Works matching AU Tsoka, Sophia

Results: 46

Optimisation-Based Feature Selection for Regression Neural Networks Towards Explainability.

Published in:

Machine Learning & Knowledge Extraction, 2025, v. 7, n. 2, p. 33, doi. 10.3390/make7020033

By:

Liapis, Georgios I.;
Tsoka, Sophia;
Papageorgiou, Lazaros G.

Publication type:

Article

Metabolic database systems for the analysis of genome-wide function.

Published in:

Biotechnology & Bioengineering, 2003, v. 84, n. 7, p. 750, doi. 10.1002/bit.10881

By:

Sophia Tsoka;
Christos A. Ouzounis

Publication type:

Article

DETECTION OF DISJOINT AND OVERLAPPING MODULES IN WEIGHTED COMPLEX NETWORKS.

Published in:

Advances in Complex Systems, 2012, v. 15, n. 5, p. 1150023-1, doi. 10.1142/S0219525911500238

By:

BENNETT, LAURA;
LIU, SONGSONG;
PAPAGEORGIOU, LAZAROS G.;
TSOKA, SOPHIA

Publication type:

Article

Optimal Piecewise Linear Regression Algorithm for QSAR Modelling.

Published in:

Molecular Informatics, 2019, v. 38, n. 3, p. N.PAG, doi. 10.1002/minf.201800028

By:

Cardoso‐Silva, Jonathan;
Papadatos, George;
Papageorgiou, Lazaros G.;
Tsoka, Sophia

Publication type:

Article

CLigOpt: controllable ligand design through target-specific optimization.

Published in:

Bioinformatics, 2024, v. 40, p. ii62, doi. 10.1093/bioinformatics/btae396

By:

Li, Yutong;
Avelar, Pedro Henrique da Costa;
Chen, Xinyue;
Zhang, Li;
Wu, Min;
Tsoka, Sophia

Publication type:

Article

PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets.

Published in:

Frontiers in Microbiology, 2019, v. 10, p. 1, doi. 10.3389/fmicb.2019.02721

By:

Janowska-Sejda, Elzbieta I.;
Lysenko, Artem;
Urban, Martin;
Rawlings, Chris;
Tsoka, Sophia;
Hammond-Kosack, Kim E.

Publication type:

Article

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 19, p. 6083, doi. 10.1093/nar/gki892

By:

Karp, Peter D.;
Ouzounis, Christos A.;
Moore-Kochlacs, Caroline;
Goldovsky, Leon;
Kaipa, Pallavi;
Ahrén, Dag;
Tsoka, Sophia;
Darzentas, Nikos;
Kunin, Victor;
López-Bigas, Núria

Publication type:

Article

Sparse Regression in Cancer Genomics: Comparing Variable Selection and Predictions in Real World Data.

Published in:

Cancer Informatics, 2021, p. 1, doi. 10.1177/11769351211056298

By:

O'Shea, Robert J;
Tsoka, Sophia;
Cook, Gary JR;
Goh, Vicky

Publication type:

Article

Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion.

Published in:

Nature Genetics, 2000, v. 26, n. 2, p. 141, doi. 10.1038/79847

By:

Tsoka, Sophia;
Ouzounis, Christos A.

Publication type:

Article

CoGenT++: an extensive and extensible data environment for computational genomics.

Published in:

Bioinformatics, 2005, v. 21, n. 19, p. 3806, doi. 10.1093/bioinformatics/bti579

By:

Leon Goldovsky;
Paul Janssen;
Dag Ahrén;
Benjamin Audit;
Ildefonso Cases;
Nikos Darzentas;
Anton J. Enright;
Núria López-Bigas;
José M. Peregrin-Alvarez;
Mike Smith;
Sophia Tsoka;
Victor Kunin;
Christos A. Ouzounis

Publication type:

Article

Modeling the percolation of annotation errors in a database of protein sequences.

Published in:

Bioinformatics, 2002, v. 18, n. 12, p. 1641, doi. 10.1093/bioinformatics/18.12.1641

By:

Gilks, Walter R.;
Audit, Benjamin;
De Angelis, Daniela;
Tsoka, Sophia;
Ouzounis, Christos A.

Publication type:

Article

CAST: an iterative algorithm for the complexity analysis of sequence tracts.

