2024-03-29T07:24:16Zhttp://oai-repositori.upf.edu/oai/requestoai:repositori.upf.edu:10230/246452018-02-19T12:31:38Zcom_10230_5963col_10230_24644
Low-complexity regions in proteins as a source of evolutionary innovation [research data]
Radó i Trilla, Núria, 1985-
Dades primàries de la tesi “Low-complexity regions as a source of evolutionary innovation”/nde Núria Radó-Trilla http://hdl.handle.net/10803/113603
2013
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/24645
eng
http://hdl.handle.net/10803/113603
http://creativecommons.org/publicdomain/zero/1.0/
info:eu-repo/semantics/openAccess
CC0 1.0 Universal
oai:repositori.upf.edu:10230/256082016-01-20T17:02:31Zcom_10230_5963col_10230_24644
A functional study of the conserved LSM proteins in C. elegans reveals their involvement in the stress response of metazoans [datasets]
Cornes Maragliano, Eric, 1987-
Research data from the thesis “A functional study of the conserved LSM proteins in C. elegans reveals their involvement in the stress response of metazoans” by Eric Cornes http://hdl.handle.net/10803/315473
2015
info:eu-repo/semantics/other
http://hdl.handle.net/10230/25608
eng
http://hdl.handle.net/10803/315473
http://creativecommons.org/publicdomain/zero/1.0/
info:eu-repo/semantics/openAccess
CC0 1.0 Universal
oai:repositori.upf.edu:10230/276362016-12-19T08:52:29Zcom_10230_5963col_10230_24644
Cancer bioMarkers database
Tamborero Noguera, David
Rubio Pérez, Carlota
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
Vivancos Prellezo, Ana
Rovira Guerín, Ana
Tusquets, Ignasi
Albanell Mestres, Joan
Rodon, Jordi
Tabernero Cartula, Josep
Dienstmann, Rodrigo
González-Pérez, Abel
López Bigas, Núria
The cancer bioMarkers database is curated and maintained by several clinical and scientific experts in the field of precision oncology supported by the European Union’s Horizon 2020 funding. This database is currently being integrated with knowledge databases of other institutions in a collaborative effort of the Global Alliance for Genomics and Health.
2016-10-17
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/27636
eng
https://www.cancergenomeinterpreter.org/biomarkers
Més informació: Cancer bioMarkers database (Cancer Genome Interpreter)
http://creativecommons.org/publicdomain/zero/1.0/
info:eu-repo/semantics/openAccess
Creative Commons CC0
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/277842017-02-27T11:44:32Zcom_10230_5963col_10230_24644
OncoPaD
Tamborero Noguera, David
López Bigas, Núria
González-Pérez, Abel
Rubio Pérez, Carlota
Déu Pons, Jordi
A tool aimed at the rational design of cancer gene panels. It estimates the cost-effectiveness of the designed panel on a cohort of tumors and provides reports on the importance of individual mutations for tumorigenesis or therapy.
2016-10-16
info:eu-repo/semantics/other
http://hdl.handle.net/10230/27784
eng
http://hdl.handle.net/10230/27942
https://bitbucket.org/bbglab/oncopad
Més informació: OncoPAD (Bitbucket)
Rubio-Perez C, Deu-Pons J, Tamborero D, Lopez-Bigas N, Gonzalez-Perez A. Rational design of cancer gene panels with OncoPaD. Genome Med. 2016; 8(98). DOI: 10.1186/s13073-016-0349-1 http://hdl.handle.net/10230/27942
http://bitbucket.org/bbglab/oncopad/raw/619011cedb025d4542b7abc54d41b69636264575/LICENSE
info:eu-repo/semantics/openAccess
OncoPAD is the property of the Universitat Pompeu Fabra (UPF), which hold the copyright thereto. Copyright® 2012-2014 Universitat Pompeu Fabra.
OncoPAD is made available to the general public subject to certain conditions described in its license. For the avoidance of doubt, you may use the software and any data accessed through UPF software for academic, non-commercial and personal use only, and you may not copy, distribute, transmit, duplicate, reduce or alter in any way for commercial purposes, or for the purpose of redistribution, without a license from the Universitat Pompeu Fabra (UPF). Requests for information regarding a license for commercial use or redistribution of IntOGen Mutations Analysis may be sent via e-mail to innovacio@upf.edu.
Third Party Software - Third Party Data
All rights in any third-party data and/or any third-party software, including all ownership rights, are reserved and remain with the respective third parties. You agree that these third parties may enforce their rights under this agreement against you directly in their own name.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/278102017-02-03T12:21:32Zcom_10230_5963col_10230_24644
IntOGen - Pipeline
González-Pérez, Abel
Pérez Llamas, Christian, 1976-
Tamborero Noguera, David
Schroeder, Michael Philipp, 1986-
Jené i Sanz, Alba, 1984-
Santos, Alberto
López Bigas, Núria
Déu Pons, Jordi
Analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes.
