Bioinformatics (BI)
Key persons
J. Vilo, M. Kull, J. Reimand, R. Vicente
Postdoc
B. Rajashekar
BIIT joint research group of
UT, Quretec and the Estonian Biocenter, Computational neuroscience research group of
UT
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, Scopus: 2-s2.0-39149098854)
- 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, Scopus: 2-s2.0-38549087902)
- 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 (Scopus:
2-s2.0-42449101770)
- 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, Scopus: 2-s2.0-56349083353)
- 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
on 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,
Scopus: 2-s2.0-48449099258)
- 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, Scopus: 2-s2.0-51049105083)
- 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, Scopus: 2-s2.0-76249090486)
- 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, Scopus: 2-s2.0-63849156615)
- 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, Scopus: 2-s2.0-72749110767)
- 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, Scopus: 2-s2.0-60049093585)
- 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,
Scopus: 2-s2.0-67849092444)
- 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, Scopus: 2-s2.0-61449159874)
- 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, Scopus: 2-s2.0-70249116787)
- 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, Scopus:
2-s2.0-65649127710)
- 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, Scopus: 2-s2.0-65449118073)
- 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, p. 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, Scopus: 2-s2.0-77955121141)
- 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, Scopus: 2-s2.0-77951150489)
- 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, Scopus: 2-s2.0-77956269672)
- 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. 16-41, 2010. article
on publisher's website (WOS:
000278003000003, Scopus: 2-s2.0-7795469679)
- 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, Scopus: 2-s2.0-78650492254)
- 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, Scopus: 2-s2.0-78650063078)
- 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, Scopus: 2-s2.0-73949090637)
- 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,
Scopus: 2-s2.0-77955817629)
- 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, Scopus: 2-s2.0-77955450675)
- 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, Scopus: 2-s2.0-78349261569)
- 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, Scopus:
2-s2.0-79952579536)
Publications 2011
- Y. Chen, M. Jørgensen, R. Kolde, X. Zhao, B. Parker,
E. Valen, J. Wen, A. Sandelin. Prediction of RNA polymerase II
recruitment, elongation and stalling from histone modification
data. BMC Genomics, v. 12, article 544, 2011. doi:
10.1186/1471-2164-12-544 (WOS:
000297666600001, Scopus: 2-s2.0-80155208160)
- 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 (WOS:
000298171400039, Scopus: 2-s2.0-82555187208)
- 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)
- 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 (webserver
issue), pp. W307-W315, 2011. doi:
10.1093/nar/gkr378 (WOS:
000292325300050, Scopus: 2-s2.0-79959923522)
- 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, Scopus: 2-s2.0-79959752193)
- 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 (Scopus:
2-s2.0-83055179346)
- 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, Scopus: 2-s2.0-79551634661)
- 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, Scopus: 2-s2.0-79960691435)
- 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,
Scopus: 2-s2.0-80051559806)
- 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 (WOS:
000299199800018, Scopus: 2-s2.0-84855225911)
- J. Aru, K. Korjus, C. Murd, T. Bachmann. Spectral
signatures of the effects of caffeine and occipitally applied
transcranial magnetic stimulation in a task-free experimental
setup. J. of Caffeine Research, v. 2, n. 1, pp. 23-30, 2012. doi:
10.1089/jcr.2011.0028
- N. V. Balmer, M. K. Weng, B. Zimmer, V. N. Ivanova,
S. M. Chambers, E. Nikolaeva, S. Jagtap, A. Sachinidis,
J. Hescheler, T. Waldmann, M. Leist. Epigenetic changes and disturbed
neural development in a human embryonic stem cell-based model relating