Published in:

Bioinformatics, 2000, v. 16, n. 10, p. 915, doi. 10.1093/bioinformatics/16.10.915

By:

Promponas, Vasilis J.;
Enright, Anton J.;
Tsoka, Sophia;
Kreil, David P.;
Leroy, Christophe;
Hamodrakas, Stavros;
Sander, Chris;
Ouzounis, Christos A.

Publication type:

Article

Chondroitin Sulfate Proteoglycan 4 and Its Potential As an Antibody Immunotherapy Target across Different Tumor Types.

Published in:

Frontiers in Immunology, 2018, p. 1, doi. 10.3389/fimmu.2017.01911

By:

Ilieva, Kristina M.;
Cheung, Anthony;
Mele, Silvia;
Chiaruttini, Giulia;
Crescioli, Silvia;
Griffin, Merope;
Nakamura, Mano;
Spicer, James F.;
Tsoka, Sophia;
Lacy, Katie E.;
Tutt, Andrew N. J.;
Karagiannis, Sophia N.

Publication type:

Article

Combined anti‐PD‐1 and anti‐CTLA‐4 checkpoint blockade: Treatment of melanoma and immune mechanisms of action.

Published in:

European Journal of Immunology, 2021, v. 51, n. 3, p. 544, doi. 10.1002/eji.202048747

By:

Willsmore, Zena N.;
Coumbe, Ben G. T.;
Crescioli, Silvia;
Reci, Sara;
Gupta, Ayushi;
Harris, Robert J.;
Chenoweth, Alicia;
Chauhan, Jitesh;
Bax, Heather J.;
McCraw, Alexa;
Cheung, Anthony;
Osborn, Gabriel;
Hoffmann, Ricarda M.;
Nakamura, Mano;
Laddach, Roman;
Geh, Jenny L. C.;
MacKenzie‐Ross, Alastair;
Healy, Ciaran;
Tsoka, Sophia;
Spicer, James F.

Publication type:

Article

Influencing tumor-associated macrophages in malignant melanoma with monoclonal antibodies.

Published in:

OncoImmunology, 2022, v. 11, n. 1, p. 1, doi. 10.1080/2162402X.2022.2127284

By:

Adams, Rebecca;
Osborn, Gabriel;
Mukhia, Bipashna;
Laddach, Roman;
Willsmore, Zena;
Chenoweth, Alicia;
Geh, Jenny L. C.;
Ross, Alastair D. MacKenzie;
Healy, Ciaran;
Barber, Linda;
Tsoka, Sophia;
Sanz-Moreno, Victoria;
Lacy, Katie E.;
Karagiannis, Sophia N.

Publication type:

Article

Enriched circulating and tumor-resident TGF-β+ regulatory B cells in patients with melanoma promote FOXP3+ Tregs.

Published in:

OncoImmunology, 2022, v. 11, n. 1, p. 1, doi. 10.1080/2162402X.2022.2104426

By:

Harris, Robert J.;
Willsmore, Zena;
Laddach, Roman;
Crescioli, Silvia;
Chauhan, Jitesh;
Cheung, Anthony;
Black, Anna;
Geh, Jenny L. C.;
Ross, Alastair D. MacKenzie;
Healy, Ciaran;
Tsoka, Sophia;
Spicer, James;
Lacy, Katie E.;
Karagiannis, Sophia N.

Publication type:

Article

Immune mediator expression signatures are associated with improved outcome in ovarian carcinoma.

Published in:

OncoImmunology, 2019, v. 8, n. 6, p. N.PAG, doi. 10.1080/2162402X.2019.1593811

By:

Nakamura, Mano;
Bax, Heather J.;
Scotto, Daniele;
Souri, Elmira Amiri;
Sollie, Sam;
Harris, Robert J.;
Hammar, Niklas;
Walldius, Goran;
Winship, Anna;
Ghosh, Sharmistha;
Montes, Ana;
Spicer, James F.;
Van Hemelrijck, Mieke;
Josephs, Debra H.;
Lacy, Katie E.;
Tsoka, Sophia;
Karagiannis, Sophia N.

Publication type:

Article

Integrative Biology Approach Identifies Cytokine Targeting Strategies for Psoriasis.

