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Items: 40

1.

Depletion of the FtsH1/3 proteolytic complex suppresses the nutrient stress response in the cyanobacterium Synechocystis PCC6803.

Krynicka V, Georg J, Jackson PJ, Dickman MJ, Hunter CN, Futschik ME, Hess WR, Komenda J.

Plant Cell. 2019 Oct 15. pii: tpc.00411.2019. doi: 10.1105/tpc.19.00411. [Epub ahead of print]

PMID:
31615847
2.

Exogenous WNT5A and WNT11 proteins rescue CITED2 dysfunction in mouse embryonic stem cells and zebrafish morphants.

Santos JMA, Mendes-Silva L, Afonso V, Martins G, Machado RSR, Lopes JA, Cancela L, Futschik ME, Sachinidis A, Gavaia P, Bragança J.

Cell Death Dis. 2019 Aug 5;10(8):582. doi: 10.1038/s41419-019-1816-6.

3.

FoxN1-dependent thymic epithelial cells promote T-cell leukemia development.

Ghezzo MN, Fernandes MT, Pacheco-Leyva I, Rodrigues PM, Machado RS, Araújo MAS, Kalathur RK, Futschik ME, Alves NL, Dos Santos NR.

Carcinogenesis. 2018 Dec 31;39(12):1463-1476. doi: 10.1093/carcin/bgy127.

PMID:
30256907
4.

Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart.

Sabour D, Machado RSR, Pinto JP, Rohani S, Sahito RGA, Hescheler J, Futschik ME, Sachinidis A.

Mol Ther Nucleic Acids. 2018 Sep 7;12:158-173. doi: 10.1016/j.omtn.2018.04.018. Epub 2018 May 4.

5.

StemMapper: a curated gene expression database for stem cell lineage analysis.

Pinto JP, Machado RSR, Magno R, Oliveira DV, Machado S, Andrade RP, Bragança J, Duarte I, Futschik ME.

Nucleic Acids Res. 2018 Jan 4;46(D1):D788-D793. doi: 10.1093/nar/gkx921.

6.

Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803.

Giner-Lamia J, Robles-Rengel R, Hernández-Prieto MA, Muro-Pastor MI, Florencio FJ, Futschik ME.

Nucleic Acids Res. 2017 Nov 16;45(20):11800-11820. doi: 10.1093/nar/gkx860.

7.

HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease.

Kalathur RKR, Pedro Pinto J, Sahoo B, Chaurasia G, Futschik ME.

Sci Rep. 2017 Jul 12;7(1):5216. doi: 10.1038/s41598-017-05224-0.

8.

Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1.

Georg J, Kostova G, Vuorijoki L, Schön V, Kadowaki T, Huokko T, Baumgartner D, Müller M, Klähn S, Allahverdiyeva Y, Hihara Y, Futschik ME, Aro EM, Hess WR.

Curr Biol. 2017 May 22;27(10):1425-1436.e7. doi: 10.1016/j.cub.2017.04.010. Epub 2017 May 4.

9.

Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells.

Macedo JA, Schrama D, Duarte I, Tavares E, Renaut J, Futschik ME, Rodrigues PM, Melo EP.

BMC Genomics. 2017 Apr 22;18(1):319. doi: 10.1186/s12864-017-3694-6.

10.

Extracellular Proteins: Novel Key Components of Metal Resistance in Cyanobacteria?

Giner-Lamia J, Pereira SB, Bovea-Marco M, Futschik ME, Tamagnini P, Oliveira P.

Front Microbiol. 2016 Jun 7;7:878. doi: 10.3389/fmicb.2016.00878. eCollection 2016.

11.

The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803.

Hernández-Prieto MA, Semeniuk TA, Giner-Lamia J, Futschik ME.

Sci Rep. 2016 Feb 29;6:22168. doi: 10.1038/srep22168.

12.

Identification of novel biomarkers in chronic immune thrombocytopenia (ITP) by microarray-based serum protein profiling.