2016-07-18
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/27810
eng
http://dx.doi.org/10.1038/nmeth.2642
https://bitbucket.org/intogen/intogen-pipeline
Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A, Lopez-Bigas N. IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods. 2013; 10 (11): 1081-2. DOI: 10.1038/nmeth.2642
Més informació: IntOGen pipeline (Bitbucket)
http://bg.upf.edu/licenses/intogen-mutations-analysis-license.txt
info:eu-repo/semantics/openAccess
IntOGen Mutations Analysis is the property of the Universitat Pompeu Fabra (UPF), which hold the copyright thereto. Copyright® 2012-2014 Universitat Pompeu Fabra./nIntOGen Mutations Analysis is made available to the general public subject to certain conditions described in its license. For the avoidance of doubt, you may use the software and any data accessed through UPF software for academic, non-commercial and personal use only, and you may not copy, distribute, transmit, duplicate, reduce or alter in any way for commercial purposes, or for the purpose of redistribution, without a license from the Universitat Pompeu Fabra (UPF). Requests for information regarding a license for commercial use or redistribution of IntOGen Mutations Analysis may be sent via e-mail to innovacio@upf.edu./nThird Party Software - Third Party Data/nThe following software may be included in the code and, unless otherwise specified, is licensed under the licenses described below. The disclaimers and copyright notices provided are based on information made available to UPF by the third party licensors listed:/n- VEP/n- Ensembl/n- LiftOver/nRegarding third-party data, you agree to comply with the terms and conditions described in the licenses provided below, based on information made available to UPF by the third party licensors listed:/n- Ensembl genes: www.ensembl.org European Bioinformatic Institute./n- Mutation assessor 2: www.mutationassessor.org Computational Biology Center/n- Memorial Sloan Kettering Cancer Center./n- KEGG: http://www.genome.jp/kegg//n- Gene Ontology: http://www.geneontology.org//n- ICGC: http://icgc.org//n- TCGA: http://cancergenome.nih.gov//nAll rights in any third-party data and/or any third-party software, including all ownership rights, are reserved and remain with the respective third parties. You agree that these third parties may enforce their rights under this agreement against you directly in their own name.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/278782018-02-19T12:30:04Zcom_10230_5963col_10230_24644
Gitools
Pérez Llamas, Christian, 1976-
López Bigas, Núria
Schroeder, Michael Philipp, 1986-
Déu Pons, Jordi
Gitools is a framework for analysis and visualization of multidimensional genomic data using interactive heat-maps
2016-07-05
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/27878
eng
http://hdl.handle.net/10230/23502
http://www.gitools.org/
Publicació relacionada: Pérez-Llamas C, López-Bigas N. Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS ONE. 2011; 6(5): e19541. DOI 10.1371/journal.pone.0019541 http://hdl.handle.net/10230/23502
Més informació: Gitools website
http://www.gnu.org/licenses/gpl-3.0.txt
info:eu-repo/semantics/openAccess
GNU General Public License v3.0. Consulteu les condicions d'ús específiques dins del document
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/279282017-01-18T11:54:06Zcom_10230_5963col_10230_24644
OncodriveFML
Mularoni, Loris
Sabarinathan, Radhakrishnan
González-Pérez, Abel
López Bigas, Núria
Déu Pons, Jordi
Method to identify genomic regions, both coding and non-coding, bearing mutations with significant shift towards high functional impact across a cohort of tumos (FMbias), which are candidates to function as cancer drivers, through a local test.
2016-06-06
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/27928
eng
http://hdl.handle.net/10230/27626
http://bitbucket.org/bbglab/oncodrivefml
Més informació: OncodriveFML (Bitbucket)
Mularoni L, Sabarinathan R, Déu Pons J, González-Pérez A, López Bigas N. OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations. Genome Biology. 2016; 17:128. DOI: 10.1186/s13059-016-0994-0 http://hdl.handle.net/10230/27626
info:eu-repo/semantics/openAccess
OncodriveFML is the property of the Universitat Pompeu Fabra (UPF), which hold the copyright thereto./nCopyright® 2012-2014 Universitat Pompeu Fabra./nOncodriveFML is made available to the general public subject to certain conditions described in its license./nFor the avoidance of doubt, you may use the software and any data accessed through UPF software for academic,/nnon-commercial and personal use only, and you may not copy, distribute, transmit, duplicate, reduce or alter/nin any way for commercial purposes, or for the purpose of redistribution, without a license from the/nUniversitat Pompeu Fabra (UPF). Requests for information regarding a license for commercial use or/nredistribution of OncodriveFML may be sent via e-mail to innovacio@upf.edu./nThird Party Software/nThe third-party software listed below is downloaded directly from its homepages and, unless otherwise specified,/nis licensed under the licenses described below. The disclaimers and copyright notices provided are based on/ninformation made available to UPF by the third party licensors listed:/nNumpy: http://www.numpy.org//nScipy: http://www.scipy.org//nPandas: https://github.com/pydata/pandas/nStatmodels: http://statsmodels.sourceforge.net//nAll rights in any third-party data and/or any third-party software, including all ownership rights, are reserved/nand remain with the respective third parties. You agree that these third parties may enforce their rights under/nthis agreement against you directly in their own name./nConsulteu les condicions d'ús específiques dins del document.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/279372017-01-19T09:56:53Zcom_10230_5963col_10230_24644
itab
Déu Pons, Jordi
Python tab files parsing and validating schema tools.
