Antti Häkkinen

22 papers Journal 22
YearRankTypeTitle / Venue / Authors
2022 J jnl
POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching.
Bioinform.
Susanna Holmström, Sampsa Hautaniemi, Antti Häkkinen
2021 J jnl
Agile workflow for interactive analysis of mass cytometry data.
Bioinform.
Julia Casado, Oskari Lehtonen, Ville Rantanen, Katja Kaipio, Luca Pasquini, Antti Häkkinen, Elenora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Mauro Biffoni, Anniina Färkkilä, Sampsa Hautaniemi
2021 J jnl
Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer.
Briefings Bioinform.
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, Kaisa Huhtinen, Sampsa Hautaniemi, Anna Vähärautio, Jing Tang, Krister Wennerberg, Tero Aittokallio
2021 J jnl
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples.
Bioinform.
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, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
2020 J jnl
qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets.
Bioinform.
Antti Häkkinen, Juha Koiranen, Julia Casado, Katja Kaipio, Oskari Lehtonen, Eleonora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Luca Pasquini, Mauro Biffoni, Rainer Lehtonen, Sampsa Hautaniemi
2019 J jnl
Anduril 2: upgraded large-scale data integration framework.
Bioinform.
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, Kari Lavikka, Lauri Lyly, Maninder Pal Singh, Sampsa Hautaniemi
2018 J jnl
Identifying differentially methylated sites in samples with varying tumor purity.
Bioinform.
Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
2018 J jnl
SCIP: a single-cell image processor toolbox.
Bioinform.
Leonardo Martins, Ramakanth Neeli-Venkata, Samuel M. D. Oliveira, Antti Häkkinen, Andre S. Ribeiro, José M. Fonseca
2016 J jnl
Characterizing rate limiting steps in transcription from RNA production times in live cells.
Bioinform.
Antti Häkkinen, Andre S. Ribeiro
2016 J jnl
Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements.
PLoS Comput. Biol.
Samuel M. D. Oliveira, Antti Häkkinen, Jason Lloyd-Price, Huy Tran, Vinodh Kandavalli, Andre S. Ribeiro
2015 J jnl
Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data.
Bioinform.
Antti Häkkinen, Andre S. Ribeiro
2014 J jnl
Estimation of fluorescence-tagged RNA numbers from spot intensities.
Bioinform.
Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, Andre S. Ribeiro
2013 J jnl
CellAging: a tool to study segregation and partitioning in division in cell lineages of
Bioinform.
Antti Häkkinen, Anantha Barathi Muthukrishnan, André Mora, José Manuel Fonseca, Andre S. Ribeiro
2013 J jnl
Effects of multimerization on the temporal variability of protein complex abundance.
BMC Syst. Biol.
Antti Häkkinen, Huy Tran, Olli Yli-Harja, Brian P. Ingalls, Andre S. Ribeiro
2012 J jnl
Detecting sequence dependent transcriptional pauses from RNA and protein number time series.
BMC Bioinform.
Frank Emmert-Streib, Antti Häkkinen, Andre S. Ribeiro
2012 J jnl
Effects of gene length on the dynamics of gene expression.
Comput. Biol. Chem.
Andre S. Ribeiro, Antti Häkkinen, Jason Lloyd-Price
2012 J jnl
Evolving kinetics of gene expression in stochastic environments.
Comput. Biol. Chem.
Antti Häkkinen, Andre S. Ribeiro
2011 J jnl
Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene.
Trans. Comp. Sys. Biology
Antti Häkkinen, Fred G. Biddle, Olli-Pekka Smolander, Olli Yli-Harja, Andre S. Ribeiro
2011 J jnl
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps.
BMC Syst. Biol.
Meenakshisundaram Kandhavelu, Henrik Mannerström, Abhishekh Gupta, Antti Häkkinen, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro
2010 J jnl
Dynamical effects of transcriptional pause-prone sites.
Comput. Biol. Chem.
Andre S. Ribeiro, Antti Häkkinen, Shannon Healy, Olli Yli-Harja
2010 J jnl
Effects of Transcriptional Pausing on Gene Expression Dynamics.
PLoS Comput. Biol.
Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro
2009 J jnl
Delayed Stochastic Model of Transcription at the Single Nucleotide Level.
J. Comput. Biol.
Andre S. Ribeiro, Olli-Pekka Smolander, Tiina Rajala, Antti Häkkinen, Olli Yli-Harja