to the fetal valproate syndrome. Hum. Mol. Genet., v. 21,
n. 18, pp. 4104-4114, 2012. doi:
10.1093/hmg/dds239 (WOS:
000308230800015, Scopus: 2-s2.0-84865776716)
- J. A. Gaspar, M. X. Doss, J. Winkler, V. Wagh, J. Hescheler,
R. Kolde, J. Vilo, H. Schulz, A. Sachinidis. Gene
expression signatures defining fundamental biological processes in
pluripotent, early, and late differentiated embryonic stem
cells. Stem Cells and Development, v. 21, n. 13, pp. 2471-2484,
2012. doi:
10.1089/scd.2011.0637 (WOS:
000308264900013, Scopus: 2-s2.0-84865742040)
- R. Kolde, S. Laur, P. Adler,
J. Vilo. Robust rank aggregation for gene list integration and
meta-analysis. Bioinformatics, v. 24, n. 4, pp. 573-580,
2012. doi:
10.1093/bioinformatics/btr709 (WOS:
000300490500017, Scopus: 2-s2.0-84857156980)
- A. Leontjeva, K. Tretyakov, J. Vilo,
T. Tamkivi. Fraud detection: methods of analysis for hypergraph
data. In Proc. of 2012 IEEE/ACM Int. Conf. on Advances in Social
Networks Analysis and Mining, ASONAM '12 (Istanbul,
Aug. 2012), pp. 1060-1064. IEEE, 2012. doi: 10.1109/asonam.2012.234 (WOS: 000320443500172, Scopus:
2-s2.0-84874266490)
- K. Lokk, T, Vooder, R. Kolde, K. Välk, U. Võsa,
R. Roosipuu, L. Milani, K. Fischer, M. Koltsina, E. Urgard, T. Annilo,
A. Metspalu, N. Tõnisson. Methylation markers of early-stage
non-small cell lung cancer. PLoS ONE, v. 7, n. 6, article
e39813, 2012. doi:
10.1371/journal.pone.0039813 (WOS:
000305892100101, Scopus: 2-s2.0-84863085270)
- P. A. Northcott, D. J. H. Shih, J. Peacock, L. Garzia,
A. S. Morrissy, T. Zichner, A. M. Stütz, A. Korshunov,
J. Reimand, S. E. Schumacher, Beroukhim, D. W. Ellison,
C. R. Marshall, A. C. Lionel, S. Mack, A. Dubuc, Y. Yao,
V. Ramaswamy, B. Luu, A. Rolider, F. M. G. Cavalli, X. Wang, M.
Remke, X. Wu, R. Y. B. Chiu, A. Chu, E. Chuah, R. D. Corbett,
G. R. Hoad, S. D. Jackman, Y. Li, A. Lo, K. L. Mungall, K. M. Nip,
J. Q. Qian, A. G. J. Raymond, N. Thiessen, R. J. Varhol, I. Birol,
R. A. Moore, A. J. Mungall, R. Holt, D. Kawauchi, M. F. Roussel,
M. Kool, D. T. W. Jones, H. Witt, A. Fernandez-L., A. M. Kenney,
R. J. Wechsler-Reya, P. Dirks, T. Aviv, W. A. Grajkowska,
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F. F. Doz, S. S. Pernet-Fattet, B.-K. Cho, S.-K. Kim, K.-C. Wang,
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G. Carlotti, R. Vibhakar, Y. S. Ra, S. Robinson, M. Zollo,
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M. Karelson, K. Abram, T. Metsalu, M. Pihlap, N. Meyer,
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Publications 2013
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alpha rhythms in mild cognitive impairment. Frontiers in Aging
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B. F. F. Ouellette, J. Reimand, R. Linding, T. Shibata,
A. Valencia, A. Butler, S. Dronov, P. Flicek, N. B. Shannon,
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variants in cancer genomes. Nature Methods, v. 10, n. 8,
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J. Vilo. A new way to protect privacy in large-scale
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pp. 886-893, 2013. doi:
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Balmer, K. Meganathan, K. Vojnits, M. Baquié, T. Waldmann,
R. Ensenat-Waser, S. Jagtap, R. M. Evans, S. Julien,
H. Peterson, D. Zagoura, S. Kadereit, D. Gerhard,
I. Sotiriadou, M. Heke, K. Natarajan, M. Henry, J. Winkler,
R. Marchan, L. Stoppini, S. Bosgra, J. Westerhout, M. Verwei,
J. Vilo, A. Kortenkamp, J. Hescheler, L. Hothorn, S. Bremer,
C. van Thriel, K.-H. Krause, J. G. Hengstler, J. Rahnenführer,
M. Leist, A. Sachinidis. Human embryonic stem cell-derived test
systems for developmental neurotoxicity: a transcriptomics
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K.-H. Krause, J. Rahnenführer, A. Sachinidis, J. Hescheler,
J. G. Hengstler. Test systems of developmental toxicity: state-of-the
art and future perspectives. Arch. of Toxicol., v. 87, n. 12,
pp. 2037-2042, 2013. doi:
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P.-Y. Dietrich, D. Tirefort, H. Chneiweiss, J.-A. Lobrinus,
K.-H. Krause, T. Virolle, O. Preynat-Seauve. The relationship between
brain tumor cell invasion of engineered neural tissues and in vivo
features of glioblastoma. Biomaterials, v. 34, n. 33, pp.
