A survey of preprocessing techniques for flow cytometry data in classification tasks.
Authors: Nunez-Nepomuceno D, Saez JA, Carmona-Saez P
09/2025 - IEEE transactions on computational biology and bioinformatics
There are no projects in the garbage can.
Omics technologies and new experimental techniques allow the simultaneous quantification of thousands of biological variables and generate large volumes of data.
This amount of information necessitates the use of appropriate analysis techniques to handle and extract knowledge from these massive datasets.
Home - Personalised Medicine Area - Strategic Line 3: Detection, Diagnostics, Monitoring and Prognostics of Diseases - Bioinformatics and Health Data Science
Omics technologies and new experimental techniques allow the simultaneous quantification of thousands of biological variables and generate large volumes of data. This amount of information necessitates the use of appropriate analysis techniques to handle and extract knowledge from these massive datasets. Our main research lines focus on developing and applying new computational and statistical methods for the integration and analysis of multi-omics and biomedical data, aiming to achieve a better understanding of the molecular mechanisms associated with complex diseases, as well as advancing their diagnosis and treatment. Specifically, we are interested in developing applications and methodologies in
different contexts:
The growth of omics techniques has led to an explosion in the availability of data in public repositories. With the appropriate methodologies, this data is an invaluable source for generating new knowledge, hypotheses, and predictive models. In our group, we have developed new methods and software based on meta-analysis techniques and data integration, applied to biomarker discovery and functional annotation analysis,among other fields.
We are creating algorithms to establish omics signatures that define new classification models and guide in predicting responses to treatments or prognosis of pathologies, also integrating information from electronic medical records. In this context, we have various collaborations with other expert groups in different pathologies such as autoimmune diseases and cancer.
One of our objectives is also to develop open-source applications that make our methodologies available to the scientific community. These applications are widely used for analyzing biomedical data. The list of developed software is available at https://compbio.ugr.es/tools/.
Our research has a highly multidisciplinary component, allowing us to establish synergies with other groups that have resulted in patents and joint projects with a clear translational focus. Some of our methodologies have also been implemented in open-source software packages, which are globally used by research groups to extract information from biomedical data and generate new knowledge in diverse areas.
We actively participate in different bioinformatics networks and consortia that enhance the center’s national and international visibility in these areas, such as TransBionet (Translational Bioinformatics Network) in which Dr. Pedro Carmona has been coIP in the “Redes de Excelencia” projects. We promote engagement in collaborative projects with other groups to address complex challenges with a strong inter- and multidisciplinary science component. We are committed to maintaining high criteria of excellence and quality in our publications, aligned with the center, with a percentage > 85% in Q1.
