Bioinformatics (BI)
Key persons
J. Vilo, M. Kull
Postdoc
B. Rajashekar
BIIT joint research group of
UT, Quretec and the Estonian Biocenter
Publications 2008
- P. Adler, J. Reimand, J. Jänes, R. Kolde, H. Peterson,
J. Vilo. KEGGanim: pathway animations for high-throughput
data. Bioinformatics, v. 24, n. 4, pp. 588-590, 2008. doi:
10.1093/bioinformatics/btm581 (WOS:
000253246300023)
- O. L. Griffith, S. B. Montgomery, B. Bernier, B. Chu, K.
Kasaian, S. Aerts, S. Mahony, M. C. Sleumer, M. Bilenky, M.
Haeussler, M. Griffith, S. M. Gallo, B. Giardine, B. Hooghe, P.
Van Loo, E. Blanco, A. Ticoll, S. Lithwick, E. Portales-Casamar,
I. J. Donaldson, G. Robertson, C. Wadelius, P. De Bleser, D.
Vlieghe, M. S. Halfon, W. Wasserman, R. Hardison, C. M. Bergman,
S. J. M. Jones, The Open Regulatory Annotation Consortium (H.
Peterson and P. Adler are part of the consortium). ORegAnno: an
open-access community-driven resource for regulatory annotation.
Nucleic Acids Res., v. 36, suppl. 1 (database issue),
pp. D107-D113, 2008. doi:
10.1093/nar/gkm967 (WOS:
000252545400020)
- M. Jäger, L. Kamm, D. Krushevskaja, H.-A. Talvik, J.
Veldemann, A. Vilgota, J. Vilo. Flexible database platform for
biomedical research with multiple user interfaces and a universal
query engine. In H.-M. Haav, A. Kalja, eds., Proc. of 8th
Int. Baltic Conf. on Databases and Information Systems, Baltic
DB&IS 2008 (Tallinn, June 2008), pp. 279-287. Tallinn Univ. of
Techn., 2008. (WOS: 000258025100023)
- M. Kull, J. Vilo. Fast approximate hierarchical clustering using
similarity heuristics. BioData Mining, v. 1, article 9, 25 pp.,
2008. doi:
10.1186/1756-0381-1-9
- O. Okun, H. Priisalu. Ensembles of nearest neighbors for gene
expression based cancer classification. In O. Okun, G. Valentini,
eds., Supervised and Unsupervised Ensemble Methods and Their
Applications, v. 126 of Studies in Comput. Intell.,
pp. 115-134. Springer, 2008. doi:
10.1007/978-3-540-78981-9_6
- O. Okun, H. Priisalu. Ensembles of k-nearest neighbors and
dimensionality reduction. In Proc. of 2008 Int. Joint Conf. on
Neural Networks, IJCNN 2008 (Hong Kong, June 2008),
pp. 2032-2039. IEEE, 2008. doi:
10.1109/ijcnn.2008.4634077 (WOS:
000263827201073)
- O. Okun, H. Priisalu. Lowering uncertainty of cancer
classification. In L. Magdalena, M. Ojeda-Aciego, J. L. Verdegay,
eds., Proc. of 12th Int. Conf. on Information Processing and
Management of Uncertainty in Knowledge Based Systems, IPMU 2008
(Malaga, June 2008), pp. 543-550. 2008. article
at conference website
- J. Reimand, L. Tooming, H. Peterson, P. Adler, J. Vilo.
