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Items: 44

1.

Machine learning of human plasma lipidomes for obesity estimation in a large population cohort.

Gerl MJ, Klose C, Surma MA, Fernandez C, Melander O, Männistö S, Borodulin K, Havulinna AS, Salomaa V, Ikonen E, Cannistraci CV, Simons K.

PLoS Biol. 2019 Oct 18;17(10):e3000443. doi: 10.1371/journal.pbio.3000443. eCollection 2019 Oct.

2.

Systems Network Genomic Analysis Reveals Cardioprotective Effect of MURC/Cavin-4 Deletion Against Ischemia/Reperfusion Injury.

Nishi M, Ogata T, Cannistraci CV, Ciucci S, Nakanishi N, Higuchi Y, Sakamoto A, Tsuji Y, Mizushima K, Matoba S.

J Am Heart Assoc. 2019 Aug 6;8(15):e012047. doi: 10.1161/JAHA.119.012047. Epub 2019 Jul 31.

3.

Controlling distinct signaling states in cultured cancer cells provides a new platform for drug discovery.

Poser SW, Otto O, Arps-Forker C, Ge Y, Herbig M, Andree C, Gruetzmann K, Adasme MF, Stodolak S, Nikolakopoulou P, Park DM, Mcintyre A, Lesche M, Dahl A, Lennig P, Bornstein SR, Schroeck E, Klink B, Leker RR, Bickle M, Chrousos GP, Schroeder M, Cannistraci CV, Guck J, Androutsellis-Theotokis A.

FASEB J. 2019 Aug;33(8):9235-9249. doi: 10.1096/fj.201802603RR. Epub 2019 May 30.

PMID:
31145643
4.

Cortical-like mini-columns of neuronal cells on zinc oxide nanowire surfaces.

Onesto V, Villani M, Narducci R, Malara N, Imbrogno A, Allione M, Costa N, Coppedè N, Zappettini A, Cannistraci CV, Cancedda L, Amato F, DI Fabrizio E, Gentile F.

Sci Rep. 2019 Mar 11;9(1):4021. doi: 10.1038/s41598-019-40548-z.

5.

Functional Brain Network Topology Discriminates between Patients with Minimally Conscious State and Unresponsive Wakefulness Syndrome.

Cacciola A, Naro A, Milardi D, Bramanti A, Malatacca L, Spitaleri M, Leo A, Muscoloni A, Cannistraci CV, Bramanti P, Calabrò RS, Anastasi GP.

J Clin Med. 2019 Mar 5;8(3). pii: E306. doi: 10.3390/jcm8030306.

6.

Navigability evaluation of complex networks by greedy routing efficiency.

Muscoloni A, Cannistraci CV.

Proc Natl Acad Sci U S A. 2019 Jan 29;116(5):1468-1469. doi: 10.1073/pnas.1817880116. Epub 2019 Jan 10. No abstract available.

7.

Lipidomics in Major Depressive Disorder.

Walther A, Cannistraci CV, Simons K, Durán C, Gerl MJ, Wehrli S, Kirschbaum C.

Front Psychiatry. 2018 Oct 15;9:459. doi: 10.3389/fpsyt.2018.00459. eCollection 2018.

8.
9.

Morphogenetic degeneracies in the actomyosin cortex.

Naganathan SR, Fürthauer S, Rodriguez J, Fievet BT, Jülicher F, Ahringer J, Cannistraci CV, Grill SW.

Elife. 2018 Oct 22;7. pii: e37677. doi: 10.7554/eLife.37677.

10.

Reward-enhanced encoding improves relearning of forgotten associations.

Miendlarzewska EA, Ciucci S, Cannistraci CV, Bavelier D, Schwartz S.

Sci Rep. 2018 Jun 4;8(1):8557. doi: 10.1038/s41598-018-26929-w.

11.

"Summer Shift": A Potential Effect of Sunshine on the Time Onset of ST-Elevation Acute Myocardial Infarction.

Cannistraci CV, Nieminen T, Nishi M, Khachigian LM, Viikilä J, Laine M, Cianflone D, Maseri A, Yeo KK, Bhindi R, Ammirati E.

J Am Heart Assoc. 2018 Apr 6;7(8). pii: e006878. doi: 10.1161/JAHA.117.006878.

12.

Ceruloplasmin replacement therapy ameliorates neurological symptoms in a preclinical model of aceruloplasminemia.

Zanardi A, Conti A, Cremonesi M, D'Adamo P, Gilberti E, Apostoli P, Cannistraci CV, Piperno A, David S, Alessio M.

EMBO Mol Med. 2018 Jan;10(1):91-106. doi: 10.15252/emmm.201708361.

13.

Machine learning meets complex networks via coalescent embedding in the hyperbolic space.

Muscoloni A, Thomas JM, Ciucci S, Bianconi G, Cannistraci CV.

Nat Commun. 2017 Nov 20;8(1):1615. doi: 10.1038/s41467-017-01825-5.

14.

Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory.

