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Pipengine: an ultra light YAML-based pipeline execution engine

Francesco Strozzi, Raoul Jean Pierre Bonnal
2017 Journal of Open Source Software  
Pipengine is written in Ruby and is available for download as a BioRuby Gem (Goto N 2010; Bonnal RJP 2012) .  ... 
doi:10.21105/joss.00341 fatcat:w4qd54fwfbh5loajnsa4qnvqdq

Identification of New Autoantigens by Protein Array Indicates a Role for IL4 Neutralization in Autoimmune Hepatitis

Chiara Zingaretti, Milena Arigò, Angela Cardaci, Monica Moro, Mariacristina Crosti, Antonella Sinisi, Elisa Sugliano, Cristina Cheroni, Francesco Marabita, Renzo Nogarotto, Raoul Jean Pierre Bonnal, Paolo Marcatili (+13 others)
2012 Molecular & Cellular Proteomics  
Autoimmune hepatitis (AIH) is an unresolving inflammation of the liver of unknown cause. Diagnosis requires the exclusion of other conditions and the presence of characteristic features such as specific autoantibodies. Presently, these autoantibodies have relatively low sensitivity and specificity and are identified via immunostaining of cells or tissues; therefore, there is a diagnostic need for better and easy-to-assess markers. To identify new AIHspecific autoantigens, we developed a protein
more » ... microarray comprising 1626 human recombinant proteins, selected in silico for being secreted or membrane associated. We screened sera from AIH patients on this microarray and compared the reactivity with that of sera from healthy donors and patients with chronic viral hepatitis C. We identified six human proteins that are specifically recognized by AIH sera. Serum reactivity to a combination of four of these autoantigens allows identification of AIH patients with high sensitivity (82%) and specificity (92%). Of the six autoantigens, the interleukin-4 (IL4) receptor fibronectin type III domain of the IL4 receptor (CD124), which is expressed on the surface of both lymphocytes and hepatocytes, showed the highest individual sensitivity and specificity for AIH. Remarkably, patients' sera inhibited STAT6 phosphorylation induced by IL4 binding to CD124, demonstrating that these autoantibodies are From the ‡Istituto Nazionale Genetica Molecolare (INGM), 20122 Milan, Italy; ¶Externautics S.p.A., 1 The abbreviations used are: AIH, autoimmune hepatitis; AUC, area under the curve; DELFIA, Dissociation-enhanced Lanthanide Fluoroscence ImmunoAssay; FNIII, fibronectin type III domain; HBV, hepatitis B virus; HCV, hepatitis C virus; HD, healthy donor; IL4R, interleukin-4 receptor; IMAC, immobilized metal ion affinity chromatography; MFI, mean fluorescence intensity; PAM, predictive analysis of microarray; ROC, Receiver Operating Characteristic. Research
doi:10.1074/mcp.m112.018713 pmid:22997428 pmcid:PMC3518104 fatcat:rq7xexgq7bet3dl6nwu7aifklu

Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ

Giulia Della Chiara, Federica Gervasoni, Michaela Fakiola, Chiara Godano, Claudia D'Oria, Luca Azzolin, Raoul Jean Pierre Bonnal, Giulia Moreni, Lorenzo Drufuca, Grazisa Rossetti, Valeria Ranzani, Ramona Bason (+27 others)
2021 Nature Communications  
AbstractCancer is characterized by pervasive epigenetic alterations with enhancer dysfunction orchestrating the aberrant cancer transcriptional programs and transcriptional dependencies. Here, we epigenetically characterize human colorectal cancer (CRC) using de novo chromatin state discovery on a library of different patient-derived organoids. By exploring this resource, we unveil a tumor-specific deregulated enhancerome that is cancer cell-intrinsic and independent of interpatient
more » ... y. We show that the transcriptional coactivators YAP/TAZ act as key regulators of the conserved CRC gained enhancers. The same YAP/TAZ-bound enhancers display active chromatin profiles across diverse human tumors, highlighting a pan-cancer epigenetic rewiring which at single-cell level distinguishes malignant from normal cell populations. YAP/TAZ inhibition in established tumor organoids causes extensive cell death unveiling their essential role in tumor maintenance. This work indicates a common layer of YAP/TAZ-fueled enhancer reprogramming that is key for the cancer cell state and can be exploited for the development of improved therapeutic avenues.
doi:10.1038/s41467-021-22544-y pmid:33879786 fatcat:mfo2jcbf75dtfhjjqkhtzeipye

Page 83 of Bookman; A Review of Books and Life Vol. 10, Issue 1 [page]

1899 Bookman; A Review of Books and Life  
Two writers, Pierre Baudier and Raoul Cadiéres, the former of whom is a mem- ber of the new cabinet, which is trying to bring about a pacification of France, have undertaken a very interesting historical  ...  Some of the most important problems of the future are treated in Jean Jaurés’s L’ Action Socialiste.  ... 

