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Items: 1 to 50 of 52

1.

Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation.

Furtado BU, Nagy I, Asp T, Tyburski J, Skorupa M, Gołębiewski M, Hulisz P, Hrynkiewicz K.

BMC Plant Biol. 2019 Oct 16;19(1):427. doi: 10.1186/s12870-019-2032-3.

2.

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.

Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J.

Methods Mol Biol. 2019;2049:285-314. doi: 10.1007/978-1-4939-9736-7_17.

PMID:
31602618
3.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.

Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D.

J Integr Bioinform. 2019 Jul 13;16(2). pii: /j/jib.2019.16.issue-2/jib-2019-0035/jib-2019-0035.xml. doi: 10.1515/jib-2019-0035.

PMID:
31301675
4.

Generating amplicon reads for microbial community assessment with next-generation sequencing.

Gołębiewski M, Tretyn A.

J Appl Microbiol. 2019 Jul 12. doi: 10.1111/jam.14380. [Epub ahead of print] Review.

PMID:
31299126
5.

Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea.

Furtado BU, Gołębiewski M, Skorupa M, Hulisz P, Hrynkiewicz K.

Appl Environ Microbiol. 2019 Jun 17;85(13). pii: e00305-19. doi: 10.1128/AEM.00305-19. Print 2019 Jul 1.

6.

Silver and Copper Nanoparticles-An Alternative in Future Mastitis Treatment and Prevention?

Kalińska A, Jaworski S, Wierzbicki M, Gołębiewski M.

Int J Mol Sci. 2019 Apr 3;20(7). pii: E1672. doi: 10.3390/ijms20071672.

7.

Salt stress vs. salt shock - the case of sugar beet and its halophytic ancestor.

Skorupa M, Gołębiewski M, Kurnik K, Niedojadło J, Kęsy J, Klamkowski K, Wójcik K, Treder W, Tretyn A, Tyburski J.

BMC Plant Biol. 2019 Feb 6;19(1):57. doi: 10.1186/s12870-019-1661-x.

8.

Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D.

Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087. Review.

9.

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters.

Deja-Sikora E, Gołębiewski M, Kalwasińska A, Krawiec A, Kosobucki P, Walczak M.

Microb Ecol. 2019 Jul;78(1):85-101. doi: 10.1007/s00248-018-1270-5. Epub 2018 Oct 19.

10.

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).

Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E.

Stand Genomic Sci. 2018 Aug 9;13:17. doi: 10.1186/s40793-018-0320-4. eCollection 2018.

11.

Characteristics of the Conjugative Transfer System of the IncM Plasmid pCTX-M3 and Identification of Its Putative Regulators.

Dmowski M, Gołębiewski M, Kern-Zdanowicz I.

J Bacteriol. 2018 Aug 24;200(18). pii: e00234-18. doi: 10.1128/JB.00234-18. Print 2018 Sep 15.

12.

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.

Gołębiewski M, Tarasek A, Sikora M, Deja-Sikora E, Tretyn A, Niklińska M.

Microb Ecol. 2019 Jan;77(1):56-75. doi: 10.1007/s00248-018-1209-x. Epub 2018 May 30.

13.

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?

Thiem D, Gołębiewski M, Hulisz P, Piernik A, Hrynkiewicz K.

Front Microbiol. 2018 Apr 18;9:651. doi: 10.3389/fmicb.2018.00651. eCollection 2018.

14.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D.

J Integr Bioinform. 2018 Mar 29;15(1). pii: /j/jib.2018.15.issue-1/jib-2018-0013/jib-2018-0013.xml. doi: 10.1515/jib-2018-0013.

15.

Quantification of Adipose Tissue and Muscle Mass Based on Computed Tomography Scans: Comparison of Eight Planimetric and Diametric Techniques Including a Step-By-Step Guide.

Irlbeck T, Janitza S, Poros B, Golebiewski M, Frey L, Paprottka PM, da Silva T, Irlbeck M, Böcker W, Weig T.