Bal G, Futschik ME, Hartl D, Ringel F, Kamhieh-Milz J, Sterzer V, Hoheisel JD, Alhamdani MS, Salama A.

Br J Haematol. 2016 Feb;172(4):602-15. doi: 10.1111/bjh.13861. Epub 2015 Dec 2.

PMID:
26628061
13.

Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State.

Pells S, Koutsouraki E, Morfopoulou S, Valencia-Cadavid S, Tomlinson SR, Kalathur R, Futschik ME, De Sousa PA.

PLoS One. 2015 Jul 7;10(7):e0131102. doi: 10.1371/journal.pone.0131102. eCollection 2015.

14.

StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.

Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RS, Machado S, Pacheco-Leyva I, Duarte I, Futschik ME.

Nucleic Acids Res. 2015 Jul 1;43(W1):W72-7. doi: 10.1093/nar/gkv529. Epub 2015 May 24.

15.

Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity.

Stroedicke M, Bounab Y, Strempel N, Klockmeier K, Yigit S, Friedrich RP, Chaurasia G, Li S, Hesse F, Riechers SP, Russ J, Nicoletti C, Boeddrich A, Wiglenda T, Haenig C, Schnoegl S, Fournier D, Graham RK, Hayden MR, Sigrist S, Bates GP, Priller J, Andrade-Navarro MA, Futschik ME, Wanker EE.

Genome Res. 2015 May;25(5):701-13. doi: 10.1101/gr.182444.114.

16.

The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach.

Kalathur RK, Giner-Lamia J, Machado S, Barata T, Ayasolla KR, Futschik ME.

Version 2. F1000Res. 2015 May 1 [revised 2016 Jan 1];4:103. doi: 10.12688/f1000research.6358.2. eCollection 2015.

17.

Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria.

Hernández-Prieto MA, Semeniuk TA, Futschik ME.

Front Genet. 2014 Jul 2;5:191. doi: 10.3389/fgene.2014.00191. eCollection 2014. Review.

18.

Targeting molecular networks for drug research.

Pinto JP, Machado RS, Xavier JM, Futschik ME.

Front Genet. 2014 Jun 4;5:160. doi: 10.3389/fgene.2014.00160. eCollection 2014. Review.

19.

StemCellNet: an interactive platform for network-oriented investigations in stem cell biology.

Pinto JP, Reddy Kalathur RK, Machado RS, Xavier JM, Bragança J, Futschik ME.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W154-60. doi: 10.1093/nar/gku455. Epub 2014 May 22.

20.

UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks.

Kalathur RK, Pinto JP, Hernández-Prieto MA, Machado RS, Almeida D, Chaurasia G, Futschik ME.

Nucleic Acids Res. 2014 Jan;42(Database issue):D408-14. doi: 10.1093/nar/gkt1100. Epub 2013 Nov 8.

21.

Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions.

Wallach T, Schellenberg K, Maier B, Kalathur RK, Porras P, Wanker EE, Futschik ME, Kramer A.

PLoS Genet. 2013 Mar;9(3):e1003398. doi: 10.1371/journal.pgen.1003398. Epub 2013 Mar 28.

22.

Iron deprivation in Synechocystis: inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profiling.

Hernández-Prieto MA, Schön V, Georg J, Barreira L, Varela J, Hess WR, Futschik ME.

G3 (Bethesda). 2012 Dec;2(12):1475-95. doi: 10.1534/g3.112.003863. Epub 2012 Dec 1.

23.

CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803.

Hernandez-Prieto MA, Futschik ME.

Bioinformation. 2012;8(13):634-8. doi: 10.6026/97320630008634. Epub 2012 Jul 6.

24.

Huntington's disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database.

Kalathur RK, Hernández-Prieto MA, Futschik ME.

BMC Neurol. 2012 Jun 28;12:47. doi: 10.1186/1471-2377-12-47.

25.