We are part of a working group to apply for an ERC Synergy grant (we have already participated in the last call, and although our proposal has not been granted, we have reinforced the research proposal for future calls). We have consolidated collaborations with different international groups, such as Dr. Julio Sáez (Head of research at EBI_EMBL) or Dr. Giusepe Jurgan (Head of Data Science for Health Unit), with joint projects and mobility of students (predoct and postdoc). We plan to launch proposals for Marie Curie actions and COST.
Authors: Nunez-Nepomuceno D, Saez JA, Carmona-Saez P
09/2025 - IEEE transactions on computational biology and bioinformatics
Authors: Caracuel-Peramos R, Rodríguez-Baena FJ, Redondo-García S, Villatoro-García JA, García-Muñoz A, Peris-Torres C, Plaza-Calonge MDC, Rubio-Gayarre A, López-Millán B, Ricciardelli C, Russell DL, Carmona-Sáez P, Rodríguez-Manzaneque JC
12/2025 - Oncoimmunology
Authors: Martorell-Marugán J, López-Domínguez R, Villatoro-García JA, Toro-Domínguez D, Chierici M, Jurman G, Carmona-Sáez P
11/2024 - Briefings in bioinformatics
Authors: Ellson I, Martorell-Marugán J, Carmona-Sáez P, Ramos-Mejia V
08/2024 - NPJ genomic medicine
Authors: López-Domínguez R, Villatoro-García JA, Marañón C, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme M, Toro-Dominguez D
01/2024 - Research square
Authors: Toro-Domínguez D, Martorell-Marugán J, Martinez-Bueno M, López-Domínguez R, Carnero-Montoro E, Barturen G, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme ME
11/2023 - Briefings in bioinformatics
Authors: Erawijantari PP, Kartal E, Liñares-Blanco J, Laajala TD, Feldman LE, FINRISK Microbiome DREAM Challenge and ML4Microbiome Communities, Carmona-Saez P, Shigdel R, Claesson MJ, Bertelsen RJ, Gomez-Cabrero D, Minot S, Albrecht J, Chung V, Inouye M, Jousilahti P, Schultz JH, Friederich HC, Knight R, Salomaa V, Niiranen T, Havulinna AS, Saez-Rodriguez J, Levinson RT, Lahti L
10/2023 - medRxiv : the preprint server for health sciences
Authors: Villatoro-García JA, López-Domínguez R, Martorell-Marugán J, Luna JD, Lorente JA, Carmona-Sáez P
11/2023 - The Science of the total environment
Authors: Domingo-Reinés J, Montes R, Garcia-Moreno A, Gallardo A, Sanchez-Manas JM, Ellson I, Lamolda M, Calabro C, López-Escamez JA, Catalina P, Carmona-Sáez P, Real PJ, Landeira D, Ramos-Mejia V
06/2023 - Cell death & disease
Authors: Asenjo HG, Alcazar-Fabra M, Espinosa-Martínez M, Lopez-Onieva L, Gallardo A, Dimitrova E, Feldmann A, Pachano T, Martorell-Marugán J, Carmona-Sáez P, Sanchez-Pozo A, Rada-Iglesias Á, Klose RJ, Landeira D
01/2023 - Nature communications
Authors: Martorell-Marugán J, Chierici M, Jurman G, Alarcón-Riquelme ME, Carmona-Sáez P
01/2023 - Computers in biology and medicine
Authors: Fernandez-Jimenez N, Fore R, Cilleros-Portet A, Lepeule J, Perron P, Kvist T, Tian FY, Lesseur C, Binder AM, Lozano M, Martorell-Marugán J, Loke YJ, Bakulski KM, Zhu Y, Forhan A, Sammallahti S, Everson TM, Chen J, Michels KB, Belmonte T, Carmona-Sáez P, Halliday J, Daniele Fallin M, LaSalle JM, Tost J, Czamara D, Fernández MF, Gómez-Martín A, Craig JM, Gonzalez-Alzaga B, Schmidt RJ, Dou JF, Muggli E, Lacasaña M, Vrijheid M, Marsit CJ, Karagas MR, Räikkönen K, Bouchard L, Heude B, Santa-Marina L, Bustamante M, Hivert MF, Bilbao JR
11/2022 - Communications biology
Authors: Femia P, Melchor J, Carmona-Saez P
08/2022 - Frontiers in physiology
Authors: Toro-Domínguez D, Martorell-Marugán J, Martinez-Bueno M, López-Domínguez R, Carnero-Montoro E, Barturen G, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme ME
09/2022 - Briefings in bioinformatics