Proceedings of Réanimation 2017, the French Intensive Care Society International Congress

Chtara Kamilia, Kais Regaieg, Najeh Baccouch, Hedi Chelly, Mabrouk Bahloul, Mounir Bouaziz, Ali Jendoubi, Ahmed Abbes, Houda Belhaouane, Oussama Nasri, Layla Jenzri, Salma Ghedira (+1089 others)
2017 Annals of Intensive Care  
A pilot study Hélène Cochet 1 , Jean Pierre Ponthus 1 , Virginie Amilien 1 , Martial Tchir 1 , Elise Barsam 1 , Mohsen Ayoub 1 , Jean Francois Georger 1 1 Réanimation polyvalente -surveillance continue  ...  Jean-Pierre Frat 1 , Remi Coudroy 1 , Stéphanie Ragot 2 , Jean-Michel Constantin 3 , Gwenael Prat 4 , Alain Mercat 5 , Thierry Boulain 6 , Christophe Girault 7 , Alexandre Demoule 8 , Jérôme Devaquet,  ...  S60 Invasive fungal infection after liver transplantation: diagnostic value of 1,3-beta-d-glucan (BG) Noorah Zaid 1 , Nawel Ait-Ammar 2 , Christine Bonnal 2 , Jean-Claude Merle 1 , Francoise Botterel 2  ... 
doi:10.1186/s13613-016-0224-7 fatcat:2iumv76ivzdszafcy6hbqkd7um

GFVO: the Genomic Feature and Variation Ontology

Joachim Baran, Bibi Sehnaaz Begum Durgahee, Karen Eilbeck, Erick Antezana, Robert Hoehndorf, Michel Dumontier
2015 PeerJ  
Raoul Jean Pierre Bonnal, Toshiaki Katayama, Francesco Strozzi brought forward suggestions to improve GFVO's practical applications.  ... 
doi:10.7717/peerj.933 pmid:26019997 pmcid:PMC4435477 fatcat:jplcinbnxfethhlzl7iqznn3cq

scRepertoire: An R-based toolkit for single-cell immune receptor analysis

Nicholas Borcherding, Nicholas L. Bormann, Gloria Kraus
2020 F1000Research  
Lorenzo Drufuca School of Medicine and Surgery, Università degli Studi di Milano Bicocca, Milan, Italy Raoul Jean Pierre Bonnal National Institute of Molecular Genetics, Milan, Italy Massimiliano Pagani  ...  Drufuca, Bonnal, and Pagani suggested we have added scRepertoire interaction with a number of R packages and changed the definition of clonotype for B cells. Per the comments made by Dr.  ... 
doi:10.12688/f1000research.22139.2 fatcat:hpmz25pplnbzbmsmp4y7cakeg4

Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma

Adrian Ally, Miruna Balasundaram, Rebecca Carlsen, Eric Chuah, Amanda Clarke, Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo (+226 others)
2017 Cell  
Verhaak, Daniel O'Brien, Jean-Pierre Kocher, Nicolas Stransky, Hiroyuki Aburatani, Yamamoto Shogo.  ...  : Reanne Bowlby, Sara Sadeghi, Karen Mungall Chandra Sekhar Pedamallu, Akinyemi I Ojesina, Matthew Meyerson, Daniel O'Brien, Jean-Pierre Kocher, Betty L. Slagle, Kyle Covington, Lawrence A.  ... 
doi:10.1016/j.cell.2017.05.046 pmid:28622513 pmcid:PMC5680778 fatcat:drfldh7h3vhb5mq3zcrqcthc3a

Kino der Ränder. Robert Guédiguians peripheres Marseille [chapter]

Transit Marseille  
Paul (Jean-Pierre Darroussin) führt seinen Eltern das eben per Kredit erworbene Taxi vor.  ...  Frédérique Bonnal) und ihren drei Kindern besteht.  ... 
doi:10.14361/9783839406991-007 fatcat:45prrwxlrvdkjan3vpvzpqmc4e

Az 1968-as májusi diákmozgalom és de Gaulle bukásának külpolitikai összefüggései [article]

Kovács Örs, Botos Máté
Salan, Raoul (1899 Raoul ( -1984 : francia tábornok, a franciák vietnámi háborúja idején az ottani erők parancsnoka, majd az algériai háború idején de Gaulle- Wilson, Harold (1916 -1995 ): 1963 -tól  ...  A Dutschke merénylettel kapcsolatban a Népszabadságban április 14-én jelent meg Rényi Péter 78 LE GOFF, Jean-Pierre: Mai 68, l'héritage impossible, Paris, La Découverte, 1998 p.100 79 HELLER Ágnes  ... 
doi:10.15774/ppke.btk.2013.013 fatcat:gludetaevrdodpjphliecrdxyu