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J. Vilo, I. Xenarios, J. Adjaye. Qualitative modeling
identifies IL-11 as a novel regulator in maintaining self-renewal in
human pluripotent stem cells. Frontiers in Physiol., v. 4,
article 303, 2013. doi:
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mutations in phosphorylation signaling predicts novel cancer
drivers. Mol. Syst. Biol., v. 9, n. 1, article 637, 2013. doi:
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of phosphorylation signaling in cancer. Sci. Rep., v. 3,
article 2651, 2013. doi:
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phase of thalamic alpha activity modulates cortical gamma-band
activity: evidence from resting-state MEG recordings. J. of
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cancer driver genes across 12 tumor types. Sci. Rep., v. 3,
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of histone acetylation and methylation as epigenetic switch between
reversible and irreversible drug effects. Arch. of Toxicol.,
v. 88, n. 7, pp. 1451-1468, 2014. doi:
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oscillations during contour integration of dynamic visual stimuli from
parietal/frontal networks. Front. in Integr. Neurosci., v. 8,
article 64, 2014. doi:
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X. M. Zhu, M. Kushida, J. Bayani, J. C. Pressey, A. Lionel,
I. D. Clarke, M. Cusimano, J. Squire, S. Scherer, M. Bernstein,
M. A. Woodin, G. D. Bader. Single cell derived clonal analysis of
human glioblastoma links functional and genomic heterogeneity.
Neuro-Oncology, v. 16, suppl. 3, p. iii14,
2014. doi:
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M. J. Roberti, M. J. Hossain, P. Adler, J. M. Fernández,
M. Krallinger, C. H. Haering, J. Vilo, A. Valencia,
J. A. Ranea, C. Orengo, J. Ellenberg, Integration of biological data
by kernels on graph nodes allows prediction of new genes involved in
mitotic chromosome condensation. Mol. Biol. of Cell, v. 25,
n. 16, pp. 2522-2536, 2014. doi:
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Gutekunst, H. van der Kuip, IMI PREDECT Consortium (J. Vilo is
part of the consortium). Three-dimensional models of cancer for
pharmacology and cancer cell biology: capturing tumor complexity in
vitro/ex vivo. Biotechnol. J., v. 9, n. 9, pp. 1115-1128,
2014. doi:
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R. Kolde, J. Vilo, E. Vasar, H. Luuk. Estimating
differential expression from multiple indicators. Nucl. Acids
Res., v. 42, n. 8, article e72, 2014. doi:
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light on global gene expression in the neuroglobin-deficient mouse
retina. Biomed. Rep., v. 2, n. 6, pp. 780-786, 2014. doi:
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S. Hutter, H. Sxeker-Cin, P. Johann, S. Bender, C. Schmidt, T. Rausch,
D. Shih, J. Reimand, L. Sieber, A. Wittmann, L. Linke,
H. Witt, U. D. Weber, M. Zapatka, R. König, R. Beroukhim,
G. Bergthold, P. Van Sluis, R. Volckmann, J. Koster, R. Versteeg,
S. Schmidt, S. Wolf, C. Lawerenz, C. C. Bartholomae, C. Von Kalle,
A. Unterberg, C. Herold-Mende, S. Hofer, A. E. Kulozik, A. Von
Deimling, W. Scheurlen, J. Felsberg, G. Reifenberger, M. Hasselblatt,
J. R. Crawford, G. A. Grant, N. Jabado, A. Perry, C. Cowdrey,
S. Croul, G. Zadeh, J. O. Korbel, F. Doz, O. Delattre, G. D. Bader,
M. G. McCabe, V. P. Collins, M. W. Kieran, Y.-J. Cho, S. L. Pomeroy,
O. Witt, B. Brors, M. D. Taylor, U. Schüller, A. Korshunov, R. Eils,
R. J. Wechsler-Reya, P. Lichter, S. M. Pfister. Genome sequencing of
SHH medulloblastoma predicts genotype-related response to smoothened
inhibition. Cancer Cell, v. 25, n. 3, pp. 393-405, 2014. doi:
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to enhance probability estimates and improve classification