Authors: Gallardo A, Molina A, Asenjo HG, Lopez-Onieva L, Martorell-Marugán J, Espinosa-Martinez M, Griñan-Lison C, Alvarez-Perez JC, Cara FE, Navarro-Marchal SA, Carmona-Sáez P, Medina PP, Marchal JA, Granados-Principal S, Sánchez-Pozo A, Landeira D
07/2022 - Oncogene
Authors: Aparicio-Puerta E, Gómez-Martín C, Giannoukakos S, Medina JM, Scheepbouwer C, García-Moreno A, Carmona-Saez P, Fromm B, Pegtel M, Keller A, Marchal JA, Hackenberg M
07/2022 - Nucleic acids research
Authors: Garcia-Moreno A, López-Domínguez R, Villatoro-García JA, Ramirez-Mena A, Aparicio-Puerta E, Hackenberg M, Pascual-Montano A, Carmona-Saez P
03/2022 - Biomedicines
Authors: Pozo-Agundo A, Villaescusa N, Martorell-Marugán J, Soriano O, Leyva S, Jódar-Reyes AB, Botella LM, Carmona-Sáez P, Blanco FJ
08/2021 - International journal of molecular sciences
Authors: Everson TM, Vives-Usano M, Seyve E, Cardenas A, Lacasaña M, Craig JM, Lesseur C, Baker ER, Fernandez-Jimenez N, Heude B, Perron P, Gónzalez-Alzaga B, Halliday J, Deyssenroth MA, Karagas MR, Íñiguez C, Bouchard L, Carmona-Sáez P, Loke YJ, Hao K, Belmonte T, Charles MA, Martorell-Marugán J, Muggli E, Chen J, Fernández MF, Tost J, Gómez-Martín A, London SJ, Sunyer J, Marsit CJ, Lepeule J, Hivert MF, Bustamante M
08/2021 - Nature communications
Authors: Martorell-Marugán J, Carmona-Sáez P
06/2021 - Bio-protocol
Authors: Peinado P, Andrades A, Martorell-Marugán J, Haswell JR, Slack FJ, Carmona-Sáez P, Medina PP
11/2021 - Human molecular genetics
Authors: Martorell-Marugán J, López-Domínguez R, García-Moreno A, Toro-Domínguez D, Villatoro-García JA, Barturen G, Martín-Gómez A, Troule K, Gómez-López G, Al-Shahrour F, González-Rumayor V, Peña-Chilet M, Dopazo J, Sáez-Rodríguez J, Alarcón-Riquelme ME, Carmona-Sáez P
06/2021 - BMC bioinformatics
Authors: Lopez-Dominguez R, Toro-Dominguez D, Martorell-Marugan J, Garcia-Moreno A, Holland CH, Saez-Rodriguez J, Goldman D, Petri MA, Alarcon-Riquelme ME, Carmona-Saez P
04/2021 - Life (Basel, Switzerland)
Authors: Barturen G, Babaei S, Català-Moll F, Martínez-Bueno M, Makowska Z, Martorell-Marugán J, Carmona-Sáez P, Toro-Domínguez D, Carnero-Montoro E, Teruel M, Kerick M, Acosta-Herrera M, Le Lann L, Jamin C, Rodríguez-Ubreva J, García-Gómez A, Kageyama J, Buttgereit A, Hayat S, Mueller J, Lesche R, Hernandez-Fuentes M, Juarez M, Rowley T, White I, Marañón C, Gomes Anjos T, Varela N, Aguilar-Quesada R, Garrancho FJ, López-Berrio A, Rodriguez Maresca M, Navarro-Linares H, Almeida I, Azevedo N, Brandão M, Campar A, Faria R, Farinha F, Marinho A, Neves E, Tavares A, Vasconcelos C, Trombetta E, Montanelli G, Vigone B, Alvarez-Errico D, Li T, Thiagaran D, Blanco Alonso R, Corrales Martínez A, Genre F, López Mejías R, Gonzalez-Gay MA, Remuzgo S, Ubilla Garcia B, Cervera R, Espinosa G, Rodríguez-Pintó I, De Langhe E, Cremer J, Lories R, Belz D, Hunzelmann N, Baerlecken N, Kniesch K, Witte T, Lehner M, Stummvoll G, Zauner M, Aguirre-Zamorano MA, Barbarroja N, Castro-Villegas MC, Collantes-Estevez E, de Ramon E, Díaz Quintero I, Escudero-Contreras A, Fernández Roldán MC, Jiménez Gómez Y, Jiménez Moleón I, Lopez-Pedrera R, Ortega-Castro R, Ortego N, Raya E, Artusi C, Gerosa M, Meroni PL, Schioppo T, De Groof A, Ducreux J, Lauwerys B, Maudoux AL, Cornec D, Devauchelle-Pensec V, Jousse-Joulin S, Jouve PE, Rouvière B, Saraux A, Simon Q, Alvarez M, Chizzolini C, Dufour A, Wynar D, Balog A, Bocskai M, Deák M, Dulic S, Kádár G, Kovács L, Cheng Q, Gerl V, Hiepe F, Khodadadi L, Thiel S, de Rinaldis E, Rao S, Benschop RJ, Chamberlain C, Dow ER, Ioannou Y, Laigle L, Marovac J, Wojcik J, Renaudineau Y, Borghi MO, Frostegård J, Martín J, Beretta L, Ballestar E, McDonald F, Pers JO, Alarcón-Riquelme ME
06/2021 - Arthritis & rheumatology (Hoboken, N.J.)
