriche. Non sono però molecole qualsiasi: hanno da uno a quattro miliardi (sì: miliardi) di anni. Sono le proteine dei nostri più antichi progenitori, che vivevano su una Terra giovanissima. Non a caso sono adatte a un ambiente ben diverso dal nostro: acque dalle temperature di quasi 50 gradi e 100 volte più acide di quelle attuali.

Bits2011 – Bits 2011: Bioinformatics Italian Society annual meeting a Pisa, 20-22 giugno

Nella sezione conferenze,  segnaliamo oggi Bits 2011, la conferenza annuale della Societa’ Italiana di Bioinformatica, che si terra’ a Pisa (Toscana, Italia, EU), dal 20 al 22 giugno 2011.

Bits 2011 Bits2011 Call for papers

BITS2011 – Pisa – June 20-22, 2011,
Area della Ricerca del CNR

First announcement

The annual meeting of the Bioinformatics Italian Society will be held in Pisa, June 20-22, 2011.


Submitted contributions should address novel bioinformatics methods, algorithms, databases, tools and applications for research and development in one or more of the following domains:

  • Genomics
  • Molecular Evolution and Comparative Genomics
  • Protein structure and function
  • Proteomics
  • Transcriptomics
  • Metagenomics
  • Systems Biology
  • Biological Databases and Biobanks
  • Algorithms for Bioinformatics
  • Biophysics and Synthetic Biology
  • Industrial Track

In addition to the usual topics of general pertinence in Bioinformatics, this meeting will cover two new areas:

  • Biophysics and Synthetic biology (as Structural biology and Origin of Life themes are in common between these disciplines and Bioinformatics)
  • Industrial track: in cooperation with Fondazione Toscana Life-Sciences, with the goal to have a parallel discussion of the possible industrial applications of the scientific subjects discussed during the sessions.

We stimulate industries not only to submit scientific contributions, that are welcome as usual, but to give short talks focused on their needs, goals and direction concerning bioinformatics, with particular emphasis at opening a dialogue with young researchers and Ph. D. students. A round table in the last congress day will collect a global assessment of how the industrial world sees the bioinformatics research.

Journal Special Issue

Selected abstracts will be invited to contribute in extended form to a special issue of BMC Bioinformatics Supplement devoted to BITS 2011.


Tutorial lectures on selected topics in Bioinformatics will be held at the Computer Science Department of the University of Pisa on June 22nd in the afternoon (more details will be posted on the conference web site).

For more information

Interviste(3): Pierre Lindenbaum dell’Universita’ di Nantes

Pubblichiamo oggi un nuovo articolo per la sezione “interviste” inaugurata qualche tempo fa. Oggi intervistiamo Pierre Lindenbaum, postdoc in genetica presso l’Universita’ di Nantes (Francia) e curatore del blog Yokofakun.

Who are you and where you work at?

I’m Pierre Lindenbaum. I got my PHD in virology in 2000 (I studied theprotein-protein interactions between the rotavirus and the host cell). During my PhD , I needed a program to quickly find the best subcloning strategies using a set of restriction enzymes. I wrote the program in ‘C’ ( and, as I had much fun in doing this, I decided to move my career to bioinformatics.
I now work as a postdoctoral researcher in UMR915/Nantes ( )

Which subjects do you study and research?

We”re working on the genetics of the cardiomyopathies. Using next-generation sequencing,  we’re trying to find what are the common genes involved in a cardiac disease.

Briefly describe your career

1996-2000: PhD at National Institute for Agronomic Research. protein-proteininteractions between the Rotavirus and the host cell
2000-2002: PostDoc at National Center of Genotyping (CNG ). Iwrote a program to find the best strategies for genotyping using mass-spectrometry.
2002-2008: Worked as a Bioinformatician at Integragen ( ). I wrote the programs/databases dedicated to our business.
2008-2009: I worked at the CEPH ( on a biological database based on the key/value datastore berkeleydb.
2010- : post doc in Nantes

What is it like in your university?