accuracy. In T. Calders, F. Esposito, E. Hüllermeier, R. Meo, eds.,
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low-frequency repetitive transcranial magnetic stimulation (rTMS) on
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W. L. Pan, G. Y. Wang, B. Rajashekar. Biotype expression and
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J. Vilo, A. Salumets, N. Tõnisson. DNA methylome profiling of
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E. Reimann, S. Kõks, K. Rull, L. Milani, G. Acharya, P. Basnet,
J. Vilo, R. Mägi, A. Metspalu, M. Peters, K. Haller-Kikkatalo,
A. Salumets. Using RNA sequencing for identifying gene imprinting and
random monoallelic expression in human placenta. Epigenetics,
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point-wise confidence bounds for ROC curves. In T. Calders,
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J. Simm, A. Velthut-Meikas, K. Samuel, T. Metsalu, H. Karro,
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approach uncovers the miRNome of peritoneal endometriotic lesions and
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magnetic stimulation evoked electroencephalography potentials between
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S. Kasvandik, J.-F. Picimbon. Molecular evidence of RNA editing in
Bombyx chemosensory protein family. PLoS ONE, v. 9,
n. 2, article e86932, 2014. doi:
10.1371/journal.pone.0086932 (WOS:
000331266000007, Scopus: 2-s2.0-84895832124)
- A. Zemmar, O. Weinmann, Y. Kellner, X. Yu, R. Vicente,
M. Gullo, H. Kasper, K. Lussi, Z. Ristic, A. R. Luft, M.
Rioult-Pedotti, Y. Zuo, M. Zagrebelsky, M. E. Schwab. Neutralization
of Nogo-A enhances synaptic plasticity in the rat motor cortex and
improves motor learning in vivo. J. of Neurosci., v. 34, n. 26,
pp. 8685-8698, 2014. doi:
10.1523/jneurosci.3817-13.2014 (WOS: 000338737800005, Scopus:
2-s2.0-84903206666)
Publications 2015
- J. Aru, J. Aru, V. Priesemann, M. Wibral, L. Lana, G. Pipa,
W. Singer, R. Vicente. Untangling cross-frequency coupling in
neuroscience. Current Opinion in Neurobiology, v. 31,
pp. 51-61, 2015. doi:
10.1016/j.conb.2014.08.002 (WOS:
000352680700010, Scopus: 2-s2.0-84907688475)
- J. Aru, T. Bachmann. Still wanted - neural mechanisms of
consciousness! Front. in Psychol., v. 6, article 5, 2015. doi:
10.3389/fpsyg.2015.00005 (WOS:
000348188700001, Scopus: 2-s2.0-84926616902)
- J. Aru, T. Bachmann, W. Singer, L. Melloni. On why the
unconscious prerequisites and consequences of consciousness might
derail us from unravelling the neural correlates of consciousness. In
S. M. Miller, ed., The Constitution of Phenomenal Consciousness:
Toward a Science and Theory, v. 92 of Advances in Consciousness
Research, pp. 205-225. John Benjamins Publ. Co., 2015. doi: 10.1075/aicr.92
- T. Bachmann, J. Aru. Comments on how Mack et
al. (2015) (do not) see iconic memory. Consciousness and
Cognition, v. 34, pp. 73-74, 2015. doi:
10.1016/j.concog.2015.03.014 (WOS:
000355054000010, Scopus: 2-s2.0-84926469279)
- E. Cosset, Y. Martinez, O. Preynat-Seauve, J.-A. Lobrinus,
C. Tapparel, S. Cordey, H. Peterson, T. J. Petty, M. Colaianna,
V. Tieng, D. Tirefort, A. Dinnyes, M. Dubois-Dauphin, L. Kaiser,
K.-H. Krause. Human three-dimensional engineered neural tissue
reveals cellular and molecular events following cytomegalovirus
infection. Biomaterials, v. 53, pp. 296-308, 2015. doi:
10.1016/j.biomaterials.2015.02.094 (Scopus: 2-s2.0-84927942085)
- G. Gómez-Herrero, W. Wu, K. Rutanen, M. C. Soriano, G. Pipa, R.
Vicente. Assessing coupling dynamics from an ensemble of time
series. Entropy, v. 17, pp. 1958-1970, 2015. doi: 10.3390/e17041958
(WOS: 000354125700021, Scopus:
2-s2.0-84930319366)
- K. Korjus, A. Uusberg, H. Uusberg, N. Kuldkepp,
K. Kreegipuu, J. Allik, R. Vicente, J. Aru. Personality
cannot be predicted from the power of resting state EEG.