Eur Surg Res. 2018;59(1-2):23-34. doi: 10.1159/000486173. Epub 2018 Jan 23.

PMID:
29393202
16.

Effect of Dairy Cow Crossbreeding on Selected Performance Traits and Quality of Milk in First Generation Crossbreds.

Puppel K, Bogusz E, Gołębiewski M, Nałęcz-Tarwacka T, Kuczyńska B, Slósarz J, Budziński A, Solarczyk P, Kunowska-Slósarz M, Przysucha T.

J Food Sci. 2018 Jan;83(1):229-236. doi: 10.1111/1750-3841.13988. Epub 2017 Nov 27.

PMID:
29178175
17.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D.

J Integr Bioinform. 2016 Dec 18;13(3):289. doi: 10.2390/biecoll-jib-2016-289.

18.

Addition of Liposome Bupivacaine to Bupivacaine HCl Versus Bupivacaine HCl Alone for Interscalene Brachial Plexus Block in Patients Having Major Shoulder Surgery.

Vandepitte C, Kuroda M, Witvrouw R, Anne L, Bellemans J, Corten K, Vanelderen P, Mesotten D, Leunen I, Heylen M, Van Boxstael S, Golebiewski M, Van de Velde M, Knezevic NN, Hadzic A.

Reg Anesth Pain Med. 2017 May/Jun;42(3):334-341. doi: 10.1097/AAP.0000000000000560.

PMID:
28157791
19.

Degrees of Antioxidant Protection: A 2-Year Study of the Bioactive Properties of Organic Milk in Poland.

Puppel K, Sakowski T, Kuczyńska B, Grodkowski G, Gołębiewski M, Barszczewski J, Wróbel B, Budziński A, Kapusta A, Balcerak M.

J Food Sci. 2017 Feb;82(2):523-528. doi: 10.1111/1750-3841.13594. Epub 2017 Jan 26.

PMID:
28125770
20.

Tideless estuaries in brackish seas as possible freshwater-marine transition zones for bacteria: the case study of the Vistula river estuary.

Gołębiewski M, Całkiewicz J, Creer S, Piwosz K.

Environ Microbiol Rep. 2017 Apr;9(2):129-143. doi: 10.1111/1758-2229.12509. Epub 2017 Jan 23.

PMID:
27935224
21.

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

Wolstencroft K, Krebs O, Snoep JL, Stanford NJ, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, van Niekerk DD, Williams AR, Malmström L, Rinn B, Müller W, Goble C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.

22.

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

Nickerson D, Atalag K, de Bono B, Geiger J, Goble C, Hollmann S, Lonien J, Müller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P.

Interface Focus. 2016 Apr 6;6(2):20150103. doi: 10.1098/rsfs.2015.0103. Review.

23.

Transcriptomic profiling of the salt stress response in excised leaves of the halophyte Beta vulgaris ssp. maritima.

Skorupa M, Gołębiewski M, Domagalski K, Kurnik K, Abu Nahia K, Złoch M, Tretyn A, Tyburski J.

Plant Sci. 2016 Feb;243:56-70. doi: 10.1016/j.plantsci.2015.11.007. Epub 2015 Nov 26.

PMID:
26795151
24.

The evolution of standards and data management practices in systems biology.

Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C.

Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053. No abstract available.

25.

Specifications of Standards in Systems and Synthetic Biology.

Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S.

J Integr Bioinform. 2015 Sep 4;12(2):258. doi: 10.2390/biecoll-jib-2015-258.

26.

Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress.

Chodak M, Gołębiewski M, Morawska-Płoskonka J, Kuduk K, Niklińska M.

Ann Microbiol. 2015;65(3):1627-1637. Epub 2014 Nov 25.

27.

Effect of supplementation of cows diet with linseed and fish oil and different variants of β-lactoglobulin on fatty acid composition and antioxidant capacity of milk.