2016-04
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/27937
eng
https://github.com/bbglab/itab
Més informació: itab (GitHub)
http://www.apache.org/licenses/LICENSE-2.0
info:eu-repo/semantics/openAccess
Copyright 2015 Universitat Pompeu Fabra/nLicensed under the Apache License, Version 2.0 (the "License");/nyou may not use this file except in compliance with the License./nYou may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0/nUnless required by applicable law or agreed to in writing, software/ndistributed under the License is distributed on an "AS IS" BASIS,/nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./nSee the License for the specific language governing permissions and/nlimitations under the License.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/279382017-03-15T09:12:48Zcom_10230_5963col_10230_24644
Mutations Needle Plot (muts-needle-plot)
Schroeder, Michael Philipp, 1986-
A needle-plot (aka stem-plot or lollipop-plot) plots each data point as a big dot and adds a vertical line that makes it appear like a needle.
2015-11
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/27938
eng
https://github.com/bbglab/muts-needle-plot
Més informació: muts-needle-plot (GitHub)
info:eu-repo/semantics/openAccess
Copyright 2015 Universitat Pompeu Fabra/nLicensed under the Apache License, Version 2.0 (the "License");/nyou may not use this file except in compliance with the License./nYou may obtain a copy of the License at/nhttp://www.apache.org/licenses/LICENSE-2.0/nUnless required by applicable law or agreed to in writing, software/ndistributed under the License is distributed on an "AS IS" BASIS,/nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./nSee the License for the specific language governing permissions and/nlimitations under the License.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/279832017-03-08T10:46:44Zcom_10230_5963col_10230_24644
OncodriveCLUST
Tamborero Noguera, David
González-Pérez, Abel
López Bigas, Núria
OncodriveCLUST is a method aimed to identify genes whose mutations are biased towards a large spatial clustering. This method is designed to exploit the feature that mutations in cancer genes, especially oncogenes, often cluster in particular positions of the protein. We consider this as a sign that mutations in these regions change the function of these proteins in a manner that provides an adaptive advantage to cancer cells and consequently are positively selected during clonal evolution of tumours, and this property can thus be used to nominate novel candidate driver genes./nThe method does not assume that the baseline mutation probability is homogeneous across all gene positions but it creates a background model using silent mutations. Coding silent mutations are supposed to be under no positive selection and may reflect the baseline clustering of somatic mutations. Given recent evidences of non-random mutation processes along the genome, the assumption of homogenous mutation probabilities is likely an oversimplication introducing bias in the detection of meaningful events.
2015-11
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/27983
eng
http://dx.doi.org/10.1093/bioinformatics/btt395
http://bitbucket.org/bbglab/oncodriveclust
Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013; 19(18): 2238-44. DOI: 10.1093/bioinformatics/btt395
Més informació: OncodriveCLUST (Bitbucket)
info:eu-repo/semantics/openAccess
Universitat Pompeu Fabra Free Source Code License Agreement. Consulteu les condicions d'ús específiques dins del document.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/279942017-03-08T10:47:20Zcom_10230_5963col_10230_24644
OncodriveFM
González-Pérez, Abel
López Bigas, Núria
OncodriveFM detects candidate cancer driver genes and pathways from catalogs of somatic mutations in a cohort of tumors by computing the bias towards the accumulation of functional mutations (FM bias).This novel approach avoids some known limitations of recurrence-based approaches, such as the difficulty to estimate background mutation rate, and the fact that they usually fail to identify lowly recurrently mutated driver genes.
2015-10
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/27994
eng
http://hdl.handle.net/10230/23344
https://bitbucket.org/bbglab/oncodrivefm
Gonzalez-Perez A, Lopez-Bigas N. Functional impact bias reveals cancer drivers. Nucleic Acids Research. 2012; 40(21): e169. DOI 10.1093/nar/gks743 http://hdl.handle.net/10230/23344
Més informació: OncodriveFM (Bitbucket)
info:eu-repo/semantics/openAccess
Universitat Pompeu Fabra Free Source Code License Agreement. Consulteu les condicions d'ús específiques dins del document.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280492017-03-10T02:30:28Zcom_10230_5963col_10230_24644
IntOGen - Cancer Drivers Database (2014)
Rubio Pérez, Carlota
Tamborero Noguera, David
Schroeder, Michael Philipp, 1986-
Antolín Hernández, Albert, 1984-
Déu Pons, Jordi
Pérez Llamas, Christian, 1976-
Mestres i López, Jordi
González-Pérez, Abel
López Bigas, Núria
This database contains information on the genes identified as drivers in Rubio-Perez and Tamborero et al. (2015). It contains information on driver identification at mutational, CNA and gene fusion level. Additional ancillary information about the role and major clonality of drivers is also included. A table is also provided with the list of datasets used for mutational driver identification.
