Sampsa Hautaniemi

39 papers Journal 34Unranked 4

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics. Bioinform. Kari Lavikka, Altti Ilari Maarala, Jaana Oikkonen, Sampsa Hautaniemi
2024	J	`jnl`	ECCB2024: The 23rd European Conference on Computational Biology. Bioinform. Anu Kukkonen-Macchi, Sampsa Hautaniemi, Katharina F. Heil, Merja Heinäniemi, Lars Juhl Jensen, Sini Junttila, Lukas Käll, Asta Laiho, Peter Maccallum, Matti Nykter, Bengt Persson, Tomi Suomi, Tim Van Den Bossche, Tommi H. Nyrönen, Laura L. Elo
2022	—	`conf`	Image Processing Pipeline to Compute Homologous Recombination Score. ICBET Haswanth Vundavilli, Manuela Tumiati, Sampsa Hautaniemi, Aniruddha Datta, Liisa Kauppi
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`	FUNGI: FUsioN Gene Integration toolset. Bioinform. 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
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`	Dynamic visualization of multi-level molecular data: The Director package in R. Comput. Methods Programs Biomed. Katherine Icay, Chengyu Liu, 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`	PerPAS: Topology-Based Single Sample Pathway Analysis Method. IEEE ACM Trans. Comput. Biol. Bioinform. Chengyu Liu, Rainer Lehtonen, Sampsa Hautaniemi
2016	J	`jnl`	Data integration to prioritize drugs using genomics and curated data. BioData Min. Riku Louhimo, Marko Laakso, Denis Belitskin, Juha Klefström, Rainer Lehtonen, Sampsa Hautaniemi
2016	J	`jnl`	SePIA: RNA and small RNA sequence processing, integration, and analysis. BioData Min. Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
2015	J	`jnl`	Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. Briefings Bioinform. Amjad Alkodsi, Riku Louhimo, Sampsa Hautaniemi
2013	J	`jnl`	Genomic Region Operation Kit for Flexible Processing of Deep Sequencing Data. IEEE ACM Trans. Comput. Biol. Bioinform. Kristian Ovaska, Lauri Lyly, Biswajyoti Sahu, Olli A. Jänne, Sampsa Hautaniemi
2013	—	`conf`	High-performance computing in biomedicine. HPCS Sampsa Hautaniemi, Marko Laakso
2013	J	`jnl`	Identification of genetic markers with synergistic survival effect in cancer. BMC Syst. Biol. Riku Louhimo, Marko Laakso, Tuomas Heikkinen, Susanna Laitinen, Pekka Manninen, Vladimir Rogojin, Minna Miettinen, Carl Blomqvist, Jianjun Liu, Heli Nevanlinna, Sampsa Hautaniemi
2013	J	`jnl`	Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links PLoS Comput. Biol. Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G. Stunnenberg, Sampsa Hautaniemi
2012	J	`jnl`	PINA v2.0: mining interactome modules. Nucleic Acids Res. Mark J. Cowley, Mark Pinese, Karin S. Kassahn, Nic Waddell, John V. Pearson, Sean M. Grimmond, Andrew V. Biankin, Sampsa Hautaniemi, Jianmin Wu
2011	J	`jnl`	CNAmet: an R package for integrating copy number, methylation and expression data. Bioinform. Riku Louhimo, Sampsa Hautaniemi
2010	J	`jnl`	Integrative platform to translate gene sets to networks. Bioinform. Marko Laakso, Sampsa Hautaniemi
2009	J	`jnl`	Advanced analysis and visualization of gene copy number and expression data. BMC Bioinform. Reija Autio, Matti Saarela, Anna-Kaarina Järvinen, Sampsa Hautaniemi, Jaakko Astola
2009	—	`ch.`	Bioinformatics of gene expression and copy number data integration. Statistics and Informatics in Molecular Cancer Research Outi Monni, Sampsa Hautaniemi
2009	J	`jnl`	Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations. BMC Bioinform. Reija Autio, Sami Kilpinen, Matti Saarela, Olli-P. Kallioniemi, Sampsa Hautaniemi, Jaakko Astola
2008	J	`jnl`	Fast Gene Ontology based clustering for microarray experiments. BioData Min. Kristian Ovaska, Marko Laakso, Sampsa Hautaniemi
2007	J	`jnl`	Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays. Bioinform. Marko Laakso, Sari Tuupanen, Auli Karhu, Rainer Lehtonen, Lauri A. Aaltonen, Sampsa Hautaniemi
2007	J	`jnl`	Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. BMC Syst. Biol. Sourabh Kharait, Sampsa Hautaniemi, Shan Wu, Akihiro Iwabu, Douglas A. Lauffenburger, Alan Wells
2006	J	`jnl`	Jointly Analyzing Gene Expression and Copy Number Data in Breast Cancer Using Data Reduction Models. IEEE ACM Trans. Comput. Biol. Bioinform. John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra, Jaakko Astola
2006	J	`jnl`	Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Process. Harri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja
2005	J	`jnl`	Modeling of signal-response cascades using decision tree analysis. Bioinform. Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, Douglas A. Lauffenburger
2004	J	`jnl`	A strategy for identifying putative causes of gene expression variation in human cancers. J. Frankl. Inst. Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Reija Autio, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Anne Kallioniemi, Olli-Pekka Kallioniemi
2004	—	`conf`	Comparative Analysis of Gene Expression and DNA Copy Number Data for Pancreatic and Breast Cancers Using an Orthogonal Decomposition. CSB John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra
2004	J	`jnl`	Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinform. John A. Berger, Sampsa Hautaniemi, Anna-Kaarina Järvinen, Henrik Edgren, Sanjit K. Mitra, Jaakko Astola
2003	J	`jnl`	A novel strategy for microarray quality control using Bayesian networks. Bioinform. Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Outi Monni
2003	J	`jnl`	Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps. Mach. Learn. Sampsa Hautaniemi, Olli Yli-Harja, Jaakko Astola, Päivikki Kauraniemi, Anne Kallioniemi, Maija Wolf, Jimmy Ruiz, Spyro Mousses, Olli-P. Kallioniemi
2003	J	`jnl`	CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinform. Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi
2003	—	`conf`	Identifying underlying factors in breast cancer using independent component analysis. NNSP John A. Berger, Sampsa Hautaniemi, Henrik Edgren, Outi Monni, Sanjit K. Mitra, Olli Yli-Harja, Jaakko Astola