Puppel K, Kuczyńska B, Nałęcz-Tarwacka T, Gołębiewski M, Sakowski T, Kapusta A, Budziński A, Balcerak M.

J Sci Food Agric. 2016 Apr;96(6):2240-8. doi: 10.1002/jsfa.7341. Epub 2015 Sep 1.

PMID:
26174000
28.

SEEK: a systems biology data and model management platform.

Wolstencroft K, Owen S, Krebs O, Nguyen Q, Stanford NJ, Golebiewski M, Weidemann A, Bittkowski M, An L, Shockley D, Snoep JL, Mueller W, Goble C.

BMC Syst Biol. 2015 Jul 11;9:33. doi: 10.1186/s12918-015-0174-y.

29.

Effect of the 5-HTTLPR polymorphism on affective temperament, depression and body mass index in obesity.

Borkowska A, Bieliński M, Szczęsny W, Szwed K, Tomaszewska M, Kałwa A, Lesiewska N, Junik R, Gołębiewski M, Sikora M, Tretyn A, Akiskal K, Akiskal H.

J Affect Disord. 2015 Sep 15;184:193-7. doi: 10.1016/j.jad.2015.05.061. Epub 2015 Jun 10.

PMID:
26093833
30.

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.

Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N.

Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019. eCollection 2015. Review.

31.

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N.

BMC Bioinformatics. 2014 Dec 14;15:369. doi: 10.1186/s12859-014-0369-z.

32.

16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils.

Gołębiewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wróbel B.

Microb Ecol. 2014 Apr;67(3):635-47. doi: 10.1007/s00248-013-0344-7. Epub 2014 Jan 9.

33.

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

34.

Challenges for an enzymatic reaction kinetics database.

Wittig U, Rey M, Kania R, Bittkowski M, Shi L, Golebiewski M, Weidemann A, Müller W, Rojas I.

FEBS J. 2014 Jan;281(2):572-82. doi: 10.1111/febs.12562. Epub 2013 Oct 25. Review.

35.

Effect of fish oil and linseed supplementation on the protein composition of milk from cows with different β-lactoglobulin phenotypes.

Puppel K, Kuczyńska B, Nałęcz-Tarwacka T, Sakowski T, Gołębiewski M, Kunowska-Slósarz M, Budziński A, Grodzki H.

J Sci Food Agric. 2014 Apr;94(6):1253-7. doi: 10.1002/jsfa.6424. Epub 2013 Nov 6.

PMID:
24114737
36.

Reduced colonic microbial diversity is associated with colitis in NHE3-deficient mice.

Larmonier CB, Laubitz D, Hill FM, Shehab KW, Lipinski L, Midura-Kiela MT, McFadden RM, Ramalingam R, Hassan KA, Golebiewski M, Besselsen DG, Ghishan FK, Kiela PR.

Am J Physiol Gastrointest Liver Physiol. 2013 Nov 15;305(10):G667-77. doi: 10.1152/ajpgi.00189.2013. Epub 2013 Sep 12.

37.

Differences in whey protein content between cow's milk collected in late pasture and early indoor feeding season from conventional and organic farms in Poland.

Kuczyńska B, Puppel K, Gołebiewski M, Metera E, Sakowski T, Słoniewski K.

J Sci Food Agric. 2012 Nov;92(14):2899-904. doi: 10.1002/jsfa.5663. Epub 2012 Apr 30.

PMID:
22549884
38.

The age of cows as a factor shaping the antioxidant level during a nutritional experiment with fish oil and linseed supplementation for increasing the antioxidant value of milk.

Puppel K, Nałecz-Tarwacka T, Kuczyńska B, Gołebiewski M, Kordyasz M, Grodzki H.

J Sci Food Agric. 2012 Sep;92(12):2494-9. doi: 10.1002/jsfa.5658. Epub 2012 Mar 29.

PMID:
22467448
39.