2015-03
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/28049
eng
http://dx.doi.org/10.1016/j.ccell.2015.02.007
https://www.intogen.org/downloads
Més informació: IntOGen (web)
Rubio-Perez C, Tamborero D, Schroeder MP, Aantolín AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell. 2015; 27(3): 382-96. DOI: 10.1016/j.ccell.2015.02.007
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280502018-01-24T08:33:12Zcom_10230_5963col_10230_24644
IntOGen - Cancer Drivers Actionability Database
Rubio Pérez, Carlota
Tamborero Noguera, David
Schroeder, Michael Philipp, 1986-
Antolín Hernández, Albert, 1984-
Déu Pons, Jordi
Pérez Llamas, Christian, 1976-
Mestres i López, Jordi
González-Pérez, Abel
López Bigas, Núria
This database contains data on the interactions with therapeutic agents an driver genes contained in Cancer Drivers Database (2014.12). It characterizes the interacting therapeutic agents in terms of clinical phase and cancer prescription, among other features. Additionally, it contains ancillary information on specific genomic alterations associated to drug effectiveness which are FDA approved or clinically being tested together with data on other genomic alterations known to be responsible of drug primary resistance.
2015-03
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/28050
eng
http://dx.doi.org/10.1016/j.ccell.2015.02.007
https://www.intogen.org/downloads
Més informació: IntOGen (web)
Rubio-Perez C, Tamborero D, Schroeder MP, Aantolín AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell. 2015; 27(3): 382-96. DOI: 10.1016/j.ccell.2015.02.007
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280092017-01-27T10:43:02Zcom_10230_5963col_10230_24644
Onexus
Déu Pons, Jordi
Onexus is a modular framework to manage the complete life cycle of data analyses. Data analyses follow these steps: analysis definition, analysis execution, results storing, results browsing and finally results publishing.
2014-11
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28009
eng
https://github.com/onexus/onexus
Més informació: Onexus (GitHub)
http://www.apache.org/licenses/LICENSE-2.0
info:eu-repo/semantics/openAccess
Copyright 2012 Universitat Pompeu Fabra./n Licensed under the Apache License, Version 2.0 (the "License");/n you may not use this file except in compliance with the License./n You may obtain a copy of the License at/n http://www.apache.org/licenses/LICENSE-2.0/n Unless required by applicable law or agreed to in writing, software/n distributed under the License is distributed on an "AS IS" BASIS,/n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./n See the License for the specific language governing permissions and/n limitations under the License./nConsulteu les condicions d'ús específiques dins del document.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280252017-02-01T10:04:00Zcom_10230_5963col_10230_24644
Wok
Pérez Llamas, Christian, 1976-
Wok is a workflow management system implemented in Python that makes very easy to structure the workflows, parallelize their execution and monitor its progress among other things. It is designed in a modular way allowing to adapt it to different infraestructures./nFor the time being it is strongly focused on clusters implementing any DRMAA compatible resource manager (i.e. Oracle Grid Engine) which working nodes have a shared folder in common. Other, more flexible infrastructures (such as the Amazon EC2) are considered for future implementations.
2014-06
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28025
eng
http://github.com/bbglab/wok
Més informació: Wok (GitHut)
http://www.gnu.org/licenses/gpl-3.0.en.html
info:eu-repo/semantics/openAccess
GNU General Public License v3.0
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280302017-02-01T11:56:15Zcom_10230_5963col_10230_24644
OncodriveRole
Schroeder, Michael Philipp, 1986-
Rubio Pérez, Carlota
Tamborero Noguera, David
González-Pérez, Abel
López Bigas, Núria
Machine-learning based approach to classify cancer driver genes into to Activating or Loss of Function roles for cancer gene development.
2014-06
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28030
eng
http://hdl.handle.net/10230/24768
http://bitbucket.org/bbglab/oncodriverole
Més informació: OncodriveRole (Bitbucket)
Schroeder MP, Rubio-Perez C, Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action. Bioinformatics. 2014 Sep 1; 30(17): i549-55. DOI: 10.1093/bioinformatics/btu467 http://hdl.handle.net/10230/24768
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280332017-02-02T10:37:01Zcom_10230_5963col_10230_24644
jHeatmap
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
López Bigas, Núria
Javascript library to create interactive heatmaps within webpages.
2014-03
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28033
eng
http://doi.org/10.1093/bioinformatics/btu094
http://jheatmap.github.io/jheatmap/
Més informació: jHeatmap (web)
Deu-Pons J, Schroeder MP, Lopez-Bigas N. jHeatmap: an interactive heatmap viewer for the web. Bioinformatics. 2014; 30(12): 1757-8. DOI: 10.1093/bioinformatics/btu094
http://www.apache.org/licenses/LICENSE-2.0
info:eu-repo/semantics/openAccess
Copyright 2011 Universitat Pompeu Fabra (http://www.upf.edu)./n Licensed under the Apache License, Version 2.0 (the "License");/n you may not use this file except in compliance with the License./n You may obtain a copy of the License at/n <http://www.apache.org/licenses/LICENSE-2.0>/n Unless required by applicable law or agreed to in writing, software/n distributed under the License is distributed on an "AS IS" BASIS,/n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./n See the License for the specific language governing permissions and/n limitations under the License.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280512017-03-10T02:30:38Zcom_10230_5963col_10230_24644
IntOGen - TCGA pan-cancer12 high confidence drivers
Tamborero Noguera, David
González-Pérez, Abel
Pérez Llamas, Christian, 1976-
Déu Pons, Jordi
Kandoth, Cyriac
Reimand, Jüri
Lawrence, Michael S.