GraphWeb: mining heterogeneous biological networks for gene modules
with functional significance, Nucleic Acids Res., v. 36,
suppl. 2 (web server issue), pp. W452-W459, 2008. doi:
10.1093/nar/gkn230 (WOS:
000258142300083)
- F. Rinaldi, T. Kappeler, K. Kaljurand, G. Schneider, M. Klenner,
S. Clematide, M. Hess, J.-M. von Allmen, P. Parisot, M. Romacker,
T. Vachon. OntoGene in BioCreative II. Genome Biol., v. 9,
suppl. 2, article S13, 2008. doi:
10.1186/gb-2008-9-s2-s13 (WOS:
000278173900013)
- A. Tkachenko, K. Tretjakov, P. Adler, J. Vilo. Text mining for
automatic annotation of microarray experiment clusters. In H.-M. Haav,
A. Kalja, eds., Proc. of 8th Int. Baltic Conf. on Databases and
Information Systems, Baltic DB&IS 2008 (Tallinn, June 2008),
pp. 423-426. Tallinn Univ. of Techn., 2008. (WOS: 000258025100038)
Publications 2009
- P. Adler, R. Kolde, M. Kull, A. Tkachenko, H. Peterson,
J. Reimand, J. Vilo. Mining for coexpression across hundreds of
datasets using novel rank aggregation and visualisation
methods. Genome Biol., v. 10, n. 12, article R139, 2009. doi:
10.1186/gb-2009-10-12-r139 (WOS: 000274289000009)
- P. Adler, H. Peterson, P. Agius, J. Reimand, J. Vilo. Ranking
genes by their co-expression to subsets of pathway members. Ann. of
New York Acad. of Sci., v. 1158, pp. 1-13, 2009. doi:
10.1111/j.1749-6632.2008.03747.x (WOS: 000265650800001)
- M. Jäger, L. Kamm, D. Krushevskaja, H.-A. Talvik, J. Veldemann,
A. Vilgota, J. Vilo. Flexible database platform for biomedical
research with multiple user interfaces and a universal query
engine. In H.-M. Haav, A. Kalja, eds. Databases and Information
Systems V, v. 187 of Frontiers of Artificial Intelligence and
Applications, pp. 301-310. IOS Press, 2009. doi:
10.3233/978-1-58603-939-4-301 (WOS:
000273295400025)
- G. Koscielny, V. L. Texier, C. Gopalakrishnan, V. Kumanduri, J. J.
Riethoven, F. Nardone, E. Stanley, C. Fallsehr, O. Hofmann, M. Kull,
E. Harrington, S. Boué, E. Eyras, M. Plass, F. Lopez, W. Ritchie,
V. Moucadel, T. Ara, H. Pospisil, A. Herrmann, J. G. Reich,
R. Guigó, P. Bork, M. V. Doeberitz, J. Vilo, W. Hide, R. Apweiler,
T. A. Thanaraj, D. Gautheret. ASTD: the alternative splicing and
transcript diversity database. Genomics, v. 93, n. 3,
pp. 213-220, 2009. doi:
10.1016/j.ygeno.2008.11.003 (WOS: 000263901000004)
- D. Krushevskaya, H. Peterson, J. Reimand, M. Kull,
J. Vilo. VisHiC - hierarchical functional enrichment analysis of
microarray data. Nucleic Acids Res., v. 37, suppl. 2 (web
server issue), pp. W587-W592, 2009. doi:
10.1093/nar/gkp435 (WOS: 000267889100102)
- O. Okun, H. Priisalu. Dataset complexity in gene expression based
cancer classification using ensembles of k-nearest
neighbors. Artif. Intell. in Medicine, v. 45, n. 2,
pp. 151-162, 2009. doi:
10.1016/j.artmed.2008.08.004 (WOS:
000264946700007)
- O. Okun, G. Valentini, H. Priisalu. Exploring the link between
bolstered classification error and dataset complexity for gene
expression based cancer classification. In T. Maeda, ed., New
Signal Processing Research, pp. 249-278. Nova Publishers,
2009.