Published in:

Science Translational Medicine, 2014, v. 6, n. 223, p. 1, doi. 10.1126/scitranslmed.3007217

By:

Perera, Gayathri K.;
Ainali, Chrysanthi;
Semenova, Ekaterina;
Hundhausen, Christian;
Barinaga, Guillermo;
Kassen, Deepika;
Williams, Andrew E.;
Mirza, Muddassar M.;
Balazs, Mercedesz;
Xiaoting Wang;
Rodriguez, Robert Sanchez;
Alendar, Andrej;
Barker, Jonathan;
Tsoka, Sophia;
Wenjun Ouyang;
Nestle, Frank O.

Publication type:

Article

Weakly supervised segmentation models as explainable radiological classifiers for lung tumour detection on CT images.

Published in:

Insights into Imaging, 2023, v. 14, n. 1, p. 1, doi. 10.1186/s13244-023-01542-2

By:

O'Shea, Robert;
Manickavasagar, Thubeena;
Horst, Carolyn;
Hughes, Daniel;
Cusack, James;
Tsoka, Sophia;
Cook, Gary;
Goh, Vicky

Publication type:

Article

Radiomic assessment of oesophageal adenocarcinoma: a critical review of 18F-FDG PET/CT, PET/MRI and CT.

Published in:

Insights into Imaging, 2022, v. 13, n. 1, p. 1, doi. 10.1186/s13244-022-01245-0

By:

O'Shea, Robert J.;
Rookyard, Chris;
Withey, Sam;
Cook, Gary J. R.;
Tsoka, Sophia;
Goh, Vicky

Publication type:

Article

Transcriptome‐based identification of novel endotypes in adult atopic dermatitis.

Published in:

Allergy, 2022, v. 77, n. 5, p. 1486, doi. 10.1111/all.15150

By:

Lefèvre‐Utile, Alain;
Saichi, Melissa;
Oláh, Péter;
Delord, Marc;
Homey, Bernhard;
Soumelis, Vassili;
Kere, Juha;
Levi‐Schaffer, Francesca;
Greco, Dario;
Ottman, Noora;
Baker, Jonathan;
Andersson, Björn;
Barrientos‐Somarribas, Mauricio;
Prast‐Nielsen, Stefanie;
Wisgrill, Lukas;
Tsoka, Sophia;
Fyhrquist, Nanna;
Alenius, Harri;
Alexander, Helen;
Schröder, Jens M

Publication type:

Article

Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites.

Published in:

Allergy, 2021, v. 76, n. 4, p. 1173, doi. 10.1111/all.14606

By:

Ottman, Noora;
Barrientos‐Somarribas, Mauricio;
Fyhrquist, Nanna;
Alexander, Helen;
Wisgrill, Lukas;
Olah, Peter;
Tsoka, Sophia;
Greco, Dario;
Levi‐Schaffer, Francesca;
Soumelis, Vassili;
Schröder, Jens M.;
Kere, Juha;
Nestle, Frank O.;
Barker, Jonathan;
Ranki, Annamari;
Lauerma, Antti;
Homey, Bernhard;
Andersson, Björn;
Alenius, Harri

Publication type:

Article

Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins.

Published in:

BMC Evolutionary Biology, 2011, v. 11, n. 1, p. 142, doi. 10.1186/1471-2148-11-142

By:

Ainali, Chrysanthi;
Simon, Michelle;
Freilich, Shiri;
Espinosa, Octavio;
Hazelwood, Lee;
Tsoka, Sophia;
Ouzounis, Christos A.;
Hancock, John M.

Publication type:

Article

IgE Activates Monocytes from Cancer Patients to Acquire a Pro-Inflammatory Phenotype.

Published in:

Cancers, 2020, v. 12, n. 11, p. 3376, doi. 10.3390/cancers12113376

By:

Nakamura, Mano;
Souri, Elmira Amiri;
Osborn, Gabriel;
Laddach, Roman;
Chauhan, Jitesh;
Stavraka, Chara;
Lombardi, Sara;
Black, Anna;
Khiabany, Atousa;
Khair, Duaa O.;
Figini, Mariangela;
Winship, Anna;
Ghosh, Sharmistha;
Montes, Ana;
Spicer, James F.;
Bax, Heather J.;
Josephs, Debra H.;
Lacy, Katie E.;
Tsoka, Sophia;
Karagiannis, Sophia N.

Publication type:

Article

An IgE antibody targeting HER2 identified by clonal selection restricts breast cancer growth via immune-stimulating activities.

