Esa Pitkänen

According to our database, Esa Pitkänen authored at least 22 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

A Unified Review of Deep Learning for Automated Medical Coding.

Shaoxiong Ji, Xiaobo Li, Wei Sun, Hang Dong, Ara Taalas, Yijia Zhang, Honghan Wu, Esa Pitkänen, Pekka Marttinen

ACM Comput. Surv., December, 2024

HistoEncoder: a digital pathology foundation model for prostate cancer.

Joona Pohjonen, Abderrahim Oussama Batouche, Antti Rannikko, Kevin Sandeman, Andrew Erickson, Esa Pitkänen, Tuomas Mirtti

CoRR, 2024

2022

Exposing and addressing the fragility of neural networks in digital pathology.

Joona Pohjonen, Carolin Stürenberg, Atte Föhr, Esa Pitkänen, Antti Rannikko, Tuomas Mirtti

CoRR, 2022

Identification of multiplicatively acting modulatory mutational signatures in cancer.

Dovydas Kiciatovas, Qingli Guo, Miika Kailas, Henri Pesonen, Jukka Corander, Samuel Kaski, Esa Pitkänen, Ville Mustonen

BMC Bioinform., 2022

2021

Training robust deep learning models for medical imaging tasks with spectral decoupling.

Joona Pohjonen, Carolin Stürenberg, Antti Rannikko, Tuomas Mirtti, Esa Pitkänen

CoRR, 2021

Comparative analysis of molecular fingerprints in prediction of drug combination effects.

Bulat Zagidullin, Ziyan Wang, Yuanfang Guan, Esa Pitkänen, Jing Tang

Briefings Bioinform., 2021

2018

Towards pan-genome read alignment to improve variation calling.

Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen

BMC Genom., 2018

2015

Service Outsourcing with Process Views.

Rik Eshuis, Alex Norta, Oliver Kopp, Esa Pitkänen

IEEE Trans. Serv. Comput., 2015

2014

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species.

Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas

PLoS Comput. Biol., 2014

2011

Minimum Mutation Algorithm for Gapless Metabolic Network Evolution.

Esa Pitkänen, Juho Rousu, Mikko Arvas

Proceedings of the BIOINFORMATICS 2011, 2011

Reconstructing Gapless Ancestral Metabolic Networks.

Esa Pitkänen, Mikko Arvas, Juho Rousu

Proceedings of the Biomedical Engineering Systems and Technologies, 2011

2010

Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks.

Esa Pitkänen

PhD thesis, 2010

Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function.

Katja Astikainen, Esa Pitkänen, Juho Rousu, Liisa Holm, Sándor Szedmák

Proceedings of the BIOINFORMATICS 2010, 2010

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels.

Katja Astikainen, Liisa Holm, Esa Pitkänen, Sándor Szedmák, Juho Rousu

Proceedings of the Biomedical Engineering Systems and Technologies, 2010

2009

Inferring branching pathways in genome-scale metabolic networks.

Esa Pitkänen, Paula Jouhten, Juho Rousu

BMC Syst. Biol., 2009

¹³C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose.

Paula Jouhten, Esa Pitkänen, Tiina Pakula, Markku Saloheimo, Merja Penttilä, Hannu Maaheimo

BMC Syst. Biol., 2009

2008

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.

Esa Pitkänen, Arto Åkerlund, Ari Rantanen, Paula Jouhten, Esko Ukkonen

J. Integr. Bioinform., 2008

A Computational Method for Reconstructing Gapless Metabolic Networks.

Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen

Proceedings of the Bioinformatics Research and Development, 2008

2006

Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation.

Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen

Trans. Comp. Sys. Biology, 2006

Ab Initio Prediction of Molecular Fragments from Tandem Mass Spectrometry Data.

Markus Heinonen, Ari Rantanen, Taneli Mielikäinen, Esa Pitkänen, Juha Kokkonen, Juho Rousu

Proceedings of the German Conference on Bioinformatics GCB 2006, 19.09. 2006, 2006

2005

Finding Feasible Pathways in Metabolic Networks.

Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen

Proceedings of the Advances in Informatics, 2005

2003

A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information.

Juho Rousu, Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Katja Saarela, Esko Ukkonen

Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003