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Tommi Jaakkola

Research Profile

Concepts & Ideas

Procedures

Devices

Oligonucleotide Array Sequence Analysis

Chemicals & Drugs

Occupations

Computational Biology

Living Beings

Saccharomyces cerevisiae

Activities & Behaviors

Genes & Molecular Sequences

Genome, Fungal

Physiology

Co-author Network

Publications

TOP 3
Tatsunori Hashimoto; Tommi S Jaakkola; Esteban O Mazzoni; Richard Sherwood; Hynek Wichterle; David Gifford
Lineage-based identification of cellular states and expression programs.
Yuchun Guo; Georgios Papachristoudis; Robert C Altshuler; Georg K Gerber; Tommi S Jaakkola; David K Gifford; Shaun Mahony
Discovering homotypic binding events at high spatial resolution.
Georg Gerber; Robin D Dowell; Tommi S Jaakkola; David K Gifford
Automated discovery of functional generality of human gene expression programs.

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All Publications

2012: Tatsunori Hashimoto; Tommi S Jaakkola; Esteban O Mazzoni; Richard Sherwood; Hynek Wichterle; David Gifford
Lineage-based identification of cellular states and expression programs.
Bioinformatics (Oxford, England) 2012;28(12):i250-7.
2010: Yuchun Guo; Georgios Papachristoudis; Robert C Altshuler; Georg K Gerber; Tommi S Jaakkola; David K Gifford; Shaun Mahony
Discovering homotypic binding events at high spatial resolution.
Bioinformatics (Oxford, England) 2010;26(24):3028-34.
2007: Georg Gerber; Robin D Dowell; Tommi S Jaakkola; David K Gifford
Automated discovery of functional generality of human gene expression programs.
PLoS computational biology 2007;3(8):e148.
2006: Yuan Qi; Alex Rolfe; Kenzie D Macisaac; Georg Gerber; Dmitry K Pokholok; Julia Zeitlinger; Timothy Danford; Robin D Dowell; Ernest Fraenkel; Tommi S Jaakkola; Richard A Young; David K Gifford
High-resolution computational models of genome binding events.
Nature biotechnology 2006;24(8):963-70.
2006: Yuan Qi; Patrycja E Missiuro; Ashish Kapoor; Craig P Hunter; Tommi S Jaakkola; David K Gifford; Hui Ge
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo.
Bioinformatics (Oxford, England) 2006;22(14):e417-23.
2006: Chen-Hsiang Yeang; Tommi S Jaakkola
Modeling the combinatorial functions of multiple transcription factors.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(2):463-80.
2005: Chen-Hsiang Yeang; H Craig Mak; Scott McCuine; Christopher T Workman; Tommi S Jaakkola; Trey Ideker
Validation and refinement of gene-regulatory pathways on a network of physical interactions.
Genome biology 2005;6(7):R62.
2004: Chen-Hsiang Yeang; Trey Ideker; Tommi S Jaakkola
Physical network models.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(2-3):243-62.
2003: Ziv Bar-Joseph; Georg Gerber; Tong Ihn Lee; Nicola J Rinaldi; Jane Y Yoo; François Robert; D Benjamin Gordon; Ernest Fraenkel; Tommi S Jaakkola; Richard A Young; David K Gifford
Computational discovery of gene modules and regulatory networks.
Nature biotechnology 2003;21(11):1337-42.
2003: Ziv Bar-Joseph; Georg Gerber; Itamar Simon; David K Gifford; Tommi S Jaakkola
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(18):10146-51.
2003: Ziv Bar-Joseph; Erik D Demaine; David K Gifford; Nathan Srebro; Angèle M Hamel; Tommi S Jaakkola
K-ary clustering with optimal leaf ordering for gene expression data.
Bioinformatics (Oxford, England) 2003;19(9):1070-8.
2003: Ziv Bar-Joseph; Georg Gerber; David K Gifford; Tommi S Jaakkola; Itamar Simon
Continuous representations of time-series gene expression data.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(3-4):341-56.
2002: Karen Sachs; David Gifford; Tommi S Jaakkola; Peter Sorger; Douglas A Lauffenburger
Bayesian network approach to cell signaling pathway modeling.
Science's STKE : signal transduction knowledge environment 2002;2002(148):pe38.
2002: Alexander J Hartemink; David K Gifford; Tommi S Jaakkola; Richard A Young
Combining location and expression data for principled discovery of genetic regulatory network models.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():437-49.
2001: Itamar Simon; J Barnett; Nancy M Hannett; Christopher T Harbison; Nicola J Rinaldi; Thomas L Volkert; John J Wyrick; Julia Zeitlinger; David K Gifford; Tommi S Jaakkola; Richard A Young
Serial regulation of transcriptional regulators in the yeast cell cycle.
Cell 2001;106(6):697-708.
2001: Ziv Bar-Joseph; David K Gifford; Tommi S Jaakkola
Fast optimal leaf ordering for hierarchical clustering.
Bioinformatics (Oxford, England) 2001;17 Suppl 1():S22-9.
2001: Alexander J Hartemink; David K Gifford; Tommi S Jaakkola; Richard A Young
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():422-33.
2000: Tommi S Jaakkola; Mark Diekhans; David Haussler
A discriminative framework for detecting remote protein homologies.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):95-114.
1999: Tommi S Jaakkola; Mark Diekhans; David Haussler
Using the Fisher kernel method to detect remote protein homologies.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():149-58.