Comparison and consolidation of microarray data sets of human tissue expression.

Russ J, Futschik ME.

BMC Genomics. 2010 May 14;11:305. doi: 10.1186/1471-2164-11-305.

26.

Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcus.

Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, Wright MA, Rector T, Steen R, McNulty N, Thompson LR, Chisholm SW.

PLoS One. 2009;4(4):e5135. doi: 10.1371/journal.pone.0005135. Epub 2009 Apr 8.

27.

Tight regulation of unstructured proteins: from transcript synthesis to protein degradation.

Gsponer J, Futschik ME, Teichmann SA, Babu MM.

Science. 2008 Nov 28;322(5906):1365-8. doi: 10.1126/science.1163581.

28.

UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome.

Chaurasia G, Malhotra S, Russ J, Schnoegl S, Hänig C, Wanker EE, Futschik ME.

Nucleic Acids Res. 2009 Jan;37(Database issue):D657-60. doi: 10.1093/nar/gkn841. Epub 2008 Nov 4.

29.

The challenge of regulation in a minimal photoautotroph: non-coding RNAs in Prochlorococcus.

Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR.

PLoS Genet. 2008 Aug 29;4(8):e1000173. doi: 10.1371/journal.pgen.1000173. Erratum in: PLoS Genet. 2008 Nov;4(11):. doi:10.1371/annotation/411b74ae-c4ce-43c9-bdd2-60c2bf60e672.

30.

Graph-theoretical comparison reveals structural divergence of human protein interaction networks.

Futschik ME, Tschaut A, Chaurasia G, Herzel H.

Genome Inform. 2007;18:141-51.

PMID:
18546482
31.

Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis.

Futschik ME, Herzel H.

Bioinformatics. 2008 Apr 15;24(8):1063-9. doi: 10.1093/bioinformatics/btn072. Epub 2008 Feb 29.

PMID:
18310054
32.

Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution.

Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW.

Nature. 2007 Sep 6;449(7158):83-6.

PMID:
17805294
33.

Systematic functional assessment of human protein-protein interaction maps.

Chaurasia G, Herzel H, Wanker EE, Futschik ME.

Genome Inform. 2006;17(1):36-45.

PMID:
17503354
34.

Comparison of human protein-protein interaction maps.

Futschik ME, Chaurasia G, Herzel H.

Bioinformatics. 2007 Mar 1;23(5):605-11. Epub 2007 Jan 19.

PMID:
17237052
35.

UniHI: an entry gate to the human protein interactome.

Chaurasia G, Iqbal Y, Hänig C, Herzel H, Wanker EE, Futschik ME.

Nucleic Acids Res. 2007 Jan;35(Database issue):D590-4. Epub 2006 Dec 7.

36.

Noise-robust soft clustering of gene expression time-course data.

Futschik ME, Carlisle B.

J Bioinform Comput Biol. 2005 Aug;3(4):965-88.

PMID:
16078370
37.

OLIN: optimized normalization, visualization and quality testing of two-channel microarray data.

Futschik ME, Crompton T.

Bioinformatics. 2005 Apr 15;21(8):1724-6. Epub 2004 Dec 7.

PMID:
15585527
38.

Prediction of clinical behaviour and treatment for cancers.

Futschik ME, Sullivan M, Reeve A, Kasabov N.

Appl Bioinformatics. 2003;2(3 Suppl):S53-8.

PMID:
15130817
39.

Evolving connectionist systems for knowledge discovery from gene expression data of cancer tissue.

Futschik ME, Reeve A, Kasabov N.

Artif Intell Med. 2003 Jun;28(2):165-89.

PMID:
12893118
40.

Association of CDH1 haplotypes with susceptibility to sporadic diffuse gastric cancer.

Humar B, Graziano F, Cascinu S, Catalano V, Ruzzo AM, Magnani M, Toro T, Burchill T, Futschik ME, Merriman T, Guilford P.

Oncogene. 2002 Nov 21;21(53):8192-5.

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