Front. in Human Neurosci., v. 9, article 63, 2015. doi:
10.3389/fnhum.2015.00063 (WOS: 000349283600001, Scopus:
2-s2.0-84923239519)
- J. G. Lees, J.-K. Hériche, I. Morilla, J. M. Fernández,
P. Adler, M. Krallinger, J. Vilo, A. Valencia,
J. Ellenberg, J. A. Ranea, C. Orengo. FUN-L: gene prioritization for
RNAi screens. Bioinform., v. 31, n. 12, pp. 2052-2053, 2015. doi:
10.1093/bioinformatics/btv073 (WOS:
000356625700070, Scopus: 2-s2.0-84931093956)
- T. Metsalu, J. Vilo. ClustVis: a web tool for
visualizing clustering of multivariate data using principal component
analysis and heatmap. Nucl. Acids Res., v. 43, suppl. 1,
pp. W566-W570, 2015. doi:
10.1093/nar/gkv468
- T. Örd, D. Örd, P. Adler, J. Vilo, T. Örd. TRIB3
enhances cell viability during glucose deprivation in HEK293-derived
cells by upregulating IGFBP2, a novel nutrient deficiency survival
factor. Biochim. et Biophys. Acta - Mol. Cell Res., v. 1853,
n. 10, pp. 2492-2505, 2015. doi:
10.1016/j.bbamcr.2015.06.006 (Scopus:
2-s2.0-84938151075)
- R. Rutiku, M. Martin, T. Bachmann, J. Aru. Does the
P300 reflect conscious perception or its consequences?
Neurosci., v. 289, pp. 180-189, 2015. doi:
10.1016/j.neuroscience.2015.04.029 (WOS:
000354783300017, Scopus: 2-s2.0-84928688564)
- M. Stamm, J. Aru, R. Rutiku, T. Bachmann. Occipital
long-interval paired pulse TMS leads to slow wave components in NREM
sleep. Consciousness and Cognition, v. 35, pp. 78-87, 2015. doi:
10.1016/j.concog.2015.04.024 (WOS: 000357000500008, Scopus:
2-s2.0-84929120048)
- L. Tserel, R. Kolde, M. Limbach, K. Tretyakov,
S. Kasela, K. Kisand, M. Saare, J. Vilo, A. Metspalu,
L. Milani, P. Peterson. Age-related profiling of DNA methylation in
CD8+ T cells reveals changes in immune response and transcriptional
regulator genes. Sci. Rep., v. 5, article 13107, 2015. doi: 10.1038/srep13107
(Scopus: 2-s2.0-84939789611)
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).
PhD defenses 2014
- R. Kolde. Methods for Re-using Public Gene Expression
Data, v. 90 of
Diss. Math. Univ. Tartuensis, 121 pp. Univ. of Tartu, 2014. handle: 10062/40689
Defense at Univ. of Tartu, 16 June 2014. Supervisor J. Vilo (Univ. of
Tartu), opponents L. J. Jensen (Univ. of Copenhagen), K. Palin
(Univ. of Helsinki).
PhD defenses 2015
- S. Ilmjärv. Estimating Differential Expression from
Multiple Indicators, v. 21 of
Diss. Neuroscient. Univ. Tartuensis, 125 pp. Univ. of Tartu, 2015. handle: 10062/45645
Defense at Univ. of Tartu, 24 April 2015. Supervisors H. Luuk,
E. Vasar, J. Vilo (Univ. of Tartu), opponent D.-A. Clevert
(Johannes-Kepler-Univ. Linz).
- H. Peterson. Exploiting High-Throughput Data for
Establishing Relationships Between Genes, v. 276 of
Diss. Biol. Univ. Tartuensis, 186 pp. Univ. of Tartu, 2015. handle: 10062/46443
Defense at Univ. of Tartu, 17 June 2015. Supervisors J. Vilo,
J. Sedman (Univ. of Tartu), opponent B. Lenhard (Imperial College
London).
- P. Adler. Analysis and Visualisation of Large Scale
Microarray Data, v. 277 of
Diss. Biol. Univ. Tartuensis, 126 pp. Univ. of Tartu, 2015. handle: 10062/47493
Defense at Univ. of Tartu, 26 August 2015. Supervisors J. Vilo,
J. Sedman (Univ. of Tartu), opponent G. Rustici (Univ. of Cambridge).
Last update 20 September 2015