- H. Schulz, R. Kolde, P. Adler, I. Aksoy, K. Anastassiadis,
M. Bader, N. Billon, H. Boeuf, P. Y. Bourillot, F. Buchholz, C. Dani,
M. X. Doss, L. Forrester, M. Gitton, D. Henrique, J. Hescheler,
H. Himmelbauer, N. Hübner, E. Karantzali, A. Kretsovali, S. Lubitz,
L. Pradier, M. Rai, J. Reimand, A. Rolletschek, A. Sachinidis,
P. Savatier, F. Stewart, M. P. Storm, M. Trouillas, J. Vilo,
M. J. Welham, J. Winkler, A. M. Wobus, A. K. Hatzopoulos, Functional
Genomics in Embryonic Stem Cells Consortium. The FunGenES database: a
genomics resource for mouse embryonic stem cell
differentiation. PLoS ONE 2009, v. 4, n. 9, article e6804. doi:
10.1371/journal.pone.0006804 (WOS:
000269522900003)
- M. P. Storm, B. Kumpfmüller, B. Thompson, R. Kolde, J. Vilo,
O. Hummel, H. Schulz, M. J. Welham. Characterization of the
phosphoinositide 3-kinase-dependent transcriptome in murine embryonic
stem cells: identification of novel regulators of
pluripotency. Stem Cells, v. 27, n. 4, pp. 764-775, 2009. doi: 10.1002/stem.3 (WOS: 000265529400003)
- M. Trouillas, C. Saucourt, B. Guillotin, X. Gauthereau, L. Ding,
F. Buchholz, M.-X. Doss, A. Sachinidis, J. Hescheler, O. Hummel,
N. Huebner, R. Kolde, J. Vilo, H. Schultz, H. Boeuf. Three
LIF-dependent signatures and gene clusters with atypical expression
profiles, identified by transcriptome studies in mouse ES cells and
early derivatives. BMC Genomics, v. 10, article 73, 2009. doi:
10.1186/1471-2164-10-73 (WOS:
000265790300001)
- T. Vooder, K. Välk, P. Palta, R. Kolde, A. Metspalu. Parallel
comparison of NSCLC CNV, survival and gene expression profiles in
Estonian population. J. of Thoracic Oncology, v. 4, n. 9,
suppl. 1, p. S932, 2009. doi:
10.1097/jto.0b013e3181b9c77e (WOS:
000269496002706)
Publications 2010
- S. Altmäe, J. Reimand, J. Vilo, O. Hovatta, A. Stavreus-Evers,
A. Salumets. Embryo-endometrium interactions at the time of
implantation. Fertility and Sterility, v. 94, n. 4, suppl. 1,
pp. S87-S87, 2010. doi:
10.1016/j.fertnstert.2010.07.334 (WOS:
000281441000294)
- N. Billon, R. Kolde, J. Reimand, M. C. Monteiro, M. Kull,
H. Peterson, K. Tretyakov, P. Adler, B. Wdziekonski, J. Vilo,
C. Dani. Comprehensive transcriptome analysis of mouse embryonic stem
cell adipogenesis unravels new processes of adipocyte
development. Genome Biol., v. 11, n. 8, article R80, 2010. doi:
10.1186/gb-2010-11-8-r80 (WOS:
000283777600001)
- M. X. Doss, V. Wagh, H. Schulz, M. Kull, R. Kolde, K. Pfannkuche,
T. Nolden, H. Himmelbauer, J. Vilo, J. Hescheler,
A. Sachinidis. Global transcriptomic analysis of murine embryonic stem
cell-derived brachyury+ (T) cells. Genes to Cells, v. 15, n. 3,
pp. 209-228, 2010. doi:
10.1111/j.1365-2443.2010.01390.x (WOS:
000275205600005)
- M. Jung, H. Peterson, L. Chavez, P. Kahlem, H. Lehrach, J. Vilo,
J. Adjaye. A data integration approach to mapping OCT4 gene regulatory
networks operative in embryonic stem cells and embryonal carcinoma
cells. PLoS ONE, v. 5, n. 5, article e10709, 2010. doi:
10.1371/journal.pone.0010709 (WOS:
000278017400009)
- P. B. Kuegler, B. Zimmer, T. Waldmann, B. Baudis, S. Ilmjärv,
J. Hescheler, P. Gaughwin, P. Brundin, W. Mundy, A. K. Bal-Price,
A. Schrattenholz, K. H. Krause, C. van Thriel, M. S. Rao, S. Kadereit,
M. Leist. Markers of murine embryonic and neural stem cells, neurons
and astrocytes: reference points for developmental neurotoxicity
testing. Altex, v. 27, n. 1/10, pp. 16-42, 2010. article
at publisher's website (WOS:
000278003000003)
- M. Kull, K. Tretyakov, J. Vilo An evolutionary model of DNA
substring distribution. In T. Elomaa, H. Mannila, P. Orponen, eds.,
Algorithms and Applications: Essays Dedicated to Esko Ukkonen on
the Occasion of His 60th Birthday, v. 6060 of Lect. Notes in
Comput. Sci., pp. 147-157. Springer, 2010. doi:
10.1007/978-3-642-12476-1_10 (WOS:
000280127600010)
- M. Lõoke, J. Reimand, T. Sedman, J. Sedman, L. Järvinen, S.