Getz, Gad
Bader, Gary D.
Ding, Li
López Bigas, Núria
This file lists the High Confidence Drivers identified as part of the pan-cancer12 initiative, published in the paper Comprehensive identification of mutational cancer driver genes across 12 tumor types" Scientific Reports 3:2650, 2013, doi:10.1038/srep02650
2013-10
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/28051
eng
http://hdl.handle.net/10230/24554
https://www.intogen.org/downloads
Més informació: IntOGen (web)
Tamborero D, González-Párez A, Pérez-Llamas C, Deu-Pons J, Kandoth C, Reimand J et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific Reports. 2013; 3: 2650. DOI 10.1038/srep02650 http://hdl.handle.net/10230/24554
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280482017-02-03T10:15:55Zcom_10230_5963col_10230_24644
C10-HDAC7
Barneda Zahonero, Bruna
Román González, Lidia
Collazo, Olga
Rafati, Haleh
Islam, Abul, 1978-
Bussmann, Lars
Di Tullio, Alessandro, 1982-
Andrés, Luisa De
Graf, T. (Thomas)
López Bigas, Núria
Mahmoudi, Tokameh
Parra, Maribel
HDAC7 is a repressor of myeloid genes whose downregulation in pre-B cells is required for transdifferentiation into macrophages.
2013-05
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28048
eng
http://hdl.handle.net/10230/23441
http://bg.upf.edu/projects/C10-HDAC7/
Més informació: C10-HDAC7 (web)
Barneda-Zahonero B, Roman-Gonzalez L, Collazo O, Rafati H, Islam ABMMK, Bussmann LH et al. HDAC7 is a repressor of myeloid genes whose downregulation is required for transdifferentiation of pre-B cells into macrophages. PLoS Genetics. 2013; 9(5): e1003503. DOI: 10.1371/journal.pgen.1003503 http://hdl.handle.net/10230/23441
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
Aquest document es troba sota llicència Creative Commons Reconeixement 3.0 Espanya (CC BY 3.0 ES)
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280812017-03-18T02:30:44Zcom_10230_5963col_10230_24644
IntOGen - Cancer driver database (2013)
González-Pérez, Abel
Pérez Llamas, Christian, 1976-
Déu Pons, Jordi
Tamborero Noguera, David
Schroeder, Michael Philipp, 1986-
Jené i Sanz, Alba, 1984-
Santos, Alberto
López Bigas, Núria
Mutations, genes and pathways involved in tumorigenesis across 4,623 cancer genomes/exomes from 13 cancer sites. IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods 10, 2013, doi:10.1038/nmeth.2642
2013-05
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/28081
eng
http://dx.doi.org/10.1038/nmeth.2642
https://www.intogen.org/downloads
Més informació: IntOGen (web)
Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A, Lopez-Bigas N. IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods. 2013;10(11):1081-2. DOI: 10.1038/nmeth.2642
http://www.intogen.org/terms
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Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280822017-02-08T10:12:42Zcom_10230_5963col_10230_24644
Oncodrive-CIS
Tamborero Noguera, David
López Bigas, Núria
González-Pérez, Abel
Oncodrive-CIS is a method aimed to identify those copy number alterations (CNAs) leading to larger in cis expression changes that may be useful in elucidating the role of these aberrations in cancer. This is based on the hypothesis that a gene driving oncogenesis through copy number changes is more prone to bias towards overexpression (or underexpression) as compared to bystanders. The effect of the gene dosage is assessed by observing expression changes not only among tumors but also taking into account normal samples data, when available./nOncodrive-CIS has several potential benefits: first, it did not examine the frequency of the CNAs across samples and therefore the detection of low-recurrent driver alterations was not impaired. Second, amplifications and deletions were evaluated separately to obtain a fair ranking of genes, because the expression change measured in deletions was lower than the one obtained from multi-copy amplifications. Third, the expression of genes in tumor samples was analyzed according to the copy number status but was also compared to normal samples, thus better revealing the gene misregulation role of CNAs in cancer cells. And finally, it should be emphasized that the relationship between expression changes and their functional impact is complex, thus Oncodrive-CIS is proposed as a method to elucidate the role of CNAs in cancer which may be complementary to analyses based on other criteria.