Authors: Garcia-Moreno A, Carmona-Saez P
08/2020 - Biomolecules
Authors: Martorell-Marugán J, Villatoro-García JA, García-Moreno A, López-Domínguez R, Requena F, Merelo JJ, Lacasaña M, de Dios Luna J, Díaz-Mochón JJ, Lorente JA, Carmona-Sáez P
01/2021 - The Science of the total environment
Authors: Troulé K, López-Fernández H, García-Martín S, Reboiro-Jato M, Carretero-Puche C, Martorell-Marugán J, Martín-Serrano G, Carmona-Sáez P, Glez-Peña D, Al-Shahrour F, Gómez-López G
05/2021 - Bioinformatics (Oxford, England)
Authors: Lopez-Caraballo L, Martorell-Marugan J, Carmona-Sáez P, Gonzalez-Munoz E
07/2020 - Cells
Authors: Lopez-Caraballo L, Martorell-Marugan J, Carmona-Saez P, Gonzalez-Muñoz E
08/2020 - iScience
Authors: Gallardo A, Molina A, Asenjo HG, Martorell-Marugán J, Montes R, Ramos-Mejia V, Sanchez-Pozo A, Carmona-Sáez P, Lopez-Onieva L, Landeira D
04/2020 - Life science alliance
Authors: Peris-Torres C, Plaza-Calonge MDC, López-Domínguez R, Domínguez-García S, Barrientos-Durán A, Carmona-Sáez P, Rodríguez-Manzaneque JC
03/2020 - Cancers
Authors: Asenjo HG, Gallardo A, López-Onieva L, Tejada I, Martorell-Marugán J, Carmona-Sáez P, Landeira D
03/2020 - Science advances
Authors: Toro-Domínguez D, Villatoro-García JA, Martorell-Marugán J, Román-Montoya Y, Alarcón-Riquelme ME, Carmona-Sáez P
03/2021 - Briefings in bioinformatics
Authors: Carrillo-Gálvez AB, Gálvez-Peisl S, González-Correa JE, de Haro-Carrillo M, Ayllón V, Carmona-Sáez P, Ramos-Mejía V, Galindo-Moreno P, Cara FE, Granados-Principal S, Muñoz P, Martin F, Anderson P
05/2020 - Stem cells translational medicine
Authors: López-Longarela B, Morrison EE, Tranter JD, Chahman-Vos L, Léonard JF, Gautier JC, Laurent S, Lartigau A, Boitier E, Sautier L, Carmona-Saez P, Martorell-Marugan J, Mellanby RJ, Pernagallo S, Ilyine H, Rissin DM, Duffy DC, Dear JW, Díaz-Mochón JJ
02/2020 - Analytical chemistry
Authors: Husi H, Martorell-Marugán J, Tabik S, Benhammou Y, del Val C, Zwir I, Herrera F, Carmona-Sáez P
11/2019 -
Authors: Toro-Domínguez D, Lopez-Domínguez R, García Moreno A, Villatoro-García JA, Martorell-Marugán J, Goldman D, Petri M, Wojdyla D, Pons-Estel BA, Isenberg D, Morales-Montes de Oca G, Trejo-Zambrano MI, García González B, Rosetti F, Gómez-Martín D, Romero-Díaz J, Carmona-Sáez P, Alarcón-Riquelme ME
10/2019 - Scientific reports
Authors: Ramos-Molina B, Sánchez-Alcoholado L, Cabrera-Mulero A, Lopez-Dominguez R, Carmona-Saez P, Garcia-Fuentes E, Moreno-Indias I, Tinahones FJ
07/2019 - Frontiers in genetics
Authors: Requena F, Asenjo HG, Barturen G, Martorell-Marugán J, Carmona-Sáez P, Landeira D
05/2019 - Scientific reports
Authors: Martorell-Marugán J, González-Rumayor V, Carmona-Sáez P
09/2019 - Bioinformatics (Oxford, England)
Authors: Rodríguez-Martínez A, de Miguel-Pérez D, Ortega FG, García-Puche JL, Robles-Fernández I, Exposito J, Martorell-Marugan J, Carmona-Sáez P, Garrido-Navas MDC, Rolfo C, Ilyine H, Lorente JA, Legueren M, Serrano MJ
02/2019 - Breast cancer research : BCR
Authors: Toro-Domínguez D, Martorell-Marugán J, López-Domínguez R, García-Moreno A, González-Rumayor V, Alarcón-Riquelme ME, Carmona-Sáez P
03/2019 - Bioinformatics (Oxford, England)
Authors: Toro-Domínguez D, Martorell-Marugán J, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme ME
12/2018 - Arthritis & rheumatology (Hoboken, N.J.)