Published in:

Journal of Experimental & Clinical Cancer Research (17569966), 2025, v. 44, n. 1, p. 1, doi. 10.1186/s13046-025-03319-5

By:

Palhares, Lais C. G. F.;
Grandits, Melanie;
Stoker, Katie;
Chauhan, Jitesh;
Sow, Heng Sheng;
Fruhwirth, Gilbert O.;
Tsoka, Sophia;
Birtley, James;
Partington, Leanne;
Wilson, Tim;
Hardaker, Elizabeth;
Karagiannis, Sophia N.;
Bax, Heather J.;
FitzGerald, Kevin

Publication type:

Article

Robustness of the p53 network and biological hackers

Published in:

FEBS Letters, 2005, v. 579, n. 14, p. 3037, doi. 10.1016/j.febslet.2005.03.101

By:

Dartnell, Lewis;
Simeonidis, Evangelos;
Hubank, Michael;
Tsoka, Sophia;
Bogle, I. David L.;
Papageorgiou, Lazaros G.

Publication type:

Article

CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks.

Published in:

BMC Systems Biology, 2015, v. 9, n. 1, p. 1, doi. 10.1186/s12918-015-0179-6

By:

Kittas, Aristotelis;
Barozet, Amélie;
Sereshti, Jekaterina;
Grabe, Niels;
Tsoka, Sophia

Publication type:

Article

Transcriptome classification reveals molecular subtypes in psoriasis.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 472, doi. 10.1186/1471-2164-13-472

By:

Ainali, Chrysanthi;
Valeyev, Najl;
Perera, Gayathri;
Williams, Andrew;
Gudjonsson, Johann E.;
Ouzounis, Christos A.;
Nestle, Frank O.;
Tsoka, Sophia

Publication type:

Article

Module detection in complex networks using integer optimisation.

Published in:

Algorithms for Molecular Biology, 2010, v. 5, p. 36, doi. 10.1186/1748-7188-5-36

By:

Gang Xu;
Bennett, Laura;
Papageorgiou, Lazaros G.;
Tsoka, Sophia

Publication type:

Article

Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework.

Published in:

BMC Bioinformatics, 2014, v. 15, n. 1, p. 299, doi. 10.1186/s12859-014-0390-2

By:

Lingjian Yang;
Ainali, Chrysanthi;
Tsoka, Sophia;
Papageorgiou, Lazaros G.

Publication type:

Article

A Systems Model for Immune Cell Interactions Unravels the Mechanism of Inflammation in Human Skin.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 12, p. 1, doi. 10.1371/journal.pcbi.1001024

By:

Valeyev, V.;
Hundhausen, Christian;
Umezawa1, Yoshinori;
Kotov, Nikolay V.;
Williams, Gareth;
Clop, Alex;
Ainali, Crysanthi;
Ouzounis, Christos;
Tsoka, Sophia;
Nestle, Frank O.

Publication type:

Article

Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 7, p. 1, doi. 10.1371/journal.pcbi.1000847

By:

Pantzartzi, Chrysa;
Drosopoulou, Elena;
Yiangou, Minas;
Drozdov, Ignat;
Tsoka, Sophia;
Ouzounis, Christos A.;
Scouras, Zacharias G.

Publication type:

Article

Interpretable optimisation-based approach for hyper-box classification.

Published in:

Machine Learning, 2025, v. 114, n. 3, p. 1, doi. 10.1007/s10994-024-06643-7

By:

Liapis, Georgios I.;
Tsoka, Sophia;
Papageorgiou, Lazaros G.

Publication type:

Article

Organizational principles of the Reactome human BioPAX model using graph theory methods.

Published in:

Journal of Complex Networks, 2016, v. 4, n. 4, p. 604, doi. 10.1093/comnet/cnw003

By:

KITTAS, ARISTOTELIS;
BENNETT, LAURA;
HERMJAKOB, HENNING;
TSOKA, SOPHIA

Publication type:

Article

B Cells in Patients With Melanoma: Implications for Treatment With Checkpoint Inhibitor Antibodies.

Published in:

Frontiers in Immunology, 2021, v. 11, p. N.PAG, doi. 10.3389/fimmu.2020.622442

By:

Willsmore, Zena N.;
Harris, Robert J.;
Crescioli, Silvia;
Hussein, Khuluud;
Kakkassery, Helen;
Thapa, Deepika;
Cheung, Anthony;
Chauhan, Jitesh;
Bax, Heather J.;
Chenoweth, Alicia;
Laddach, Roman;
Osborn, Gabriel;
McCraw, Alexa;
Hoffmann, Ricarda M.;
Nakamura, Mano;
Geh, Jenny L.;
MacKenzie-Ross, Alastair;
Healy, Ciaran;
Tsoka, Sophia;
Spicer, James F.