Durán C, Daminelli S, Thomas JM, Haupt VJ, Schroeder M, Cannistraci CV.

Brief Bioinform. 2018 Nov 27;19(6):1183-1202. doi: 10.1093/bib/bbx041.

15.

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies.

Ciucci S, Ge Y, Durán C, Palladini A, Jiménez-Jiménez V, Martínez-Sánchez LM, Wang Y, Sales S, Shevchenko A, Poser SW, Herbig M, Otto O, Androutsellis-Theotokis A, Guck J, Gerl MJ, Cannistraci CV.

Sci Rep. 2017 Mar 13;7:43946. doi: 10.1038/srep43946.

16.

Can local-community-paradigm and epitopological learning enhance our understanding of how local brain connectivity is able to process, learn and memorize chronic pain?

Narula V, Zippo AG, Muscoloni A, Biella GEM, Cannistraci CV.

Appl Netw Sci. 2017;2(1):28. doi: 10.1007/s41109-017-0048-x. Epub 2017 Aug 30.

17.

Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients.

Paroni Sterbini F, Palladini A, Masucci L, Cannistraci CV, Pastorino R, Ianiro G, Bugli F, Martini C, Ricciardi W, Gasbarrini A, Sanguinetti M, Cammarota G, Posteraro B.

Appl Environ Microbiol. 2016 Oct 27;82(22):6633-6644. Print 2016 Nov 15.

18.

Serological immune response against ADAM10 pro-domain is associated with favourable prognosis in stage III colorectal cancer patients.

Álvarez-Fernández SM, Barbariga M, Cannizzaro L, Cannistraci CV, Hurley L, Zanardi A, Conti A, Sanvito F, Innocenzi A, Pecorelli N, Braga M, Alessio M.

Oncotarget. 2016 Nov 29;7(48):80059-80076. doi: 10.18632/oncotarget.11181.

19.

Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome.

Sales S, Graessler J, Ciucci S, Al-Atrib R, Vihervaara T, Schuhmann K, Kauhanen D, Sysi-Aho M, Bornstein SR, Bickle M, Cannistraci CV, Ekroos K, Shevchenko A.

Sci Rep. 2016 Jun 14;6:27710. doi: 10.1038/srep27710.

20.

Drug target prioritization by perturbed gene expression and network information.

Isik Z, Baldow C, Cannistraci CV, Schroeder M.

Sci Rep. 2015 Nov 30;5:17417. doi: 10.1038/srep17417.

21.

Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data.

Alessio M, Cannistraci CV.

Methods Mol Biol. 2016;1384:289-98. doi: 10.1007/978-1-4939-3255-9_16.

PMID:
26611421
22.

Image Pretreatment Tools I: Algorithms for Map Denoising and Background Subtraction Methods.

Cannistraci CV, Alessio M.

Methods Mol Biol. 2016;1384:79-89. doi: 10.1007/978-1-4939-3255-9_5.

PMID:
26611410
23.

Erratum: From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks.

Cannistraci CV, Alanis-Lobato G, Ravasi T.

Sci Rep. 2015 Jul 21;5:9794. doi: 10.1038/srep09794. No abstract available.

24.

Highlighting nonlinear patterns in population genetics datasets.

Alanis-Lobato G, Cannistraci CV, Eriksson A, Manica A, Ravasi T.

Sci Rep. 2015 Jan 30;5:8140. doi: 10.1038/srep08140.

25.

Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra.

Cannistraci CV, Abbas A, Gao X.

Sci Rep. 2015 Jan 26;5:8017. doi: 10.1038/srep08017.

26.

The co-transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions.

Mavromatis CH, Bokil NJ, Totsika M, Kakkanat A, Schaale K, Cannistraci CV, Ryu T, Beatson SA, Ulett GC, Schembri MA, Sweet MJ, Ravasi T.

Cell Microbiol. 2015 May;17(5):730-46. doi: 10.1111/cmi.12397. Epub 2015 Jan 24.

27.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater.

Bayer K, Moitinho-Silva L, Brümmer F, Cannistraci CV, Ravasi T, Hentschel U.

FEMS Microbiol Ecol. 2014 Dec;90(3):832-43. doi: 10.1111/1574-6941.12441. Epub 2014 Nov 10.

28.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

29.

Increased expression of Myosin binding protein H in the skeletal muscle of amyotrophic lateral sclerosis patients.

Conti A, Riva N, Pesca M, Iannaccone S, Cannistraci CV, Corbo M, Previtali SC, Quattrini A, Alessio M.

Biochim Biophys Acta. 2014 Jan;1842(1):99-106. doi: 10.1016/j.bbadis.2013.10.013. Epub 2013 Oct 30.

30.

Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea.

Moitinho-Silva L, Bayer K, Cannistraci CV, Giles EC, Ryu T, Seridi L, Ravasi T, Hentschel U.

Mol Ecol. 2014 Mar;23(6):1348-63. doi: 10.1111/mec.12365. Epub 2013 Aug 20.

