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2020 – today
- 2021
[j21]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:
Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer. Briefings Bioinform. 22(6) (2021)- [j20]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:
Agile workflow for interactive analysis of mass cytometry data. Bioinform. 37(9): 1263-1268 (2021) - [j19]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:
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples. Bioinform. 37(18): 2882-2888 (2021) - 2020
- [j18]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:
qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets. Bioinform. 36(20): 5086-5092 (2020)
2010 – 2019
- 2019
- [j17]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:
Anduril 2: upgraded large-scale data integration framework. Bioinform. 35(19): 3815-3817 (2019) - 2018
- [j16]Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi:
Identifying differentially methylated sites in samples with varying tumor purity. Bioinform. 34(18): 3078-3085 (2018) - [j15]Leonardo Martins, Ramakanth Neeli-Venkata, Samuel M. D. Oliveira, Antti Häkkinen, Andre S. Ribeiro, José M. Fonseca:
SCIP: a single-cell image processor toolbox. Bioinform. 34(24): 4318-4320 (2018) - 2016
- [j14]Antti Häkkinen, Andre S. Ribeiro:
Characterizing rate limiting steps in transcription from RNA production times in live cells. Bioinform. 32(9): 1346-1352 (2016) - [j13]Samuel M. D. Oliveira, Antti Häkkinen, Jason Lloyd-Price, Huy Tran, Vinodh Kandavalli, Andre S. Ribeiro:
Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. PLoS Comput. Biol. 12(10) (2016) - 2015
- [j12]Antti Häkkinen, Andre S. Ribeiro:
Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. Bioinform. 31(1): 69-75 (2015) - 2014
- [j11]Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, Andre S. Ribeiro:
Estimation of fluorescence-tagged RNA numbers from spot intensities. Bioinform. 30(8): 1146-1153 (2014) - 2013
- [j10]Antti Häkkinen, Anantha Barathi Muthukrishnan, André Mora, José Manuel Fonseca, Andre S. Ribeiro:
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli. Bioinform. 29(13): 1708-1709 (2013) - [j9]Antti Häkkinen, Huy Tran, Olli Yli-Harja, Brian P. Ingalls, Andre S. Ribeiro:
Effects of multimerization on the temporal variability of protein complex abundance. BMC Syst. Biol. 7(S-1): S3 (2013) - 2012
- [j8]Frank Emmert-Streib, Antti Häkkinen, Andre S. Ribeiro:
Detecting sequence dependent transcriptional pauses from RNA and protein number time series. BMC Bioinform. 13: 152 (2012) - [j7]Antti Häkkinen, Andre S. Ribeiro:
Evolving kinetics of gene expression in stochastic environments. Comput. Biol. Chem. 37: 11-16 (2012) - [j6]Andre S. Ribeiro, Antti Häkkinen, Jason Lloyd-Price:
Effects of gene length on the dynamics of gene expression. Comput. Biol. Chem. 41: 1-9 (2012) - 2011
- [j5]Meenakshisundaram Kandhavelu, Henrik Mannerström, Abhishekh Gupta, Antti Häkkinen, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro:
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. 5: 149 (2011) - [j4]Antti Häkkinen, Fred G. Biddle, Olli-Pekka Smolander, Olli Yli-Harja, Andre S. Ribeiro:
Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. Trans. Comp. Sys. Biology 13: 1-12 (2011) - 2010
- [j3]Andre S. Ribeiro, Antti Häkkinen, Shannon Healy, Olli Yli-Harja:
Dynamical effects of transcriptional pause-prone sites. Comput. Biol. Chem. 34(3): 143-148 (2010) - [j2]Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro:
Effects of Transcriptional Pausing on Gene Expression Dynamics. PLoS Comput. Biol. 6(3) (2010)
2000 – 2009
- 2009
- [j1]Andre S. Ribeiro, Olli-Pekka Smolander, Tiina Rajala, Antti Häkkinen, Olli Yli-Harja:
Delayed Stochastic Model of Transcription at the Single Nucleotide Level. J. Comput. Biol. 16(4): 539-553 (2009)
Coauthor Index
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