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mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle.
Published in:
BMC Systems Biology, 2009, v. 3, p. 1, doi. 10.1186/1752-0509-3-18
By:
- Soranzo, Nicola;
- Zampieri, Mattia;
- Farina, Lorenzo;
- Altafini, Claudio
Publication type:
Article
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.
Published in:
Nucleic Acids Research, 2016, v. 44, n. W1, p. W3, doi. 10.1093/nar/gkw343
By:
- Afgan, Enis;
- Baker, Dannon;
- den Beek, Marius van;
- Blankenberg, Daniel;
- Bouvier, Dave;
- Čech, Martin;
- Chilton, John;
- Clements, Dave;
- Coraor, Nate;
- Eberhard, Carl;
- Grüning, Björn;
- Guerler, Aysam;
- Hillman-Jackson, Jennifer;
- Von Kuster, Greg;
- Rasche, Eric;
- Soranzo, Nicola;
- Turaga, Nitesh;
- Taylor, James;
- Nekrutenko, Anton;
- Goecks, Jeremy
Publication type:
Article
A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.
Published in:
GigaScience, 2020, v. 9, n. 10, p. 1, doi. 10.1093/gigascience/giaa102
By:
- Tekman, Mehmet;
- Batut, Bérénice;
- Ostrovsky, Alexander;
- Antoniewski, Christophe;
- Clements, Dave;
- Ramirez, Fidel;
- Etherington, Graham J;
- Hotz, Hans-Rudolf;
- Scholtalbers, Jelle;
- Manning, Jonathan R;
- Bellenger, Lea;
- Doyle, Maria A;
- Heydarian, Mohammad;
- Huang, Ni;
- Soranzo, Nicola;
- Moreno, Pablo;
- Mautner, Stefan;
- Papatheodorou, Irene;
- Nekrutenko, Anton;
- Taylor, James
Publication type:
Article
A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses.
Published in:
GigaScience, 2019, v. 8, n. 12, p. N.PAG, doi. 10.1093/gigascience/giz144
By:
- Etherington, Graham J;
- Soranzo, Nicola;
- Mohammed, Suhaib;
- Haerty, Wilfried;
- Davey, Robert P;
- Palma, Federica Di
Publication type:
Article
Aequatus: an open-source homology browser.
Published in:
GigaScience, 2018, v. 7, n. 11, p. N.PAG, doi. 10.1093/gigascience/giy128
By:
- Thanki, Anil S;
- Soranzo, Nicola;
- Herrero, Javier;
- Haerty, Wilfried;
- Davey, Robert P
Publication type:
Article
ReGaTE: Registration of Galaxy Tools in Elixir.
Published in:
GigaScience, 2017, v. 6, n. 6, p. 1, doi. 10.1093/gigascience/gix022
By:
- Doppelt-Azeroual, Olivia;
- Mareuil, Fabien;
- Deveaud, Eric;
- Kalaš, Matúš;
- Soranzo, Nicola;
- van den Beek, Marius;
- Grüning, Björn;
- Ison, Jon;
- Ménager, Hervé
Publication type:
Article
From Knockouts to Networks: Establishing Direct Cause- Effect Relationships through Graph Analysis.
Published in:
PLoS ONE, 2010, v. 5, n. 10, p. 1, doi. 10.1371/journal.pone.0012912
By:
- Pinna, Andrea;
- Soranzo, Nicola;
- de la Fuente, Alberto
Publication type:
Article
Origin of Co-Expression Patterns in E.coli and S.cerevisiae Emerging from Reverse Engineering Algorithms.
Published in:
PLoS ONE, 2008, v. 3, n. 8, p. 1, doi. 10.1371/journal.pone.0002981
By:
- Zampieri, Mattia;
- Soranzo, Nicola;
- Bianchini, Daniele;
- Altafini, Claudio
Publication type:
Article
LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis.
Published in:
Microbiome, 2022, v. 10, n. 1, p. 1, doi. 10.1186/s40168-022-01365-1
By:
- Özkurt, Ezgi;
- Fritscher, Joachim;
- Soranzo, Nicola;
- Ng, Duncan Y. K.;
- Davey, Robert P.;
- Bahram, Mohammad;
- Hildebrand, Falk
Publication type:
Article
Galaxy Training: A powerful framework for teaching!
Published in:
PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010752
By:
- Hiltemann, Saskia;
- Rasche, Helena;
- Gladman, Simon;
- Hotz, Hans-Rudolf;
- Larivière, Delphine;
- Blankenberg, Daniel;
- Jagtap, Pratik D.;
- Wollmann, Thomas;
- Bretaudeau, Anthony;
- Goué, Nadia;
- Griffin, Timothy J.;
- Royaux, Coline;
- Le Bras, Yvan;
- Mehta, Subina;
- Syme, Anna;
- Coppens, Frederik;
- Droesbeke, Bert;
- Soranzo, Nicola;
- Bacon, Wendi;
- Psomopoulos, Fotis
Publication type:
Article
Discerning static and causal interactions in genome-wide reverse engineering problems.
