Sampsa Hautaniemi

Publication Activity (10 Years)

Years Active: 2003-2022
Publications (10 Years): 13

Top Topics

Parameter Tuning

Biologically Meaningful

Tumor Segmentation

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Briefings Bioinform.

Publications

Haswanth Vundavilli, Manuela Tumiati, Sampsa Hautaniemi, Aniruddha Datta, Liisa Kauppi
Image Processing Pipeline to Compute Homologous Recombination Score. ICBET (2022)
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) (2021)
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)
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) (2021)
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) (2021)
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) (2020)
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) (2019)
Katherine Icay, Chengyu Liu, Sampsa Hautaniemi
Dynamic visualization of multi-level molecular data: The Director package in R. Comput. Methods Programs Biomed. 153 (2018)
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) (2018)
Chengyu Liu, Rainer Lehtonen, Sampsa Hautaniemi
PerPAS: Topology-Based Single Sample Pathway Analysis Method. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (3) (2018)
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 (2016)
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 (2016)
Amjad Alkodsi, Riku Louhimo, Sampsa Hautaniemi
Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. Briefings Bioinform. 16 (2) (2015)
Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G. Stunnenberg, Sampsa Hautaniemi
to Poor Survival in Breast Cancer. PLoS Comput. Biol. 9 (6) (2013)
Sampsa Hautaniemi, Marko Laakso
High-performance computing in biomedicine. HPCS (2013)
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) (2013)
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) (2013)
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) (2012)
Riku Louhimo, Sampsa Hautaniemi
CNAmet: an R package for integrating copy number, methylation and expression data. Bioinform. 27 (6) (2011)
Marko Laakso, Sampsa Hautaniemi
Integrative platform to translate gene sets to networks. Bioinform. 26 (14) (2010)
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)
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)
Kristian Ovaska, Marko Laakso, Sampsa Hautaniemi
Fast Gene Ontology based clustering for microarray experiments. BioData Min. 1 (2008)
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 (2007)
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) (2007)
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) (2006)
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) (2006)
Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, Douglas A. Lauffenburger
Modeling of signal-response cascades using decision tree analysis. Bioinform. 21 (9) (2005)
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 (2004)
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)
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) (2004)
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)
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) (2003)
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) (2003)
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) (2003)