Authors: Alvarez-Cubero MJ, Santiago O, Martínez-Labarga C, Martínez-García B, Marrero-Díaz R, Rubio-Roldan A, Pérez-Gutiérrez AM, Carmona-Saez P, Lorente JA, Martinez-Gonzalez LJ
06/2018 - Scientific reports
Authors: Martorell-Marugan J, Toro-Dominguez D, Alarcon-Riquelme ME, Carmona-Saez P
12/2017 - BMC bioinformatics
Authors: Herrera-Merchan A, Cuadros M, Rodriguez MI, Rodriguez S, Torres R, Estecio M, Coira IF, Loidi C, Saiz M, Carmona-Saez P, Medina PP
10/2017 - Oncotarget
Authors: Carmona-Sáez P, Varela N, Luque MJ, Toro-Domínguez D, Martorell-Marugan J, Alarcón-Riquelme ME, Marañón C
12/2017 - Bioinformatics (Oxford, England)
Authors: Toro-Domínguez D, Carmona-Sáez P, Alarcón-Riquelme ME
03/2017 - Arthritis research & therapy
Authors: Díaz-Villamarín X, Dávila-Fajardo CL, Martínez-González LJ, Carmona-Sáez P, Sánchez-Ramos J, Álvarez Cubero MJ, Salmerón-Febres LM, Cabeza Barrera J, Fernández-Quesada F
08/2016 - Pharmacogenomics
Authors: Melero JT, Ortega FG, Gonzalez AM, Carmona-Saez P, Garcia Puche JL, Sugarbaker PH, Delgado M, Lorente JA, Serrano MJ
03/2016 - Surgery
Authors: Alvarez-Cubero MJ, Martinez-Gonzalez LJ, Saiz M, Carmona-Saez P, Alvarez JC, Pascual-Geler M, Lorente JA, Cozar JM
08/2015 - Experimental & molecular medicine
Authors: Gómez Peña C, Dávila-Fajardo CL, Martínez-González LJ, Carmona-Sáez P, Soto Pino MJ, Sánchez Ramos J, Moreno Escobar E, Blancas I, Fernández JJ, Fernández D, Correa C, Cabeza Barrera J
08/2015 - Pharmacogenetics and genomics
Authors: Toro-Domínguez D, Carmona-Sáez P, Alarcón-Riquelme ME
12/2014 - Arthritis research & therapy
Authors: Vazquez M, Nogales-Cadenas R, Arroyo J, Botías P, García R, Carazo JM, Tirado F, Pascual-Montano A, Carmona-Saez P
07/2010 - Nucleic acids research
Authors: Kökény S, Papp J, Weber G, Vaszkó T, Carmona-Saez P, Oláh E
06/2009 - Anticancer research
Authors: Nogales-Cadenas R, Carmona-Saez P, Vazquez M, Vicente C, Yang X, Tirado F, Carazo JM, Pascual-Montano A
07/2009 - Nucleic acids research
Authors: Vazquez M, Carmona-Saez P, Nogales-Cadenas R, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A
07/2009 - Nucleic acids research
Authors: Recuero M, Vicente MC, Martínez-García A, Ramos MC, Carmona-Saez P, Sastre I, Aldudo J, Vilella E, Frank A, Bullido MJ, Valdivieso F
04/2009 - Aging cell
Authors: Mejía-Roa E, Carmona-Saez P, Nogales R, Vicente C, Vázquez M, Yang XY, García C, Tirado F, Pascual-Montano A
07/2008 - Nucleic acids research
Authors: Abascal F, Carmona-Saez P, Carazo JM, Pascual-Montano A
05/2008 - Bioinformatics (Oxford, England)
Authors: Anton MA, Gorostiaga D, Guruceaga E, Segura V, Carmona-Saez P, Pascual-Montano A, Pio R, Montuenga LM, Rubio A
01/2008 - Genome biology
Authors: Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A
01/2007 - Genome biology
Authors: Pascual-Montano A, Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Marqui RD
07/2006 - BMC bioinformatics
Authors: Chagoyen M, Carmona-Saez P, Gil C, Carazo JM, Pascual-Montano A
07/2006 - BMC bioinformatics
Authors: Hernández-Vargas H, Ballestar E, Carmona-Saez P, von Kobbe C, Bañón-Rodríguez I, Esteller M, Moreno-Bueno G, Palacios J
09/2006 - International journal of cancer
Authors: Carmona-Saez P, Pascual-Marqui RD, Tirado F, Carazo JM, Pascual-Montano A
02/2006 - BMC bioinformatics
Authors: Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A
02/2006 - BMC bioinformatics
Authors: Chagoyen M, Carmona-Saez P, Shatkay H, Carazo JM, Pascual-Montano A
01/2006 - BMC bioinformatics
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