A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information. - Juho Rousu; Ari Rantanen; Hannu Maaheimo; Esa Pitkänen; Katja Saarela; Esko Ukkonen (CMSB, 2003)

Finding Feasible Pathways in Metabolic Networks. - Esa Pitkänen; Ari Rantanen; Juho Rousu; Esko Ukkonen (Panhellenic Conference on Informatics, 2005)

Ab Initio Prediction of Molecular Fragments from Tandem Mass Spectrometry Data. - Markus Heinonen; Ari Rantanen; Taneli Mielikäinen; Esa Pitkänen; Juha Kokkonen; Juho Rousu (German Conference on Bioinformatics, 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)

A Computational Method for Reconstructing Gapless Metabolic Networks. - Esa Pitkänen; Ari Rantanen; Juho Rousu; Esko Ukkonen (BIRD, 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)

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)

Inferring branching pathways in genome-scale metabolic networks. - Esa Pitkänen; Paula Jouhten; Juho Rousu (BMC Syst. Biol., 2009)

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels. - Katja Astikainen; Liisa Holm; Esa Pitkänen; Sándor Szedmák; Juho Rousu (BIOSTEC (Selected Papers), 2010)

Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function. - Katja Astikainen; Esa Pitkänen; Juho Rousu; Liisa Holm; Sándor Szedmák (BIOINFORMATICS, 2010)

Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks. - Esa Pitkänen (2010)

Reconstructing Gapless Ancestral Metabolic Networks. - Esa Pitkänen; Mikko Arvas; Juho Rousu (BIOSTEC (Selected Papers), 2011)

Minimum Mutation Algorithm for Gapless Metabolic Network Evolution. - Esa Pitkänen; Juho Rousu; Mikko Arvas (BIOINFORMATICS, 2011)

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. - Esa Pitkänen; Paula Jouhten; Jian Hou 007; Muhammad Fahad Syed; Peter Blomberg; Jana Kludas; Merja Oja; Liisa Holm; Merja Penttilä; Juho Rousu; Mikko Arvas (PLoS Comput. Biol., 2014)

Service Outsourcing with Process Views. - Rik Eshuis; Alex Norta; Oliver Kopp; Esa Pitkänen (IEEE Trans. Serv. Comput., 2015)

Towards pan-genome read alignment to improve variation calling. - Daniel Valenzuela 001; Tuukka Norri; Niko Välimäki; Esa Pitkänen; Veli Mäkinen (BMC Genom., 2018)

Comparative analysis of molecular fingerprints in prediction of drug combination effects. - Bulat Zagidullin; Ziyan Wang; Yuanfang Guan; Esa Pitkänen; Jing Tang 002 (Briefings Bioinform., 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)

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)

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)

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)

A Unified Review of Deep Learning for Automated Medical Coding. - Shaoxiong Ji; Xiaobo Li 007; Wei Sun 046; Hang Dong 002; Ara Taalas; Yijia Zhang 001; Honghan Wu; Esa Pitkänen; Pekka Marttinen (ACM Comput. Surv., 2024)