2013-02
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28082
eng
http://hdl.handle.net/10230/23565
http://bg.upf.edu/group/projects/oncodrive-cis.php
Més informació: Oncodrive-CIS (Biomedical Genomics)
Tamborero D, López-Bigas N, González-Pérez A. Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression. PLoS ONE. 2013; 8(2): e55489. DOI 10.1371/journal.pone.0055489 http://hdl.handle.net/10230/23565
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Dades sita llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280952017-02-09T09:10:26Zcom_10230_5963col_10230_24644
SVGMap
Rafael Palou, Xavier
Schroeder, Michael Philipp, 1986-
López Bigas, Núria
The aim of SVGMap is helping in the visualisation of experimental data which are associated with some graphical representation. Thus SVGMap browser allows to generate images with colored areas corresponding to the chosen data and color scale./nThe data is represented as a table and is searchable. All data as well as the generated images/figures can be exported easily through the interface./nAdditionally the tool allows to manage (add, edit or delete) experiments and configure the front-end user search appearance such as the number of images to be displayed, the scale types to use and more.
2012-01
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28095
eng
http://dx.doi.org/10.1093/bioinformatics/btr581
http://bitbucket.org/bbglab/svgmap/wiki/Home
Més informació: SVGMap (Bitbucket)
Rafael-Palou X, Schroeder MP, Lopez-Bigas N. SVGMap: configurable image browser for experimental data. Bioinformatics. 2011;28(1):119-20. DOI: 10.1093/bioinformatics/btr581
http://www.opensource.org/licenses/osl-3.0
info:eu-repo/semantics/openAccess
Copyright 2011 Universitat Pompeu Fabra./nThis software is open source and is licensed under the Open Software License version 3.0./nYou may obtain a copy of the License at/nhttp://www.opensource.org/licenses/osl-3.0/nThis software also includes image examples licensed under Creative Commons license./nUnless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./nSee the License for the specific language governing permissions and limitations under the License.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/280972017-02-09T11:52:49Zcom_10230_5963col_10230_24644
p27
Pippa, Raffaella
Espinosa Blay, Lluís
Gundem, Gunes
Garcia Escudero, Ramon
Dominguez, Ana
Orlando, S.
Gallastegui, E.
Saiz, Cristina
Besson, Arnaud
Pujol, Maria Jesus
López Bigas, Núria
Paramio, Jesus M.
Bigas Salvans, Anna
Bachs Valldeneu, Oriol
The cyclin-cdk (cyclin-dependent kinase) inhibitor p27(Kip1) (p27) has a crucial negative role on cell cycle progression. In addition to its classical role as a cyclin-cdk inhibitor, it also performs cyclin-cdk-independent functions as the regulation of cytoskeleton rearrangements and cell motility. p27 deficiency has been associated with tumor aggressiveness and poor clinical outcome, although the mechanisms underlying this participation still remain elusive. We report here a new cellular function of p27 as a transcriptional regulator in association with p130/E2F4 complexes that could be relevant for tumorigenesis. We observed that p27 associates with specific promoters of genes involved in important cellular functions as processing and splicing of RNA, mitochondrial organization and respiration, translation and cell cycle. On these promoters p27 co-localizes with p130, E2F4 and co-repressors as histone deacetylases (HDACs) and mSIN3A. p27 co-immunoprecipitates with these proteins and by affinity chromatography, we demonstrated a direct interaction of p27 with p130 and E2F4 through its carboxyl-half. We have also shown that p130 recruits p27 on the promoters, and there p27 is needed for the subsequent recruitment of HDACs and mSIN3A. Expression microarrays and luciferase assays revealed that p27 behaves as transcriptional repressor of these p27-target genes (p27-TGs). Finally, in human tumors, we established a correlation with overexpression of p27-TGs and poor survival. Thus, this new function of p27 as a transcriptional repressor could have a role in the major aggressiveness of tumors with low levels of p27.
2011-12
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28097
eng
http://dx.doi.org/10.1038/onc.2011.582
http://bg.upf.edu/p27/home/
Més informació: Transcriptional regulatory role of p27Kip1 (web)
Pippa R, Espinosa L, Gundem G, García-Escudero R, Dominguez A, Orlando S, Gallastegui E, Saiz C, Besson A, Pujol MJ, López-Bigas N, Paramio JM, Bigas A, Bachs O. p27Kip1 represses transcription by direct interaction with p130/E2F4 at the promoters of target genes. Oncogene. 2012;31(38):4207-20. DOI: 10.1038/onc.2011.582
http://creativecommons.org/licenses/by/3.0/es/
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Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281072017-03-18T02:30:45Zcom_10230_5963col_10230_24644
IntOGen - Arrays
Gundem, Gunes
Pérez Llamas, Christian, 1976-
Jené i Sanz, Alba, 1984-
Kedzierska, Anna
Islam, Abul, 1978-
Déu Pons, Jordi
Furney, Simon J.
López Bigas, Núria
Genes and pathways affected by expression and copy number changes in tumors across projects and cancer types.
2010-02
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/28107
eng
http://dx.doi.org/10.1038/nmeth0210-92
https://www.intogen.org/downloads
Més informació: IntOGen (web)
Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N. IntOGen: integration and data mining of multidimensional oncogenomic data. Nat Methods. 2010;7(2):92-3. DOI: 10.1038/nmeth0210-92
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281252017-02-20T09:55:00Zcom_10230_5963col_10230_24644
RBP2
López Bigas, Núria
Kisiel, Tomasz A.
