Niina Haiminen
| Researcher, PhD | |
|
Computational Genomics Group USA |
 |
Research Interests:
- Algorithm design and analysis
- Computational biology
- Data mining
- Cacao genome sequencing: cacaogenomedb.org
Teaching:
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Scientific writing group instructor (in Finnish), Fall 2007
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Information retrieval methods course assistant, Spring 2007
- Computational complexity course assistant, Fall 2005
- Approximation algorithms course assistant, Fall 2004
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Opettajatuutorointi, Syksy 2005
Publications etc.
- N Haiminen, D N Kuhn, L Parida, I Rigoutsos:
Evaluation of Methods for de novo Genome Assembly from High-throughput Sequencing Reads Reveals Dependencies that Affect the Quality of the Results.
PLoS ONE, in press. - Kallio, Vuokko, Ojala, Haiminen, Mannila:
Randomization techniques for assessing the significance of gene periodicity results.
BMC Bioinformatics 12:330, 2011. [online, open access] - F A Feltus, C A Saski, K Mockaitis, N Haiminen, L Parida, Z Smith, J Ford, M E Staton, S P Ficklin, B P Blackmon, C-H Cheng, R J Schnell, D N Kuhn and J-C Motamayor:
Sequencing of a QTL-rich Region of the Theobroma cacao Genome using Pooled BACs and the Identification of Trait Specific Candidate Genes.
BMC Genomics 12:379, 2011. [online, open access] - Laxmi Parida, Niina Haiminen: Discovering evolutionary patterns from gene order.
In Evolutionary genomics: statistical and computational methods (in series Methods in Molecular Biology), Springer Humana, in press. - Niina Haiminen, F. Alex Feltus, Laxmi Parida: Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.
BMC Genomics 12:194, 2011. [online, open access] - Aristotelis Tsirigos, Niina Haiminen, Erhan Bilal: Genomic Regions Tools for High-throughput Analytics in Genomics.
IBM Research Report RC25125, 2011. [link] - Presentation at PAG XIV (Jan 2011) on Whole-Genome Sequencing And Assembly Simulation With High-Throughput Technologies: talk abstract
- Presentation at ECCB10, Ghent, Belgium (Sept 2010): How robust are NGS whole-genome assemblies: A case study with plant genomes.
- Arvas, Haiminen, Smit, Rautio, Vitikainen, Wiebe, Martinez, Chee, Kunkel, Sanche, Nelson, Pakula, Saloheimo, Penttila, Kivioja:
Detecting novel genes with sparse arrays.
Gene 467:1-2, pp. 41-51, 2010. [link] - Presentation at PAG-XVIII (Jan 2010) on Genome Assembly Validation: talk abstract and poster abstract
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Markus Ojala, Niko Vuokko, Aleksi Kallio, Niina Haiminen, Heikki Mannila:
Randomization Methods for Assessing Data Analysis Results on Real-Valued Matrices.
Statistical Analysis and Data Mining 2:4, pp. 209-230, 2009. [link] -
Niina Haiminen, Heikki Mannila, Evimaria Terzi:
Determining significance of pairwise co-occurrences of events in bursty sequences.
BMC Bioinformatics 9:336, 2008. [online, open access] -
Niina Haiminen, Heikki Mannila:
Evaluation of BIC and cross validation for model selection on sequence segmentations.
International Journal of Data Mining and Bioinformatics (IJDMB) 4:6, pp. 675-700, 2010. -
Niina Haiminen:
Mining Sequential Data &ndash in Search of Segmental Structures.
PhD Thesis, Department of Computer Science, University of Helsinki, 60+78 pp., March 2008. [pdf][abstracts][printed copies available upon request] -
Markus Ojala, Niko Vuokko, Aleksi Kallio, Niina Haiminen, Heikki Mannila:
Randomization of real-valued matrices for assessing
the significance of data mining results.
Proc. SIAM Conference on Data Mining (SDM08), pp. 494-505, 2008. [pdf] -
Niina Haiminen, Aristides Gionis, Kari Laasonen:
Algorithms for unimodal segmentation with applications to unimodality detection.
Knowledge and Information Systems 14:1, pp. 39-57, 2008. [online via SpringerLink]
- an extended versio of -
Niina Haiminen, Aristides Gionis: Unimodal segmentation of sequences.
Proc. Fourth IEEE International Conference on Data Mining (ICDM04), pp.106-113, 2004. [.ps] [pdf] -
Niina Haiminen, Heikki Mannila, Evimaria Terzi:
Comparing segmentations by applying randomization techniques.
BMC Bioinformatics 8:171, 2007. [online, open access] -
Niina Haiminen, Heikki Mannila:
Discovering isochores by least-squares optimal segmentation.
Gene 394:1-2, pp. 53-60, 2007. [online via ScienceDirect] -
Ella Bingham, Aristides Gionis, Niina Haiminen, Heli Hiisilä, Heikki Mannila, Evimaria Terzi:
Segmentation and dimensionality reduction.
Proc. SIAM Conference on Data Mining (SDM06), pp. 372-383, 2006. [pdf] Matlab codes
- Justin Lessler, Niina Haiminen, James Kaufman, Donald Burke:
A Computational Model of Evolvable Viruses in Populations: System and Applications.
Poster in DIMACS Workshop on Facing the Challenge of Infectious Diseases in Africa: The Role of Mathematical Modeling, 2006. [workshop link]
- Niina Haiminen: Discovering recurrent sources in genomic sequences. MSc Thesis, Department of Computer Science, University of Helsinki, 66 pp., March 2004. [link]
Other:
- PhD degree, May 2008
- Reviewed papers for the Journal of Discrete Algorithms, Genome Biology, BMC Bioinformatics, IEE TCBB, Knowledge and Information Systems, and KDD & PKDD & SDM conferences
- Board member in Bioinformatiikan seura (Finnish Society for Bioinformatics), 2006
- Internship at IBM Almaden Research Center, San Jose, CA, USA, June - Sept 2006
- Internship at IBM T.J. Watson Research Center, New York, NY, USA, May - Aug 2005
- Student at ComBi graduate school, Jan 2005 - May 2008
- ICDM Student travel award, Nov 2004
- MSc degree, May 2004
- Employed at HIIT, May 2003 - Sept 2008
- Studied Dutch (Nederlands) in Tilburg, the Netherlands, Jan - July 1999
- Enrolled at University of Helsinki, Sept 1998 - May 2008