Delayed Stochastic Model of Transcription at the Single Nucleotide Level. - Andre S. Ribeiro; Olli-Pekka Smolander; Tiina Rajala; Antti Häkkinen; Olli Yli-Harja (J. Comput. Biol., 2009)

Dynamical effects of transcriptional pause-prone sites. - Andre S. Ribeiro; Antti Häkkinen; Shannon Healy; Olli Yli-Harja (Comput. Biol. Chem., 2010)

Effects of Transcriptional Pausing on Gene Expression Dynamics. - Tiina Rajala; Antti Häkkinen; Shannon Healy; Olli Yli-Harja; Andre S. Ribeiro (PLoS Comput. Biol., 2010)

In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. - Meenakshisundaram Kandhavelu; Henrik Mannerström; Abhishekh Gupta; Antti Häkkinen; Jason Lloyd-Price; Olli Yli-Harja; Andre S. Ribeiro (BMC Syst. Biol., 2011)

Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. - Antti Häkkinen; Fred G. Biddle; Olli-Pekka Smolander; Olli Yli-Harja; Andre S. Ribeiro (Trans. Comp. Sys. Biology, 2011)

Detecting sequence dependent transcriptional pauses from RNA and protein number time series. - Frank Emmert-Streib; Antti Häkkinen; Andre S. Ribeiro (BMC Bioinform., 2012)

Evolving kinetics of gene expression in stochastic environments. - Antti Häkkinen; Andre S. Ribeiro (Comput. Biol. Chem., 2012)

Effects of gene length on the dynamics of gene expression. - Andre S. Ribeiro; Antti Häkkinen; Jason Lloyd-Price (Comput. Biol. Chem., 2012)

CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli. - Antti Häkkinen; Anantha Barathi Muthukrishnan; André Mora; José Manuel Fonseca; Andre S. Ribeiro (Bioinform., 2013)

Effects of multimerization on the temporal variability of protein complex abundance. - Antti Häkkinen; Huy Tran; Olli Yli-Harja; Brian P. Ingalls; Andre S. Ribeiro (BMC Syst. Biol., 2013)

Estimation of fluorescence-tagged RNA numbers from spot intensities. - Antti Häkkinen; Meenakshisundaram Kandhavelu; Stefania Garasto; Andre S. Ribeiro (Bioinform., 2014)

Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. - Antti Häkkinen; Andre S. Ribeiro (Bioinform., 2015)

Characterizing rate limiting steps in transcription from RNA production times in live cells. - Antti Häkkinen; Andre S. Ribeiro (Bioinform., 2016)

Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. - Samuel M. D. Oliveira; Antti Häkkinen; Jason Lloyd-Price; Huy Tran; Vinodh Kandavalli; Andre S. Ribeiro (PLoS Comput. Biol., 2016)

Identifying differentially methylated sites in samples with varying tumor purity. - Antti Häkkinen; Amjad Alkodsi; Chiara Facciotto; Kaiyang Zhang; Katja Kaipio; Sirpa Leppä; Olli Carpén; Seija Grénman; Johanna Hynninen; Sakari Hietanen; Rainer Lehtonen; Sampsa Hautaniemi (Bioinform., 2018)

SCIP: a single-cell image processor toolbox. - Leonardo Martins; Ramakanth Neeli-Venkata; Samuel M. D. Oliveira; Antti Häkkinen; Andre S. Ribeiro; José M. Fonseca 001 (Bioinform., 2018)

Anduril 2: upgraded large-scale data integration framework. - Alejandra Cervera; Ville Rantanen; Kristian Ovaska; Marko Laakso; Javier Nuñez-Fontarnau; Amjad Alkodsi; Julia Casado; Chiara Facciotto; Antti Häkkinen; Riku Louhimo; Sirkku Karinen; Kaiyang Zhang; et al. (Bioinform., 2019)

qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets. - Antti Häkkinen; Juha Koiranen; Julia Casado; Katja Kaipio; Oskari Lehtonen; Eleonora Petrucci; Johanna Hynninen; Sakari Hietanen; Olli Carpén; Luca Pasquini; Mauro Biffoni; Rainer Lehtonen; et al. (Bioinform., 2020)

Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer. - Liye He; Daria Bulanova; Jaana Oikkonen; Antti Häkkinen; Kaiyang Zhang; Shuyu Zheng; Wenyu Wang; Erdogan Pekcan Erkan; Olli Carpén; Titta Joutsiniemi; Sakari Hietanen; Johanna Hynninen; et al. (Briefings Bioinform., 2021)

Agile workflow for interactive analysis of mass cytometry data. - Julia Casado; Oskari Lehtonen; Ville Rantanen; Katja Kaipio; Luca Pasquini; Antti Häkkinen; Elenora Petrucci; Johanna Hynninen; Sakari Hietanen; Olli Carpén; Mauro Biffoni; Anniina Färkkilä; et al. (Bioinform., 2021)

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples. - Antti Häkkinen; Kaiyang Zhang; Amjad Alkodsi; Noora Andersson; Erdogan Pekcan Erkan; Jun Dai; Katja Kaipio; Tarja Lamminen; Naziha Mansuri; Kaisa Huhtinen; Anna Vähärautio; Olli Carpén; et al. (Bioinform., 2021)

POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching. - Susanna Holmström; Sampsa Hautaniemi; Antti Häkkinen (Bioinform., 2022)