Värv, K. Peil, K. Kristjuhan, J. Vilo, A. Kristjuhan. Relicensing of
transcriptionally inactivated replication origins in budding
yeast. J. of Biol. Chem., v. 285, n. 51, pp. 40004-40011,
2010. doi:
10.1074/jbc.m110.148924(WOS:
000285185500045)
- E. Maron, K. Kallassalu, A. Tammiste, R. Kolde, J. Vilo, I. Tõru,
V. Vasar, J. Shlik, A. Metspalu. Peripheral gene expression profiling
of CCK-4-induced panic in healthy subjects. Amer. J. of
Med. Genet. B: Neuropsychiatr. Genet., v. 153B, n. 1, pp. 269-274,
2010. doi:
10.1002/ajmg.b.30898 (WOS:
000273440500031)
- A. Rebane, L. Tserel, K. Kisand, L. Backhoff, T. Runnel,
R. Kolde, H. Peterson, J. Vilo, P. Peterson. Balanced expression of
miRNA-S secures differentiation and maturation of human blood monocyte
derived dendritic cells. Scand. J. of Immunol., v. 71, n. 6,
pp. 512-513, 2010. doi:
10.1111/j.1365-3083.2010.02398.x (WOS:
000277608600080)
- J. Reimand, J. M. Vaquerizas, A. E. Todd, J. Vilo,
N. M. Luscombe. Comprehensive reanalysis of transcription factor
knockout expression data in Saccharomyces cerevisiae reveals many new
targets. Nucleic Acids Research, v. 38, n. 14, pp. 4768-4777,
2010. doi:
10.1093/nar/gkq232 (WOS:
000280922400027)
- F. Rinaldi, G. Schneider, K. Kaljurand, S. Clematide, T. Vachon,
M. Romacker. OntoGene in BioCreative II.5. IEEE/ACM Trans. on
Comput. Biol. and Bioinform., v. 7, n. 3, pp. 472-480, 2010. doi:
10.1109/tcbb.2010.50 (WOS:
000280494300009)
- F. S. Roque, L. Slaughter, A. Tkatšenko. A comparison of
several key information visualization systems for secondary use of
electronic health record content. In Proc. of NAACL HLT 2010 2nd
Louhi Wksh. on Text and Data Mining of Health Documents (Los Angeles,
CA, June 2010), pp. 76-83. ACL, 2010. article at
publisher's website
- L. Tserel, R. Kolde, A. Rebane, K. Kisand, T. Org, H. Peterson,
J. Vilo, P. Peterson. Gene expression and epigenetic changes in
differentiation of human macrophages and dendritic
cells. Scand. J. of Immunol., v. 71, n. 6, p. 526, 2010. doi:
10.1111/j.1365-3083.2010.02398.x (WOS: 000277608600108)
- L. Tserel, R. Kolde, A. Rebane, K. Kisand, T. Org, H. Peterson,
J. Vilo, P. Peterson. Genome-wide promoter analysis of histone
modifications in human monocyte-derived antigen presenting
cells. BMC Genomics, v. 11, article 642, 2010. doi:
10.1186/1471-2164-11-642 (WOS:
000284880400001)
- T. Vooder, K. Välk, R. Kolde, R. Roosipuu, J. Vilo,
A. Metspalu. Gene expression-based approaches in differentiation of
metastases and second primary tumour. Case Rep. in Oncol.,
v. 3, n. 2, pp. 255-261, 2010. doi:
10.1159/000318010
- K. Välk, T. Vooder, R. Kolde, M.-A. Reintam, C. Petzold, J. Vilo,
A. Metspalu. Gene expression profiles of non-small cell lung cancer:
survival prediction and new biomarkers. Oncology, v. 79,
n. 3-4, pp. 283-292, 2010. doi:
10.1159/000322116 (WOS:
000289108100019)
Publications 2011
- C. A. Hundahl, H. Luuk, S. Ilmjärv, B. Falktoft, Z. Raida,
J. Vikesaa, L. Friis-Hansen, A. Hay-Schmidt. Neuroglobin-deficiency
exacerbates Hif1A and c-FOS response, but does not affect neuronal
survival during severe hypoxia in vivo. PLoS ONE, v. 6, n. 12,
article e28160, 2011. doi:
10.1371/journal.pone.0028160
- J. Reimand, T. Arak, J. Vilo. g:Profiler - a web
server for functional interpretation of gene lists (2011
update). Nucleic Acids Research, v. 39, suppl. 2,
pp. W307-W315, 2011. doi:
10.1093/nar/gkr378 (WOS:
000292325300050)
- M. Peters, S. Altmäe, J. Reimand, T. Laisk, M. Saare, O. Hovatta,
R. Kolde, J. Vilo, A. Stavreus-Evers, A. Salumets. Human
embryo-endometrium interactions at the time of implantation. Human
Reproduction, v. 26, suppl. 1, p. I216, 2011. doi:
10.1093/humrep/26.s1.80 (WOS:
000294450500541)
- F. Rinaldi, K. Kaljurand, R. Sætre. Terminological
resources for text mining over biomedical scientific
literature. Artif. Intell. in Medicine, v. 52, n. 2,
pp. 107-114, 2011. doi:
10.1016/j.artmed.2011.04.011 (WOS:
000293101100007)
- K. Tretyakov, A. Armas-Cervantes, L. García-Bañuelos,
J. Vilo, M. Dumas. Fast fully dynamic landmark-based
estimation of shortest path distances in very large graphs. In
Proc. of Int. Conf. on Information and Knowledge Management, CIKM
2011 (Glasgow, Oct. 2011), pp. 1785-1794. ACM Press, 2011. doi:
10.1145/2063576.2063834
- K. Tretyakov, S. Laur, J. Vilo. G = MAT: linking transcription
factor expression and DNA binding data. PLoS ONE, v. 6, n. 1,
article e14559, 2011. doi:
10.1371/journal.pone.0014559 (WOS:
000286834300001)
- L. Tserel, T. Runnel, K. Kisand, M. Pihlap, L. Bakhoff, R. Kolde,
H. Peterson, J. Vilo, P. Peterson, A. Rebane. MicroRNA expression
profiles of human blood monocyte-derived dendritic cells and
macrophages reveal miR-511 as putative positive regulator of toll-like
receptor 4. J. of Biol. Chem., v. 286, n. 30, pp. 26487-26495,
2011. doi:
10.1074/jbc.m110.213561 (WOS:
000286834300001)
- U. Võsa, T. Vooder, R. Kolde, K. Fischer, K. Välk,
N. Tõnisson, R. Roosipuu, J. Vilo, A. Metspalu,
T. Annilo. Identification of miR-374a as a prognostic marker for
survival in patients with early-stage nonsmall cell lung
cancer. Genes, Chromosomes and Cancer, v. 50, n. 10,
pp. 812-822, 2011. doi:
10.1002/gcc.20902 (WOS:
000294177300006)
- K. Välk, T. Vooder, R. Kolde, R. Roosipuu, J. Vilo,
A. Metspalu. Gene expression-based approaches in differentiation of
metastases and second primary tumour. J. of Thoracic Oncology,
v. 6, n. 6, suppl. 2, pp. S1055-S1056, 2011. doi:
10.1097/01.jto.0000399290.73317.eb (WOS:
000291769800223)
Publications 2012
- S. Altmäe, J. Reimand, O. Hovatta, P. Zhang, J. Kere,
T. Laisk, M. Saare, M. Peters, J. Vilo, A. Stavreus-Evers,
A. Salumets. Research resource: interactome of human embryo
implantation: identification of gene expression pathways, regulation,
and integrated regulatory networks. Molecular Endocrinology,
v. 26, n. 1, pp. 203-217, 2012. doi:
10.1210/me.2011-1196
- R. Kolde, S. Laur, P. Adler,
J. Vilo. Robust rank aggregation for gene list integration and
meta-analysis
Bioinformatics, to appear. doi:
10.1093/bioinformatics/btr709
PhD defenses 2010
- J. Reimand. Functional Analysis of Gene Lists, Networks and
Regulatory Systems, v. 61 of Diss. Math. Univ. Tartuensis,
153 pp. Univ. of Tartu, 2010. handle: 10062/14852
Defense at Univ. of Tartu, 17 June 2010. Supervisor J. Vilo (Univ. of
Tartu), opponents S. Kaski (Aalto Univ.), T. Neumann (Tallinn Univ. of
Technology).
PhD defenses 2011
- M. Kull. Statistical Enrichment Analysis in Algorithms for
Studying Gene Regulation, v. 74 of
Diss. Math. Univ. Tartuensis, 151 pp. Univ. of Tartu, 2011. handle: 10062/18098
Defense at Univ. of Tartu, 26 Aug. 2011. Supervisor J. Vilo (Univ. of
Tartu), opponents J. Dopazo (Principe Felipe Research Centre,
Valencia), J. Rousu (Univ. of Helsinki).
Last update 21 January 2012