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ORCIDSampsa Hautaniemi
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2020 – today
- 2024
[j33]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:
ECCB2024: The 23rd European Conference on Computational Biology. Bioinform. 40(Supplement_2): ii1-ii3 (2024)- 2022
- [j32]Susanna Holmström, Sampsa Hautaniemi, Antti Häkkinen:
POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching. Bioinform. 38(9): 2474-2480 (2022) - [c4]Haswanth Vundavilli, Manuela Tumiati, Sampsa Hautaniemi
, Aniruddha Datta, Liisa Kauppi:
Image Processing Pipeline to Compute Homologous Recombination Score. ICBET 2022: 51-56 - 2021
- [j31]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) - [j30]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) - [j29]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) - [j28]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:
FUNGI: FUsioN Gene Integration toolset. Bioinform. 37(19): 3353-3355 (2021) - 2020
- [j27]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
- [j26]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
- [j25]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) - [j24]Katherine Icay, Chengyu Liu, Sampsa Hautaniemi:
Dynamic visualization of multi-level molecular data: The Director package in R. Comput. Methods Programs Biomed. 153: 129-136 (2018) - [j23]Chengyu Liu, Rainer Lehtonen, Sampsa Hautaniemi:
PerPAS: Topology-Based Single Sample Pathway Analysis Method. IEEE ACM Trans. Comput. Biol. Bioinform. 15(3): 1022-1027 (2018) - 2016
- [j22]Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi:
SePIA: RNA and small RNA sequence processing, integration, and analysis. BioData Min. 9: 20 (2016) - [j21]Riku Louhimo, Marko Laakso, Denis Belitskin, Juha Klefström, Rainer Lehtonen, Sampsa Hautaniemi:
Data integration to prioritize drugs using genomics and curated data. BioData Min. 9: 21 (2016) - 2015
- [j20]Amjad Alkodsi, Riku Louhimo, Sampsa Hautaniemi:
Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. Briefings Bioinform. 16(2): 242-254 (2015) - 2013
- [j19]Riku Louhimo, Marko Laakso, Tuomas Heikkinen, Susanna Laitinen, Pekka Manninen, Vladimir Rogojin, Minna Miettinen, Carl Blomqvist, Jianjun Liu, Heli Nevanlinna, Sampsa Hautaniemi:
Identification of genetic markers with synergistic survival effect in cancer. BMC Syst. Biol. 7(S-1): S2 (2013) - [j18]Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G. Stunnenberg, Sampsa Hautaniemi:
Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer. PLoS Comput. Biol. 9(6) (2013) - [j17]Kristian Ovaska, Lauri Lyly, Biswajyoti Sahu, Olli A. Jänne, Sampsa Hautaniemi:
Genomic Region Operation Kit for Flexible Processing of Deep Sequencing Data. IEEE ACM Trans. Comput. Biol. Bioinform. 10(1): 200-206 (2013) - [c3]Sampsa Hautaniemi, Marko Laakso:
High-performance computing in biomedicine. HPCS 2013: 233 - 2012
- [j16]Mark J. Cowley, Mark Pinese, Karin S. Kassahn, Nic Waddell, John V. Pearson, Sean M. Grimmond, Andrew V. Biankin, Sampsa Hautaniemi, Jianmin Wu:
PINA v2.0: mining interactome modules. Nucleic Acids Res. 40(Database-Issue): 862-865 (2012) - 2011
- [j15]Riku Louhimo, Sampsa Hautaniemi:
CNAmet: an R package for integrating copy number, methylation and expression data. Bioinform. 27(6): 887-888 (2011) - 2010
- [j14]Marko Laakso, Sampsa Hautaniemi:
Integrative platform to translate gene sets to networks. Bioinform. 26(14): 1802-1803 (2010)
2000 – 2009
- 2009
- [j13]Reija Autio, Sami Kilpinen, Matti Saarela, Olli-P. Kallioniemi, Sampsa Hautaniemi, Jaakko Astola:
Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations. BMC Bioinform. 10(S-1) (2009) - [j12]Reija Autio, Matti Saarela, Anna-Kaarina Järvinen, Sampsa Hautaniemi, Jaakko Astola:
Advanced analysis and visualization of gene copy number and expression data. BMC Bioinform. 10(S-1) (2009) - [p1]Outi Monni, Sampsa Hautaniemi:
Bioinformatics of gene expression and copy number data integration. Statistics and Informatics in Molecular Cancer Research 2009: 78-101 - 2008
- [j11]Kristian Ovaska, Marko Laakso, Sampsa Hautaniemi:
Fast Gene Ontology based clustering for microarray experiments. BioData Min. 1 (2008) - 2007
- [j10]Marko Laakso, Sari Tuupanen, Auli Karhu, Rainer Lehtonen, Lauri A. Aaltonen, Sampsa Hautaniemi:
Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays. Bioinform. 23(15): 1952-1961 (2007) - [j9]Sourabh Kharait, Sampsa Hautaniemi, Shan Wu, Akihiro Iwabu, Douglas A. Lauffenburger, Alan Wells:
Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. BMC Syst. Biol. 1: 9 (2007) - 2006
- [j8]Harri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja:
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Process. 86(4): 814-834 (2006) - [j7]John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra, Jaakko Astola:
Jointly Analyzing Gene Expression and Copy Number Data in Breast Cancer Using Data Reduction Models. IEEE ACM Trans. Comput. Biol. Bioinform. 3(1): 2-16 (2006) - 2005
- [j6]Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, Douglas A. Lauffenburger:
Modeling of signal-response cascades using decision tree analysis. Bioinform. 21(9): 2027-2035 (2005) - 2004
- [j5]John A. Berger, Sampsa Hautaniemi, Anna-Kaarina Järvinen, Henrik Edgren, Sanjit K. Mitra, Jaakko Astola:
Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinform. 5: 194 (2004) - [j4]Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Reija Autio, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Anne Kallioniemi, Olli-Pekka Kallioniemi:
A strategy for identifying putative causes of gene expression variation in human cancers. J. Frankl. Inst. 341(1-2): 77-88 (2004) - [c2]John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra:
Comparative Analysis of Gene Expression and DNA Copy Number Data for Pancreatic and Breast Cancers Using an Orthogonal Decomposition. CSB 2004: 584-585 - 2003
- [j3]Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi:
CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinform. 19(13): 1714-1715 (2003) - [j2]Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Outi Monni:
A novel strategy for microarray quality control using Bayesian networks. Bioinform. 19(16): 2031-2038 (2003) - [j1]Sampsa Hautaniemi, Olli Yli-Harja, Jaakko Astola, Päivikki Kauraniemi, Anne Kallioniemi, Maija Wolf, Jimmy Ruiz, Spyro Mousses, Olli-P. Kallioniemi:
Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps. Mach. Learn. 52(1-2): 45-66 (2003) - [c1]John A. Berger, Sampsa Hautaniemi, Henrik Edgren, Outi Monni, Sanjit K. Mitra, Olli Yli-Harja, Jaakko Astola:
Identifying underlying factors in breast cancer using independent component analysis. NNSP 2003: 81-90
Coauthor Index
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