DeWaal, Dannielle C.
Holmes, Katherine B.
Volkert, Tom L.
Gupta, Sumeet
Love, Jennifer
Murray, Heather L.
Young, Richard A.
Benevolenskaya, Elizaveta V.
Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.
2008-09
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28125
eng
http://dx.doi.org/10.1016/j.molcel.2008.08.004
Lopez-Bigas N, Kisiel TA, DeWaal DC, Holmes KB, Volkert TL, Gupta S, Love J, Murray HL, Young RA, Benevolenskaya EV. Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation. Mol Cell. 2008; 31(4):520–30. DOI: 10.1016/j.molcel.2008.08.004
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
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Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281262017-02-21T08:59:36Zcom_10230_5963col_10230_24644
CGProp
Furney, Simon J.
Madden, Stephen F.
Kisiel, Tomasz A.
Higgins, Desmond G.
López Bigas, Núria
Cancer gene properties.
2007-12
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28126
eng
http://hdl.handle.net/10230/16420
Furney SJ, Higgins DG, Ouzounis CA, López-Bigas N. Structural and functional properties of genes involved in human cancer. BMC Genomics. 2006; 7: 3. DOI: 10.1186/1471-2164-7-3 http://hdl.handle.net/10230/16420
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
Dades sota llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281272017-02-21T10:23:29Zcom_10230_5963col_10230_24644
funcSTAR
Shikhagaie, Medya
López Bigas, Núria
Web tool for the selection of SNPs from the STAR project with potential functional effect.
2007-10
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28127
eng
http://dx.doi.org/10.1038/ng.124
http://bg.upf.edu/funcSTAR/
Més informació: funcSTAR (web)
STAR Consortium. SNP and haplotype mapping for genetic analysis in the rat. Nat Genet. 2008;40(5):560-6. DOI: 10.1038/ng.124
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
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Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281282017-02-21T11:17:48Zcom_10230_5963col_10230_24644
Evolvavility
López Bigas, Núria
De, Subhajyoti
Teichmann, Sarah A.
Mutations, genes and pathways involved in tumorigenesis across 4,623 cancer genomes/exomes from 13 cancer sites. IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods 10, 2013, doi:10.1038/nmeth.2642
2007-10
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28128
eng
http://dx.doi.org/10.1186/gb-2008-9-2-r33
Lopez-Bigas N, De S, Teichmann SA. Functional protein divergence in the evolution of Homo sapiens. Genome Biol. 2008; 9:R33. DOI: 10.1186/gb-2008-9-2-r33
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
Dades en llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281292017-02-21T11:56:13Zcom_10230_5963col_10230_24644
iDGP
Furney, Simon J.
Albà Soler, Mar
López Bigas, Núria
Database of human genes prioritized for their probability of involvement in dominant or recessive hereditary diseases.
2006-07
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28129
eng
http://hdl.handle.net/10230/16419
Furney SJ, Albà MM, López-Bigas N. Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics. 2006; 7: 165. DOI: 10.1186/1471-2164-7-165 http://hdl.handle.net/10230/16419
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
Dades sota llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281312017-03-18T02:33:04Zcom_10230_5963col_10230_24644
OncodriveMUT
Tamborero Noguera, David
Rubio Pérez, Carlota
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
Vivancos Prellezo, Ana
Rovira Guerín, Ana
Tusquets, Ignasi
Albanell Mestres, Joan
Rodon, Jordi
Tabernero Cartula, Josep
Dienstman, Rodrigo
González-Pérez, Abel
López Bigas, Núria
Bioinformatics method to identify individual driver mutations.
2016-01
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28131
eng
http://bitbucket.org/intogen/intogen-pipeline/raw/a2569e57124108eabd6695009e8a6a682154e49e/LICENSE
info:eu-repo/semantics/openAccess
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281332017-03-18T02:33:06Zcom_10230_5963col_10230_24644
TCGI prescription
Tamborero Noguera, David
Rubio Pérez, Carlota
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
Vivancos Prellezo, Ana
Rovira Guerín, Ana
Tusquets, Ignasi
Albanell Mestres, Joan
Rodon, Jordi
Tabernero Cartula, Josep
Dienstman, Rodrigo
González-Pérez, Abel
López Bigas, Núria
CGI drug prescription assigns targeted drugs to a tumor, based on its genomic alterations, according different levels of evidence (from pre-clinical assays to clinical guidelines).
2016-10
info:eu-repo/semantics/other
Software
http://hdl.handle.net/10230/28133
eng
http://bitbucket.org/intogen/intogen-pipeline/raw/a2569e57124108eabd6695009e8a6a682154e49e/LICENSE
info:eu-repo/semantics/openAccess
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/281382017-03-18T02:33:03Zcom_10230_5963col_10230_24644
Intogen - Catalog of driver mutations
Tamborero Noguera, David
Rubio Pérez, Carlota
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
Vivancos Prellezo, Ana
Rovira Guerín, Ana
Tusquets, Ignasi
Albanell Mestres, Joan
Tabernero Cartula, Josep
Dienstman, Rodrigo
González-Pérez, Abel
López Bigas, Núria
This database contains the results of the driver analysis performed by the Cancer Genome Interpreter across 6,792 exomes of a pan-cancer cohort of 28 tumor types. Validated oncogenic mutations are identified according to the state-of-the-art clinical and experimental data, whereas the effect of the mutations of unknown significance is predicted by the OncodriveMUT method.
