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Items: 22

1.

Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks.

Madrid-Mencía M, Raineri E, Cao TBN, Pancaldi V.

Nucleic Acids Res. 2020 Mar 17. pii: gkaa159. doi: 10.1093/nar/gkaa159. [Epub ahead of print]

PMID:
32182345
2.

Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization.

Greco A, Sanchez Valle J, Pancaldi V, Baudot A, Barillot E, Caselle M, Valencia A, Zinovyev A, Cantini L.

Int J Mol Sci. 2019 Jun 26;20(13). pii: E3114. doi: 10.3390/ijms20133114.

3.

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.

Ben Zouari Y, Molitor AM, Sikorska N, Pancaldi V, Sexton T.

Genome Biol. 2019 May 22;20(1):102. doi: 10.1186/s13059-019-1706-3.

4.

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer.

Forés-Martos J, Catalá-López F, Sánchez-Valle J, Ibáñez K, Tejero H, Palma-Gudiel H, Climent J, Pancaldi V, Fañanás L, Arango C, Parellada M, Baudot A, Vogt D, Rubenstein JL, Valencia A, Tabarés-Seisdedos R.

Mol Autism. 2019 Apr 8;10:17. doi: 10.1186/s13229-019-0262-8. eCollection 2019.

5.

Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity.

Ecker S, Pancaldi V, Valencia A, Beck S, Paul DS.

Bioessays. 2018 Feb;40(2). doi: 10.1002/bies.201700148. Epub 2017 Dec 18. Review.

PMID:
29251357
6.

Automatic identification of informative regions with epigenomic changes associated to hematopoiesis.

Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A; BLUEPRINT Consortium.

Nucleic Acids Res. 2017 Sep 19;45(16):9244-9259. doi: 10.1093/nar/gkx618.

7.

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.

Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A; BLUEPRINT Consortium, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS.

Genome Biol. 2017 Jan 26;18(1):18. doi: 10.1186/s13059-017-1156-8.

8.

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N.

Cell. 2016 Nov 17;167(5):1398-1414.e24. doi: 10.1016/j.cell.2016.10.026.

9.

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.

Pancaldi V, Carrillo-de-Santa-Pau E, Javierre BM, Juan D, Fraser P, Spivakov M, Valencia A, Rico D.

Genome Biol. 2016 Jul 8;17(1):152. doi: 10.1186/s13059-016-1003-3.

10.

Chromatin Regulators as a Guide for Cancer Treatment Choice.

Gurard-Levin ZA, Wilson LO, Pancaldi V, Postel-Vinay S, Sousa FG, Reyes C, Marangoni E, Gentien D, Valencia A, Pommier Y, Cottu P, Almouzni G.

Mol Cancer Ther. 2016 Jul;15(7):1768-77. doi: 10.1158/1535-7163.MCT-15-1008. Epub 2016 May 16.

11.

AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast.

Bitton DA, Schubert F, Dey S, Okoniewski M, Smith GC, Khadayate S, Pancaldi V, Wood V, Bähler J.

Front Genet. 2015 Nov 16;6:330. doi: 10.3389/fgene.2015.00330. eCollection 2015.

12.

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.

Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Pascual M, Agirre X, Prosper F, Alignani D, Paiva B, Caron G, Fest T, Muench MO, Fomin ME, Lee ST, Wiemels JL, Valencia A, Gut M, Flicek P, Stunnenberg HG, Siebert R, Küppers R, Gut IG, Campo E, Martín-Subero JI.

Nat Genet. 2015 Jul;47(7):746-56. doi: 10.1038/ng.3291. Epub 2015 Jun 8.

13.

A Boolean gene regulatory model of heterosis and speciation.

Emmrich PM, Roberts HE, Pancaldi V.

BMC Evol Biol. 2015 Feb 24;15:24. doi: 10.1186/s12862-015-0298-0.

14.

Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia.

Ecker S, Pancaldi V, Rico D, Valencia A.

Genome Med. 2015 Jan 28;7(1):8. doi: 10.1186/s13073-014-0125-z. eCollection 2015.

15.

Biological noise to get a sense of direction: an analogy between chemotaxis and stress response.

Pancaldi V.

Front Genet. 2014 Mar 13;5:52. doi: 10.3389/fgene.2014.00052. eCollection 2014. No abstract available.

16.

Systematic screen for mutants resistant to TORC1 inhibition in fission yeast reveals genes involved in cellular ageing and growth.

Rallis C, López-Maury L, Georgescu T, Pancaldi V, Bähler J.

Biol Open. 2014 Feb 15;3(2):161-71. doi: 10.1242/bio.20147245.

17.

Stress induces remodelling of yeast interaction and co-expression networks.

Lehtinen S, Marsellach FX, Codlin S, Schmidt A, Clément-Ziza M, Beyer A, Bähler J, Orengo C, Pancaldi V.

Mol Biosyst. 2013 Jul;9(7):1697-707. doi: 10.1039/c3mb25548d. Epub 2013 Mar 7.

PMID:
23471351
18.

Topology of functional networks predicts physical binding of proteins.

Saraç OS, Pancaldi V, Bähler J, Beyer A.

Bioinformatics. 2012 Aug 15;28(16):2137-45. doi: 10.1093/bioinformatics/bts351. Epub 2012 Jun 19.

PMID:
22718785
19.

Predicting the fission yeast protein interaction network.

Pancaldi V, Saraç OS, Rallis C, McLean JR, Převorovský M, Gould K, Beyer A, Bähler J.

G3 (Bethesda). 2012 Apr;2(4):453-67. doi: 10.1534/g3.111.001560. Epub 2012 Apr 1.

20.

In silico characterization and prediction of global protein-mRNA interactions in yeast.

Pancaldi V, Bähler J.

Nucleic Acids Res. 2011 Aug;39(14):5826-36. doi: 10.1093/nar/gkr160. Epub 2011 Apr 1.

21.

Meta-analysis of genome regulation and expression variability across hundreds of environmental and genetic perturbations in fission yeast.

Pancaldi V, Schubert F, Bähler J.

Mol Biosyst. 2010 Mar;6(3):543-52. doi: 10.1039/b913876p. Epub 2009 Dec 15.

PMID:
20174682
22.

Hierarchical coarse-graining transform.

Pancaldi V, King PR, Christensen K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Mar;79(3 Pt 2):036704. Epub 2009 Mar 18.

PMID:
19392078

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