Publication type:

Article

Optimisation Models for Pathway Activity Inference in Cancer.

Published in:

Cancers, 2023, v. 15, n. 6, p. 1787, doi. 10.3390/cancers15061787

By:

Chen, Yongnan;
Liu, Songsong;
Papageorgiou, Lazaros G.;
Theofilatos, Konstantinos;
Tsoka, Sophia

Publication type:

Article

Selective Flocculation and Precipitation for the Improvement of Virus-Like Particle Recovery from Yeast Homogenate.

Published in:

Biotechnology Progress, 2000, v. 16, n. 4, p. 661, doi. 10.1021/bp0000407

By:

Tsoka, Sophia;
Ciniawskyj, Ohla C.;
Thomas, Owen R. T.;
Titchener-Hooker, Nigel J.;
Hoare, Michael

Publication type:

Article

Network-based piecewise linear regression for QSAR modelling.

Published in:

Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 9, p. 831, doi. 10.1007/s10822-019-00228-6

By:

Cardoso-Silva, Jonathan;
Papageorgiou, Lazaros G.;
Tsoka, Sophia

Publication type:

Article

Community Structure Detection for Overlapping Modules through Mathematical Programming in Protein Interaction Networks.

Published in:

PLoS ONE, 2014, v. 9, n. 11, p. 1, doi. 10.1371/journal.pone.0112821

By:

Bennett, Laura;
Kittas, Aristotelis;
Liu, Songsong;
Papageorgiou, Lazaros G.;
Tsoka, Sophia

Publication type:

Article

DyCoNet: A Gephi Plugin for Community Detection in Dynamic Complex Networks.

Published in:

PLoS ONE, 2014, v. 9, n. 7, p. 1, doi. 10.1371/journal.pone.0101357

By:

Kauffman, Julie;
Kittas, Aristotelis;
Bennett, Laura;
Tsoka, Sophia

Publication type:

Article

Network-Based Data Integration for Selecting Candidate Virulence Associated Proteins in the Cereal Infecting Fungus Fusarium graminearum.

Published in:

PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0067926

By:

Lysenko, Artem;
Urban, Martin;
Bennett, Laura;
Tsoka, Sophia;
Janowska-Sejda, Elzbieta;
Rawlings, Chris J.;
Hammond-Kosack, Kim E.;
Saqi, Mansoor

Publication type:

Article

Functional and Topological Properties in Hepatocellular Carcinoma Transcriptome.

Published in:

PLoS ONE, 2012, v. 7, n. 4, p. 1, doi. 10.1371/journal.pone.0035510

By:

Drozdov, Ignat;
Bornschein, Jan;
Wex, Thomas;
Valeyev, Najl V.;
Tsoka, Sophia;
Malfertheiner, Peter

Publication type:

Article

Detection of Composite Communities in Multiplex Biological Networks.

Published in:

Scientific Reports, 2015, p. 10345, doi. 10.1038/srep10345

By:

Bennett, Laura;
Papageorgiou, Lazaros G.;
Kittas, Aristotelis;
Muirhead, Gareth;
Tsoka, Sophia

Publication type:

Article

Community Structure Detection for Directed Networks through Modularity Optimisation.

Published in:

Algorithms, 2016, v. 9, n. 4, p. 73, doi. 10.3390/a9040073

By:

Lingjian Yang;
Silva, Jonathan C.;
Papageorgiou, Lazaros G.;
Tsoka, Sophia

Publication type:

Article

Genome-wide expression patterns in physiological cardiac hypertrophy.

Published in:

BMC Genomics, 2010, v. 11, n. 1, p. 1, doi. 10.1186/1471-2164-11-557

By:

Drozdov, Ignat;
Tsoka, Sophia;
Ouzounis, Christos A;
Shah, Ajay M

Publication type:

Article

Genome-wide expression patterns in physiological cardiac hypertrophy.

Published in:

BMC Genomics, 2010, v. 11, p. 557, doi. 10.1186/1471-2164-11-557

By:

Drozdov, Ignat;
Tsoka, Sophia;
Ouzounis, Christos A.;
Shah, Ajay M.

Publication type:

Article