2016-10
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/28138
eng
https://www.intogen.org/downloads
Més informació: IntOGen (web).
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document.
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/282012021-12-22T07:54:40Zcom_10230_5963col_10230_34003col_10230_24644
Performance of low-cost monitors to assess household air pollution [dataset]
Curto Tirado, Ariadna, 1987-
Donaire González, David
Barrera Gómez, Jose
Marshall, Julian D.
Nieuwenhuijsen, Mark J.
Wellenius, Gregory A.
Tonne, Cathryn
Raw data of PM2.5 and CO from an indoor wood-combustion experiment.
We evaluated the performance of two low-cost sensors measuring fine particulate matter (PM2.5) (HAPEX Nano, Climate Solutions Consulting, and TZOA-R Model RD02, MyTZOA) and one measuring carbon monoxide (CO) (EL-USB-CO, Lascar Electronics Ltd.) in a real-world wood-combustion experiment. PM2.5 devices were compared against a DustTrak (Model 8534, TSI Inc.) and a BGI pump (BGI4004, BGI Inc.) and the EL-USB-CO data-logger was compared against a Q-Trak (Model 7575, TSI Inc.). Sampling was conducted in a single-family house in Terrassa (Spain) during five non-consecutive days. All devices were co-located 1 meter away from an indoor fireplace and 0.6 meters above the ground. Fire was set once per day with hardwood logs and kept burning for 12 hours including a minimum of 2 hours with an opened window. The data provided is the raw output from all the devices tested for the 5 sampling days aiming interested researchers to play with the data and reproduce our findings.
2016-02-22
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/28201
eng
http://hdl.handle.net/10230/33850
info:eu-repo/grantAgreement/EC/FP7/336167
Publicació relacionada: Curto A, Donaire-Gonzalez D, Barrera-Gómez J, Marshall JD, Nieuwenhuijsen MJ, Wellenius GA, Tonne C. Performance of low-cost monitors to assess household air pollution. Environ Res. 2018;163: 53-63. DOI: 10.1016/j.envres.2018.01.024 http://hdl.handle.net/10230/33850
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oai:repositori.upf.edu:10230/337432018-02-19T10:59:08Zcom_10230_5963col_10230_24644
Quantitative predictions of protein interactions with long noncoding RNAs
Cirillo, Davide
Long noncoding RNAs (lncRNAs, which comprise 68% of the human transcriptome with average length of 1,000 nt) interact with various RNA-binding proteins (RBPs) to mediate cellular functions. Here we introduce Global Score as a tool to predict protein interactions with lncRNAs (http://service.tartaglialab.com/new_submission/globalscore). We used enhanced CLIP (eCLIP) to test the binding of the lncRNA Xist to the RBPs HnrnpK (Global Score of 0.99), Ptbp1 (0.99), Lbr (0.79), HnrnpU (Saf-A) (0.66), Spen (Sharp) (0.59) and negative control Dkc1 (0.01). Global Score prediction correlates with the eCLIP binding profile (Pearson correlation = 0.93). As for the binding sites, Spen and HnrnpK, Ptbp1, and Lbr interact respectively with Xist A, B, and E repeats and adjacent regions, while HnrnpU binds across the whole transcript, and Dkc1 does not interact with Xist.
2016
info:eu-repo/semantics/other
Dataset
http://hdl.handle.net/10230/33743
eng
http://hdl.handle.net/10803/403537
Publicació relacionada: Cirillo, Davide. Prediction of protein and nucleic acid interactions. 2016. http://hdl.handle.net/10803/403537
http://creativecommons.org/publicdomain/zero/1.0/
info:eu-repo/semantics/openAccess
CC0 1.0 Universal
Universitat Pompeu Fabra
oai:repositori.upf.edu:10230/345072018-04-28T01:30:12Zcom_10230_5963col_10230_24644
The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape [supplementary information]
Dobon, Begoña
Hassan, Hisham Y.
Laayouni, Hafid, 1968-
Luisi, Pierre, 1985-
Ricaño Ponce, Isis
Zhernakova, Alexandra
Wijmenga, Cisca
Tahir, Hanan
Comas, David, 1969-
Netea, Mihai G
Bertranpetit, Jaume, 1952-
2018-04-27
info:eu-repo/semantics/other
http://hdl.handle.net/10230/34507
eng
http://hdl.handle.net/10230/25768
Publicació relacionada: Dobon B, Hassan HY, Laayouni H, Luisi P, Ricaño-Ponce I, Zhernakova A et al. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape. Scientific Reports. 2015; 5: 9996. DOI 10.1038/srep09996 http://hdl.handle.net/10230/25768
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
This work is licensed under a Creative Commons Attribution 4.0 International License.
Universitat Pompeu Fabra