Works by Satagopam, Venkata P.

Results: 28

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets.

Published in:

GigaScience, 2020, v. 9, n. 11, p. 1, doi. 10.1093/gigascience/giaa127

By:

Kratochvíl, Miroslav;
Hunewald, Oliver;
Heirendt, Laurent;
Verissimo, Vasco;
Vondrášek, Jiří;
Satagopam, Venkata P;
Schneider, Reinhard;
Trefois, Christophe;
Ollert, Markus

Publication type:

Article

COBREXA 2: tidy and scalable construction of complex metabolic models.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf056

By:

Kratochvíl, Miroslav;
Wilken, St Elmo;
Ebenhöh, Oliver;
Schneider, Reinhard;
Satagopam, Venkata P

Publication type:

Article

COBREXA.jl: constraint-based reconstruction and exascale analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 4, p. 1171, doi. 10.1093/bioinformatics/btab782

By:

Kratochvíl, Miroslav;
Heirendt, Laurent;
Wilken, St Elmo;
Pusa, Taneli;
Arreckx, Sylvain;
Noronha, Alberto;
Aalst, Marvin van;
Satagopam, Venkata P;
Ebenhöh, Oliver;
Schneider, Reinhard;
Trefois, Christophe;
Gu, Wei

Publication type:

Article

Martini: using literature keywords to compare gene sets.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 1, p. 26, doi. 10.1093/nar/gkp876

By:

Soldatos, Theodoros G.;
O’Donoghue, Seán I.;
Satagopam, Venkata P.;
Jensen, Lars J.;
Brown, Nigel P.;
Barbosa-Silva, Adriano;
Schneider, Reinhard

Publication type:

Article

Optimal Control of Stochastic Dynamic Systems with Semi-Markov Parameters.

Published in:

Symmetry (20738994), 2025, v. 17, n. 4, p. 498, doi. 10.3390/sym17040498

By:

Lukashiv, Taras;
Malyk, Igor V.;
Hemedan, Ahmed Abdelmonem;
Satagopam, Venkata P.

Publication type:

Article

nala: text mining natural language mutation mentions.

Published in:

Bioinformatics, 2017, v. 33, n. 12, p. 1852, doi. 10.1093/bioinformatics/btx083

By:

Cejuela, Juan Miguel;
Bojchevski, Aleksandar;
Uhlig, Carsten;
Bekmukhametov, Rustem;
Karn, Sanjeev Kumar;
Mahmuti, Shpend;
Baghudana, Ashish;
Dubey, Ankit;
Satagopam, Venkata P.;
Rost, Burkhard

Publication type:

Article

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery.

Published in:

Bioinformatics, 2014, v. 30, n. 22, p. 3249, doi. 10.1093/bioinformatics/btu524

By:

Papanikolaou, Nikolas;
Pavlopoulos, Georgios A.;
Pafilis, Evangelos;
Theodosiou, Theodosios;
Schneider, Reinhard;
Satagopam, Venkata P.;
Promponas, Vasilis J.;
Iliopoulos, Ioannis;
Ouzounis, Christos A.;
Eliopoulos, Aristides G.

Publication type:

Article

Deciphering shared molecular dysregulation across Parkinson's disease variants using a multi-modal network-based data integration and analysis.

Published in:

NPJ Parkinson's Disease, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41531-025-00914-3

By:

Zagare, Alise;
Balaur, Irina;
Rougny, Adrien;
Saraiva, Claudia;
Gobin, Matthieu;
Monzel, Anna S.;
Ghosh, Soumyabrata;
Satagopam, Venkata P.;
Schwamborn, Jens C.

Publication type:

Article

Genome-wide identification and functional analyses of micro RNA signatures associated with cancer pain.

Published in:

EMBO Molecular Medicine, 2013, v. 5, n. 11, p. 1740, doi. 10.1002/emmm.201302797

By:

Bali, Kiran Kumar;
Selvaraj, Deepitha;
Satagopam, Venkata P.;
Lu, Jianning;
Schneider, Reinhard;
Kuner, Rohini

Publication type:

Article

Caipirini: using gene sets to rank literature.

Published in:

BioData Mining, 2012, v. 5, n. 1, p. 1, doi. 10.1186/1756-0381-5-1

By:

Soldatos, Theodoros G.;
O'Donoghue, Seán I.;
Satagopam, Venkata P.;
Barbosa-Silva, Adriano;
Pavlopoulos, Georgios A.;
Wanderley-Nogueira, Ana Carolina;
Soares-Cavalcanti, Nina Mota;
Schneide, Reinhard

Publication type:

Article

Arena3D: visualization of biological networks in 3D.

Published in:

BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-104

By:

Pavlopoulos, Georgios A.;
O'Donoghue, Seán I.;
Satagopam, Venkata P.;
Soldatos, Theodoros G.;
Pafilis, Evangelos;
Schneider, Reinhard

Publication type:

Article

Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human.