SABIO-RK--database for biochemical reaction kinetics.

Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauer-Danzwith H, Mir S, Krebs O, Bittkowski M, Wetsch E, Rojas I, Müller W.

Nucleic Acids Res. 2012 Jan;40(Database issue):D790-6. doi: 10.1093/nar/gkr1046. Epub 2011 Nov 18.

40.

Controlled vocabularies and semantics in systems biology.

Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N.

Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77.

41.

Adaptative potential of the Lactococcus lactis IL594 strain encoded in its 7 plasmids.

Górecki RK, Koryszewska-Bagińska A, Gołębiewski M, Żylińska J, Grynberg M, Bardowski JK.

PLoS One. 2011;6(7):e22238. doi: 10.1371/journal.pone.0022238. Epub 2011 Jul 18.

42.

Caspase recruitment domain 15 gene haplotypes in sarcoidosis.

Pabst S, Golebiewski M, Herms S, Karpushova A, Díaz-Lacava A, Walier M, Zimmer S, Cichon S, Wienker TF, Nöthen MM, Nickenig G, Meyer R, Skowasch D, Grohé C.

Tissue Antigens. 2011 Apr;77(4):333-7. doi: 10.1111/j.1399-0039.2010.01628.x.

PMID:
21388357
43.

Enzyme kinetics informatics: from instrument to browser.

Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Müller W, Paton NW, Rojas I.

FEBS J. 2010 Sep;277(18):3769-79. doi: 10.1111/j.1742-4658.2010.07778.x. Epub 2010 Aug 3.

44.

Who is really caring for your environment of care? Developing standardized cleaning procedures and effective monitoring techniques.

Dumigan DG, Boyce JM, Havill NL, Golebiewski M, Balogun O, Rizvani R.

Am J Infect Control. 2010 Jun;38(5):387-92. doi: 10.1016/j.ajic.2009.07.005.

PMID:
20435376
45.

Monitoring the effectiveness of hospital cleaning practices by use of an adenosine triphosphate bioluminescence assay.

Boyce JM, Havill NL, Dumigan DG, Golebiewski M, Balogun O, Rizvani R.

Infect Control Hosp Epidemiol. 2009 Jul;30(7):678-84. doi: 10.1086/598243.

PMID:
19489715
46.

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A.

Bioinformatics. 2009 Jun 1;25(11):1455-6. doi: 10.1093/bioinformatics/btp170. Epub 2009 Mar 23.

47.

Analysis of the complete genome sequence of the lactococcal bacteriophage bIBB29.

Hejnowicz MS, Gołebiewski M, Bardowski J.

Int J Food Microbiol. 2009 Apr 30;131(1):52-61. doi: 10.1016/j.ijfoodmicro.2008.06.010. Epub 2008 Jun 15.

PMID:
18644641
48.

Storing and annotating of kinetic data.

Rojas I, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Wittig U.

In Silico Biol. 2007;7(2 Suppl):S37-44.

PMID:
17822389
49.

Complete nucleotide sequence of the pCTX-M3 plasmid and its involvement in spread of the extended-spectrum beta-lactamase gene blaCTX-M-3.

Gołebiewski M, Kern-Zdanowicz I, Zienkiewicz M, Adamczyk M, Zylinska J, Baraniak A, Gniadkowski M, Bardowski J, Cegłowski P.

Antimicrob Agents Chemother. 2007 Nov;51(11):3789-95. Epub 2007 Aug 13.

50.

Mosaic structure of p1658/97, a 125-kilobase plasmid harboring an active amplicon with the extended-spectrum beta-lactamase gene blaSHV-5.

Zienkiewicz M, Kern-Zdanowicz I, Gołebiewski M, Zyliñska J, Mieczkowski P, Gniadkowski M, Bardowski J, Cegłowski P.

Antimicrob Agents Chemother. 2007 Apr;51(4):1164-71. Epub 2007 Jan 12.

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