PMID:
23957633
31.

Still need for compelling evidence to support the circadian dependence of infarct size after ST-elevation myocardial infarction.

Ammirati E, Maseri A, Cannistraci CV.

Circ Res. 2013 Aug 2;113(4):e43-4. doi: 10.1161/CIRCRESAHA.113.301908. No abstract available.

PMID:
23908336
32.

Exploitation of genetic interaction network topology for the prediction of epistatic behavior.

Alanis-Lobato G, Cannistraci CV, Ravasi T.

Genomics. 2013 Oct;102(4):202-8. doi: 10.1016/j.ygeno.2013.07.010. Epub 2013 Jul 25.

33.

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding.

Cannistraci CV, Alanis-Lobato G, Ravasi T.

Bioinformatics. 2013 Jul 1;29(13):i199-209. doi: 10.1093/bioinformatics/btt208.

34.

Questing for circadian dependence in ST-segment-elevation acute myocardial infarction: a multicentric and multiethnic study.

Ammirati E, Cristell N, Cianflone D, Vermi AC, Marenzi G, De Metrio M, Uren NG, Hu D, Ravasi T, Maseri A, Cannistraci CV.

Circ Res. 2013 May 10;112(10):e110-4. doi: 10.1161/CIRCRESAHA.112.300778.

PMID:
23661713
35.

From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks.

Cannistraci CV, Alanis-Lobato G, Ravasi T.

Sci Rep. 2013;3:1613. doi: 10.1038/srep01613. Erratum in: Sci Rep. 2015;5:9794.

36.

Working memory load attenuates emotional enhancement in recognition memory.

Miendlarzewska EA, van Elswijk G, Cannistraci CV, van Ee R.

Front Psychol. 2013 Mar 18;4:112. doi: 10.3389/fpsyg.2013.00112. eCollection 2013.

37.

Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies.

Cannistraci CV, Ogorevc J, Zorc M, Ravasi T, Dovc P, Kunej T.

BMC Med Genomics. 2013 Feb 14;6:5. doi: 10.1186/1755-8794-6-5.

38.

Identification and predictive value of interleukin-6+ interleukin-10+ and interleukin-6- interleukin-10+ cytokine patterns in ST-elevation acute myocardial infarction.

Ammirati E, Cannistraci CV, Cristell NA, Vecchio V, Palini AG, Tornvall P, Paganoni AM, Miendlarzewska EA, Sangalli LM, Monello A, Pernow J, Björnstedt Bennermo M, Marenzi G, Hu D, Uren NG, Cianflone D, Ravasi T, Manfredi AA, Maseri A.

Circ Res. 2012 Oct 26;111(10):1336-48. doi: 10.1161/CIRCRESAHA.111.262477. Epub 2012 Aug 29.

PMID:
22931953
39.

Acclimation increases freezing stress response of Arabidopsis thaliana at proteome level.

Fanucchi F, Alpi E, Olivieri S, Cannistraci CV, Bachi A, Alpi A, Alessio M.

Biochim Biophys Acta. 2012 Jun;1824(6):813-25. doi: 10.1016/j.bbapap.2012.03.015. Epub 2012 Apr 6.

PMID:
22510494
40.

Ceruloplasmin oxidation, a feature of Parkinson's disease CSF, inhibits ferroxidase activity and promotes cellular iron retention.

Olivieri S, Conti A, Iannaccone S, Cannistraci CV, Campanella A, Barbariga M, Codazzi F, Pelizzoni I, Magnani G, Pesca M, Franciotta D, Cappa SF, Alessio M.

J Neurosci. 2011 Dec 14;31(50):18568-77. doi: 10.1523/JNEUROSCI.3768-11.2011.

41.

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes.

Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M.

Bioinformatics. 2010 Sep 15;26(18):i531-9. doi: 10.1093/bioinformatics/btq376.

42.

An atlas of combinatorial transcriptional regulation in mouse and man.

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y.

Cell. 2010 Mar 5;140(5):744-52. doi: 10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr 16;141(2):369. Kamburov, Atanas [added]; Kaur, Mandeep [added]; MacPherson, Cameron Ross [added]; Radovanovic, Aleksandar [added]; Schwartz, Ariel [added].

43.

Median-modified Wiener filter provides efficient denoising, preserving spot edge and morphology in 2-DE image processing.

Cannistraci CV, Montevecchi FM, Alessio M.

Proteomics. 2009 Nov;9(21):4908-19. doi: 10.1002/pmic.200800538.

PMID:
19862762
44.

Protein fingerprints of cultured CA3-CA1 hippocampal neurons: comparative analysis of the distribution of synaptosomal and cytosolic proteins.

Corti V, Sanchez-Ruiz Y, Piccoli G, Bergamaschi A, Cannistraci CV, Pattini L, Cerutti S, Bachi A, Alessio M, Malgaroli A.

BMC Neurosci. 2008 Apr 10;9:36. doi: 10.1186/1471-2202-9-36.

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