Published in:

Nature Communications, 2016, v. 7, n. 2, p. 10706, doi. 10.1038/ncomms10706

By:

Ramilowski, Jordan A.;
Goldberg, Tatyana;
Harshbarger, Jayson;
Kloppmann, Edda;
Lizio, Marina;
Satagopam, Venkata P.;
Itoh, Masayoshi;
Kawaji, Hideya;
Carninci, Piero;
Rost, Burkhard;
Forrest, Alistair R. R.

Publication type:

Article

A draft network of ligand-receptor-mediated multicellular signalling in human.

Published in:

Nature Communications, 2015, v. 6, n. 7, p. 7866, doi. 10.1038/ncomms8866

By:

Ramilowski, Jordan A.;
Goldberg, Tatyana;
Harshbarger, Jayson;
Kloppman, Edda;
Lizio, Marina;
Satagopam, Venkata P.;
Itoh, Masayoshi;
Kawaji, Hideya;
Carninci, Piero;
Rost, Burkhard;
Forrest, Alistair R. R.

Publication type:

Article

Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-141

By:

Barbosa-Silva, Adriano;
Satagopam, Venkata P.;
Schneider, Reinhard;
Ortega, J. Miguel

Publication type:

Article

Transcriptional mechanisms underlying sensitization of peripheral sensory neurons by Granulocyte-/Granulocyte-macrophage colony stimulating factors.

Published in:

Molecular Pain, 2013, v. 9, n. 1, p. 1, doi. 10.1186/1744-8069-9-48

By:

Bali, Kiran Kumar;
Venkataramani, Varun;
Satagopam, Venkata P.;
Gupta, Pooja;
Schneider, Reinhard;
Kuner, Rohini

Publication type:

Article

The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1003951

By:

Davey, Norman E.;
Satagopam, Venkata P.;
Santiago-Mozos, Salvador;
Villacorta-Martin, Carlos;
Bharat, Tanmay A. M.;
Schneider, Reinhard;
Briggs, John A. G.

Publication type:

Article

The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

Published in:

2013

By:

de Ridder, Jeroen;
Bromberg, Yana;
Michaut, Magali;
Satagopam, Venkata P.;
Corpas, Manuel;
Macintyre, Geoff;
Alexandrov, Theodore

Publication type:

Opinion

Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1371/journal.pcbi.1002834

By:

de Ridder, Jeroen;
Abeel, Thomas;
Michaut, Magali;
Satagopam, Venkata P.;
Gehlenborg, Nils

Publication type:

Article

Confronting the catalytic dark matter encoded by sequenced genomes.

Published in:

Nucleic Acids Research, 2017, v. 45, n. 20, p. 11495, doi. 10.1093/nar/gkx937

By:

Ellens, Kenneth W.;
Christian, Nils;
Singh, Charandeep;
Satagopam, Venkata P.;
May, Patrick;
Linster, Carole L.

Publication type:

Article

Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research.

Published in:

Frontiers in Neurology, 2020, p. 1, doi. 10.3389/fneur.2020.00524

By:

Rajan, Roopa;
Divya, K. P.;
Kandadai, Rukmini Mridula;
Yadav, Ravi;
Satagopam, Venkata P.;
Madhusoodanan, U. K.;
Agarwal, Pankaj;
Kumar, Niraj;
Ferreira, Teresa;
Kumar, Hrishikesh;
Sreeram Prasad, A. V.;
Shetty, Kuldeep;
Mehta, Sahil;
Desai, Soaham;
Kumar, Suresh;
Prashant, L. K.;
Bhatt, Mohit;
Wadia, Pettarusp;
Ramalingam, Sudha;
Wali, G. M.

Publication type:

Article

The Luxembourg Parkinson's Study: A Comprehensive Approach for Stratification and Early Diagnosis.

Published in:

Frontiers in Aging Neuroscience, 2018, p. N.PAG, doi. 10.3389/fnagi.2018.00326

By:

Hipp, Geraldine;
Vaillant, Michel;
Diederich, Nico J.;
Roomp, Kirsten;
Satagopam, Venkata P.;
Banda, Peter;
Sandt, Estelle;
Mommaerts, Kathleen;
Schmitz, Sabine K.;
Longhino, Laura;
Schweicher, Alexandra;
Hanff, Anne-Marie;
Nicolai, Béatrice;
Kolber, Pierre;
Reiter, Dorothea;
Pavelka, Lukas;
Binck, Sylvia;
Pauly, Claire;
Geffers, Lars;
Betsou, Fay

Publication type:

Article

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques.