Published in:
Bioinformatics, 2008, v. 24, n. 13, p. 1510, doi. 10.1093/bioinformatics/btn220
By:
- Mattia Zampieri;
- Nicola Soranzo;
- Claudio Altafini
Publication type:
Article
Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data.
Published in:
Bioinformatics, 2007, v. 23, n. 13, p. 1640, doi. 10.1093/bioinformatics/btm163
By:
- Nicola Soranzo;
- Ginestra Bianconi;
- Claudio Altafini
Publication type:
Article
Expanding the Galaxy's reference data.
Published in:
Bioinformatics Advances, 2022, v. 2, n. 1, p. 1, doi. 10.1093/bioadv/vbac030
By:
- VijayKrishna, Nagampalli;
- Joshi, Jayadev;
- Coraor, Nate;
- Hillman-Jackson, Jennifer;
- Bouvier, Dave;
- van den Beek, Marius;
- Eguinoa, Ignacio;
- Coppens, Frederik;
- Davis, John;
- Stolarczyk, Michał;
- Sheffield, Nathan C;
- Gladman, Simon;
- Cuccuru, Gianmauro;
- Grüning, Björn;
- Soranzo, Nicola;
- Rasche, Helena;
- Langhorst, Bradley W;
- Bernt, Matthias;
- Fornika, Dan;
- Morais, David Anderson de Lima
Publication type:
Article
NCBI BLAST+ integrated into Galaxy.
Published in:
GigaScience, 2015, v. 4, n. 1, p. 1, doi. 10.1186/s13742-015-0080-7
By:
- Cock, Peter J. A.;
- Chilton, John M.;
- Grüning, Björn;
- Johnson, James E.;
- Soranzo, Nicola
Publication type:
Article
Transcriptomic profiles of aging in purified human immune cells.
Published in:
BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1522-4
By:
- Reynolds, Lindsay M.;
- Jingzhong Ding;
- Taylor, Jackson R.;
- Lohman, Kurt;
- Soranzo, Nicola;
- de la Fuente, Alberto;
- Tie Fu Liu;
- Johnson, Craig;
- Barr, R. Graham;
- Register, Thomas C.;
- Donohue, Kathleen M.;
- Talor, Monica V.;
- Cihakova, Daniela;
- Gu, Charles;
- Divers, Jasmin;
- Siscovick, David;
- Burke, Gregory;
- Post, Wendy;
- Shea, Steven;
- Jacobs.Jr, David R.
Publication type:
Article
BioBlend.objects: metacomputing with Galaxy.
Published in:
Bioinformatics, 2014, v. 30, n. 19, p. 2816, doi. 10.1093/bioinformatics/btu386
By:
- Leo, Simone;
- Pireddu, Luca;
- Cuccuru, Gianmauro;
- Lianas, Luca;
- Soranzo, Nicola;
- Afgan, Enis;
- Zanetti, Gianluigi
Publication type:
Article
Orione, a web-based framework for NGS analysis in microbiology.
Published in:
Bioinformatics, 2014, v. 30, n. 13, p. 1928, doi. 10.1093/bioinformatics/btu135
By:
- Cuccuru, Gianmauro;
- Orsini, Massimiliano;
- Pinna, Andrea;
- Sbardellati, Andrea;
- Soranzo, Nicola;
- Travaglione, Antonella;
- Uva, Paolo;
- Zanetti, Gianluigi;
- Fotia, Giorgio
Publication type:
Article
Decompositions of large-scale biological systems based on dynamical properties.
Published in:
Bioinformatics, 2012, v. 28, n. 1, p. 76, doi. 10.1093/bioinformatics/btr620
By:
- Soranzo, Nicola;
- Ramezani, Fahimeh;
- Iacono, Giovanni;
- Altafini, Claudio
Publication type:
Article
Simulating systems genetics data with SysGenSIM.
Published in:
Bioinformatics, 2011, v. 27, n. 17, p. 2459, doi. 10.1093/bioinformatics/btr407
By:
- Pinna, Andrea;
- Soranzo, Nicola;
- Hoeschele, Ina;
- de la Fuente, Alberto
Publication type:
Article
ERNEST: a toolbox for chemical reaction network theory.
Published in:
Bioinformatics, 2009, v. 25, n. 21, p. 2853, doi. 10.1093/bioinformatics/btp513
By:
- Soranzo, Nicola;
- Altafini, Claudio
Publication type:
Article
Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease.
Published in:
2015
By:
- Jingzhong Ding;
- Reynolds, Lindsay M.;
- Zeller, Tanja;
- Müller, Christian;
- Lohman, Kurt;
- Nicklas, Barbara J.;
- Kritchevsky, Stephen B.;
- Zhiqing Huang;
- de la Fuente, Alberto;
- Soranzo, Nicola;
- Settlage, Robert E.;
- Chia-Chi Chuang;
- Howard, Timothy;
- Ning Xu;
- Goodarzi, Mark O.;
- Chen, Y.-D. Ida;
- Rotter, Jerome I.;
- Siscovick, David S.;
- Parks, John S.;
- Murphy, Susan
Publication type:
journal article

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