I’m working in a new building close to the “Hotel-Dieu hospital”
( ) and facing the “Loire” ( )
We’re also close to a heliport, so it often smells the gazoline.

What is it like in your research lab?

There is a really good atmosphereand people are nice. We counted 14 king ‘s cakes in January for celebrating the epiphany.  😛
There a large number of phd students as well as some physicians: so we’re closeto the patients and their problems.
Some views of my desk & my lab here:

What is it like in your country?

Right now, it’s raining.

Are you plannin’ and go elsewhere to work in the future?

Ask my wife, she decides all 😛

How did it come to your mind to open a bioinformatics blog?

I was in a very bad mood.
The day I started my blog, I told people about but they did notcare. Furthermore I was asked something like “Can you blast the Genome vs itself to see if there is something interesting ? Can we have the result tomorrow in a nice Excel spreadsheet”.  So I started my blog to tell the world about the things I like.

Which are the most important functionalities of it?

It’s my notebook. I can use it to see how I solved a problem some months ago. It also reflects my skills an my interests.

Which advantages did you get durin’ your career for havin’ it?

Thanks to my blog I got an invitation to scifoo2007 ( ) and two invitations to attend the BioHackathons in Japan

D’you think bioinformatics blog are too few around?

At least for French bioinformaticians, I can say they are rare. Why ? I don’t know.

D’you think bioinformaticians should get more in contact thru the web?

Not necessarily, if people come to work with their usual professional network. In my case, I had some nice experiences with FriendFeed
–  After a discussion about RDF
( , I got an invitation to be one of the authors of a chapter  of “Beautiful Data”

– Andrew Su (  asked for a bioinformatician to help
him with the GeneWiki effort ( ). At the end, I was the second author of an article published in an issue of Nucleic Acids Research.

Which bioinformatics organizations are you a member?


Do you visit and want to signal some other bioinformatics blog or website? is currently one of my favorite destination because some of the questions asked  here can be very challenging, fun  and it gives an overview of the other’s problems.
For the blogs, you will find the usual suspects at:



Ringraziamo Pierre per la sua disponibilita’!

Citizen Science, Rosett@home e Foldit

Avete mai sentito parlare di Citizen Science?
E’ il nome con cui i media nordamericani trattano il nuovo fenomeno della scienza partecipata sul web, nella quale internauti anonimi mettono a disposizione il proprio tempo, il proprio pc ed il proprio entusiasmo per usufruire/giocare con una qualche applicazione software a contenuto scientifico disponibile sul web.

Tra i primi progetti di “citizen science“, fa la parte del leone proprio la bioinformatica: ben 2 software sono disponibili online (Rosetta@home e Foldit). Ma riportiamo cos’ha scritto qualche giorno fa:

Da rete di computer a network di cervelli. Dalla stessa famiglia di software è nato anche Rosetta@home, un programma di calcolo distribuito per l’elaborazione della struttura tridimensionale delle proteine. Come riporta un recente articolo di Nature, è stato questo programma ad aver mostrato la via verso la “citizen science”. Il software, infatti, simulava il ripiegamento di una catena di amminoacidi sul monitor procedendo per tentativi, senza dare agli utenti la possibilità di intervenire. Con il tempo si è capito che il programma raggiungeva i risultati migliori combinando le funzionalità della macchina alla capacità, tipica degli esseri umani, di risolvere il puzzle per intuizione. Ecco allora che gli internauti sono diventati parte attiva del processo grazie a Foldit, un gioco online dove gli utenti competono, collaborano e creano strategie per la costruzione di proteine in 3D.

(l’articolo completo su

CIBB 2011 – 8th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics – CIBB2011

Segnalo a tutti questa importantissima conferenza su bioinformatica ed intelligenza computazionale che si terra’ a Gargnano sul Lago di Garda, in data 30 giugno, 1° luglio, 2 luglio.