Published in:

Database: The Journal of Biological Databases & Curation, 2010, v. 2010, p. 1, doi. 10.1093/database/baq019

By:

Satagopam, Venkata P.;
Theodoropoulou, Margarita C.;
Stampolakis, Christos K.;
Pavlopoulos, Georgios A.;
Papandreou, Nikolaos C.;
Bagos, Pantelis G.;
Schneider, Reinhard;
Hamodrakas, Stavros J.

Publication type:

Article

Defective Lamin A-Rb Signaling in Hutchinson-Gilford Progeria Syndrome and Reversal by Farnesyltransferase Inhibition.

Published in:

PLoS ONE, 2010, v. 5, n. 6, p. 1, doi. 10.1371/journal.pone.0011132

By:

Marji, Jackleen;
O'Donoghue, Seán I.;
McClintock, Dayle;
Satagopam, Venkata P.;
Schneider, Reinhard;
Ratner, Desiree;
Worman, Howard J.;
Gordon, Leslie B.;
Djabali, Karima

Publication type:

Article

Lessons learned from the COVID-19 pandemic: identifying hesitant groups and exploring reasons for vaccination hesitancy, from adolescence to late adulthood.

Published in:

Frontiers in Public Health, 2025, p. 1, doi. 10.3389/fpubh.2024.1456265

By:

Pauly, Laure;
Residori, Caroline;
Bulut, Hamid;
Bulaev, Dmitry;
Ghosh, Soumyabrata;
O'Sullivan, Marc P.;
Fritz, Joëlle V.;
Vaillant, Michel;
Rommes, Basile;
Samuel, Robin;
Satagopam, Venkata P.;
Krüger, Rejko;
Leist, Anja K.

Publication type:

Article

siRNA screen identifies QPCT as a druggable target for Huntington's disease.

Published in:

Nature Chemical Biology, 2015, v. 11, n. 5, p. 347, doi. 10.1038/nchembio.1790

By:

Jimenez-Sanchez, Maria;
Lam, Wun;
Hannus, Michael;
Sönnichsen, Birte;
Imarisio, Sara;
Fleming, Angeleen;
Tarditi, Alessia;
Menzies, Fiona;
Ed Dami, Teresa;
Xu, Catherine;
Gonzalez-Couto, Eduardo;
Lazzeroni, Giulia;
Heitz, Freddy;
Diamanti, Daniela;
Massai, Luisa;
Satagopam, Venkata P;
Marconi, Guido;
Caramelli, Chiara;
Nencini, Arianna;
Andreini, Matteo

Publication type:

Article

Constitutive activation of oncogenic PDGFRα-mutant proteins occurring in GIST patients induces receptor mislocalisation and alters PDGFRa signalling characteristics.

Published in:

Cell Communication & Signaling, 2015, v. 13, n. 1, p. 1, doi. 10.1186/s12964-015-0096-8

By:

Bahlawane, Christelle;
Eulenfeld, René;
Wiesinger, Monique Y.;
Jiali Wang;
Muller, Arnaud;
Girod, Andreas;
Nazarov, Petr V.;
Felsch, Kathrin;
Vallar, Laurent;
Sauter, Thomas;
Satagopam, Venkata P.;
Haan, Serge

Publication type:

Article

ImmUniverse Consortium: Multi-omics integrative approach in personalized medicine for immune-mediated inflammatory diseases.

Published in:

Frontiers in Immunology, 2022, v. 13, p. 01, doi. 10.3389/fimmu.2022.1002629

By:

Vetrano, Stefania;
Bouma, Gerben;
Benschop, Robert J.;
Birngruber, Thomas;
Costanzo, Antonio;
D'Haens, G. R. A. M.;
Frasca, Loredana;
Hillenbrand, Rainer;
Iversen, Lars;
Johansen, Claus;
Kaser, Arthur;
Koenen, Hans J. P. M.;
Noehammer, Christa;
Peyrin-Biroulet, Laurent;
Raes, Jeroen;
Ricotti, Leonardo;
Rosenstiel, Philip;
Satagopam, Venkata P.;
Schreiber, Stefan;
Vermeire, Severine

Publication type:

Article

Grand challenges in bioinformatics education and training.

Published in:

Nature Biotechnology, 2023, v. 41, n. 8, p. 1171, doi. 10.1038/s41587-023-01891-9

By:

Işık, Esra Büşra;
Brazas, Michelle D.;
Schwartz, Russell;
Gaeta, Bruno;
Palagi, Patricia M.;
van Gelder, Celia W. G.;
Suravajhala, Prashanth;
Singh, Harpreet;
Morgan, Sarah L.;
Zahroh, Hilyatuz;
Ling, Maurice;
Satagopam, Venkata P.;
McGrath, Annette;
Nakai, Kenta;
Tan, Tin Wee;
Gao, Ge;
Mulder, Nicola;
Schönbach, Christian;
Zheng, Yun;
De Las Rivas, Javier

Publication type:

Article