Sampsa Hautaniemi

According to our database, Sampsa Hautaniemi authored at least 36 papers between 2003 and 2022.

Collaborative distances:

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

2022

Image Processing Pipeline to Compute Homologous Recombination Score.

Haswanth Vundavilli, Manuela Tumiati, Sampsa Hautaniemi, Aniruddha Datta, Liisa Kauppi

Proceedings of the ICBET 2022: 12th International Conference on Biomedical Engineering and Technology, Tokyo, Japan, April 20, 2022

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, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi

Bioinform., 2021

FUNGI: FUsioN Gene Integration toolset.

Alejandra Cervera, Heidi Rausio, Tiia Kähkönen, Noora Andersson, Gabriele Partel, Ville Rantanen, Giulia Paciello, Elisa Ficarra, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Rainer Lehtonen, Sampsa Hautaniemi, Kaisa Huhtinen

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, Sampsa Hautaniemi

Bioinform., 2021

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, Kaisa Huhtinen, Sampsa Hautaniemi, Anna Vähärautio, Jing Tang, Krister Wennerberg, Tero Aittokallio

Briefings Bioinform., 2021

2020

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, Sampsa Hautaniemi

Bioinform., 2020

2019

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, Kari Lavikka, Lauri Lyly, Maninder Pal Singh, Sampsa Hautaniemi

Bioinform., 2019

2018

PerPAS: Topology-Based Single Sample Pathway Analysis Method.

Chengyu Liu, Rainer Lehtonen, Sampsa Hautaniemi

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Dynamic visualization of multi-level molecular data: The Director package in R.

Katherine Icay, Chengyu Liu, Sampsa Hautaniemi

Comput. Methods Programs Biomed., 2018

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

2016

Data integration to prioritize drugs using genomics and curated data.

Riku Louhimo, Marko Laakso, Denis Belitskin, Juha Klefström, Rainer Lehtonen, Sampsa Hautaniemi

BioData Min., 2016

SePIA: RNA and small RNA sequence processing, integration, and analysis.

Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi

BioData Min., 2016

2015

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data.

Amjad Alkodsi, Riku Louhimo, Sampsa Hautaniemi

Briefings Bioinform., 2015

2013

Genomic Region Operation Kit for Flexible Processing of Deep Sequencing Data.

Kristian Ovaska, Lauri Lyly, Biswajyoti Sahu, Olli A. Jänne, Sampsa Hautaniemi

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links <i>ATAD3B</i> to Poor Survival in Breast Cancer.

Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G. Stunnenberg, Sampsa Hautaniemi

PLoS Comput. Biol., 2013

Identification of genetic markers with synergistic survival effect in cancer.

Riku Louhimo, Marko Laakso, Tuomas Heikkinen, Susanna Laitinen, Pekka Manninen, Vladimir Rogojin, Minna Miettinen, Carl Blomqvist, Jianjun Liu, Heli Nevanlinna, Sampsa Hautaniemi

BMC Syst. Biol., 2013

High-performance computing in biomedicine.

Sampsa Hautaniemi, Marko Laakso

Proceedings of the International Conference on High Performance Computing & Simulation, 2013

2012

PINA v2.0: mining interactome modules.

Mark J. Cowley, Mark Pinese, Karin S. Kassahn, Nic Waddell, John V. Pearson, Sean M. Grimmond, Andrew V. Biankin, Sampsa Hautaniemi, Jianmin Wu

Nucleic Acids Res., 2012

2011

CNAmet: an R package for integrating copy number, methylation and expression data.

Riku Louhimo, Sampsa Hautaniemi

Bioinform., 2011

2010

Integrative platform to translate gene sets to networks.

Marko Laakso, Sampsa Hautaniemi

Bioinform., 2010

2009

Advanced analysis and visualization of gene copy number and expression data.

Reija Autio, Matti Saarela, Anna-Kaarina Järvinen, Sampsa Hautaniemi, Jaakko Astola

BMC Bioinform., 2009

Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations.

Reija Autio, Sami Kilpinen, Matti Saarela, Olli-P. Kallioniemi, Sampsa Hautaniemi, Jaakko Astola

BMC Bioinform., 2009

Bioinformatics of gene expression and copy number data integration.

Outi Monni, Sampsa Hautaniemi

Proceedings of the Statistics and Informatics in Molecular Cancer Research., 2009

2008

Fast Gene Ontology based clustering for microarray experiments.

Kristian Ovaska, Marko Laakso, Sampsa Hautaniemi

BioData Min., 2008

2007

Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility.

Sourabh Kharait, Sampsa Hautaniemi, Shan Wu, Akihiro Iwabu, Douglas A. Lauffenburger, Alan Wells

BMC Syst. Biol., 2007

Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays.

Marko Laakso, Sari Tuupanen, Auli Karhu, Rainer Lehtonen, Lauri A. Aaltonen, Sampsa Hautaniemi

Bioinform., 2007

2006

Jointly Analyzing Gene Expression and Copy Number Data in Breast Cancer Using Data Reduction Models.

John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra, Jaakko Astola

IEEE ACM Trans. Comput. Biol. Bioinform., 2006

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks.

Harri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja

Signal Process., 2006

2005

Modeling of signal-response cascades using decision tree analysis.

Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, Douglas A. Lauffenburger

Bioinform., 2005

2004

A strategy for identifying putative causes of gene expression variation in human cancers.

Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Reija Autio, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Anne Kallioniemi, Olli-Pekka Kallioniemi

J. Frankl. Inst., 2004

Optimized LOWESS normalization parameter selection for DNA microarray data.

John A. Berger, Sampsa Hautaniemi, Anna-Kaarina Järvinen, Henrik Edgren, Sanjit K. Mitra, Jaakko Astola

BMC Bioinform., 2004

Comparative Analysis of Gene Expression and DNA Copy Number Data for Pancreatic and Breast Cancers Using an Orthogonal Decomposition.

John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003

Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps.

Sampsa Hautaniemi, Olli Yli-Harja, Jaakko Astola, Päivikki Kauraniemi, Anne Kallioniemi, Maija Wolf, Jimmy Ruiz, Spyro Mousses, Olli-P. Kallioniemi

Mach. Learn., 2003

A novel strategy for microarray quality control using Bayesian networks.

Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Outi Monni

Bioinform., 2003

CGH-Plotter: MATLAB toolbox for CGH-data analysis.

Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi

Bioinform., 2003

Identifying underlying factors in breast cancer using independent component analysis.

John A. Berger, Sampsa Hautaniemi, Henrik Edgren, Outi Monni, Sanjit K. Mitra, Olli Yli-Harja, Jaakko Astola

Proceedings of the NNSP 2003, 2003