Siete tutti invitati ad inviare all’organizzazione i vostri articoli e le vostre proposte di tutorial agli organizzatori scrivendo a


Call for papers:
==========================================================The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in bioinformatics, systems biology, medical informatics and biostatistics with a particular focus on Neural Networks, Computational Learning, Fuzzy Logic, and Evolutionary Computation, methods and their relationships with Statistical Pattern Recognition, Non-Parametric Inference and Computational Statistics

CIBB 2011 is jointly organized by:

INNS International Neural Network Society SIG Bioinformatics
INNS International Neural Network Society  SIG Biopattern
IEEE-CIS-BBTC Task force on Neural Networks

Technical areas addressed by CIBB 2010 include, but are not limited to:

Sequence analysis, promoter analysis and identification of transcription factor binding sites; Gene expression data analysis; Methods for the integration of clinical and genetic data; Algorithms for alternative splicing analysis; Methods for the functional classification of genes; Methods for the unsupervised analysis, validation and visualization of structures discovered in bio-molecular data; Prediction of secondary and tertiary protein structures; Mass spectrometry data analysis in proteomics; Methods for comparative genomics; Algorithms for molecular evolution and phylogenetic analysis; Mathematical modelling and simulation of biological systems; Heterogeneous data integration and data fusion for diagnostics; Bio-molecular databases and data mining; Algorithms for pharmacogenetics; Bio-medical text mining and imaging; Modeling and evaluation methods for diagnosis and prognosis; Software tools for bioinformatics

The scientific program will include, besides some plenary talks, contributed papers that will be presented in plenary oral and poster sessions. Accepted papers will be published in the compact disk of conference proceedings. A
selection of papers presented at CIBB 2011 will be published a in post conference volume printed by an international publisher. Moreover, we are planning to publish the best papers in extended form in a special issue of an
international scientific journal.

Important Dates:

Tutorial  Proposals:          1 April 2011
Paper submission deadline:    1 April 2011
Notification of acceptance:   1 May   2011
Final paper due:              15 May   2011
Conference:                   30 June  2011

Tutorial proposals:


Tutorial proposals including title, one page long abstract, and short cv of
presenters, are due by 30 April 2010  Please, send the proposals to

Paper submission:


Papers must be prepared following the guidelines illustrated on the CIBB web site and should be not longer than 10 pages Papers must be uploaded using the conference website (http:/

General Chairs

Elia Biganzoli (Italy)
Andrea Tettamanzi (Italy)
Alfredo Vellido (Spain)

Biostatistic Technical Chair

Valeria Edefonti (Italy)

Bioinformatics Technical Chair

Claudia Angelini (Italy)

Program Chairs

Luciano Milanesi (Italy)
Roberto Tagliaferri (Italy)

Scientific Committee

S Auephanwiriyakul (Thailand)
G Bernot (France)
C Bi (USA)
P Boracchi (Italy)
M Cannataro (Italy)
A Decarli (Italy)
A Ferro (Italy)
E Formenti (France)
C Friedrich (Germany)
S Gaglio (Italy)
A Giordano (Italy&USA)
P Lio’ (UK)
P Lisboa (UK)
G Mauri (Italy)
N Pasquier (France)
D Pelta (Spain)
L Peterson (USA)
G Pollastri (Italy)
M Popescu (USA)
R Rizzo (Italy)
V Roth (Switzerland)
G Russo (USA)
F Stefanini (Italy)
G Valentini (Italy)
Y Zhang (USA)

Local Organizing Committee:

F Ambrogi (Italy)
N Bassani (Italy)
F Napolitano(Italy)

Steering Committee

P Baldi (USA)
A Floares (Romania)
J Garibaldi (UK)
F Masulli (Italy & USA)
R Tagliaferri (Italy)

CIBB 2011
Gargnano del Garda (Italy), 30 June – 2 July 2011
Conference Website