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Items: 1 to 50 of 96

1.

Case of Microcephaly after Congenital Infection with Asian Lineage Zika Virus, Thailand.

Wongsurawat T, Athipanyasilp N, Jenjaroenpun P, Jun SR, Kaewnapan B, Wassenaar TM, Leelahakorn N, Angkasekwinai N, Kantakamalakul W, Ussery DW, Sutthent R, Nookaew I, Horthongkham N.

Emerg Infect Dis. 2018 Sep 17;24(9). doi: 10.3201/eid2409.180416. [Epub ahead of print]

2.

Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients.

Wongsurawat T, Woo CC, Giannakakis A, Lin XY, Cheow ESH, Lee CN, Richards M, Sze SK, Nookaew I, Kuznetsov VA, Sorokin V.

Data Brief. 2018 Feb 6;17:1112-1135. doi: 10.1016/j.dib.2018.01.108. eCollection 2018 Apr.

3.

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate.

Poudel S, Giannone RJ, Basen M, Nookaew I, Poole FL 2nd, Kelly RM, Adams MWW, Hettich RL.

Biotechnol Biofuels. 2018 Mar 23;11:80. doi: 10.1186/s13068-018-1076-1. eCollection 2018.

4.

Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW.

Microb Ecol. 2018 Feb 14. doi: 10.1007/s00248-018-1155-7. [Epub ahead of print]

PMID:
29445826
5.

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome.

Timm CM, Carter KR, Carrell AA, Jun SR, Jawdy SS, Vélez JM, Gunter LE, Yang Z, Nookaew I, Engle NL, Lu TS, Schadt CW, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Pelletier DA, Weston DJ.

mSystems. 2018 Jan 23;3(1). pii: e00070-17. doi: 10.1128/mSystems.00070-17. eCollection 2018 Jan-Feb.

6.

Distinctive molecular signature and activated signaling pathways in aortic smooth muscle cells of patients with myocardial infarction.

Wongsurawat T, Woo CC, Giannakakis A, Lin XY, Cheow ESH, Lee CN, Richards M, Sze SK, Nookaew I, Kuznetsov VA, Sorokin V.

Atherosclerosis. 2018 Apr;271:237-244. doi: 10.1016/j.atherosclerosis.2018.01.024. Epub 2018 Jan 31.

7.

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D.

Jenjaroenpun P, Wongsurawat T, Pereira R, Patumcharoenpol P, Ussery DW, Nielsen J, Nookaew I.

Nucleic Acids Res. 2018 Apr 20;46(7):e38. doi: 10.1093/nar/gky014.

8.

dBBQs: dataBase of Bacterial Quality scores.

Wanchai V, Patumcharoenpol P, Nookaew I, Ussery D.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):483. doi: 10.1186/s12859-017-1900-9.

9.

Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us?

Jun SR, Wassenaar TM, Wanchai V, Patumcharoenpol P, Nookaew I, Ussery DW.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):471. doi: 10.1186/s12859-017-1894-3.

10.

Low-complexity microbiota in the duodenum of children with newly diagnosed ulcerative colitis.

Sjöberg F, Barkman C, Nookaew I, Östman S, Adlerberth I, Saalman R, Wold AE.

PLoS One. 2017 Oct 19;12(10):e0186178. doi: 10.1371/journal.pone.0186178. eCollection 2017.

11.

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons.

Wang J, Jenjaroenpun P, Bhinge A, Angarica VE, Del Sol A, Nookaew I, Kuznetsov VA, Stanton LW.

Genome Res. 2017 Nov;27(11):1783-1794. doi: 10.1101/gr.223313.117. Epub 2017 Oct 13.

12.

Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production.

Thammarongtham C, Nookaew I, Vorapreeda T, Srisuk T, Land ML, Jeennor S, Laoteng K.

Curr Microbiol. 2018 Jan;75(1):57-70. doi: 10.1007/s00284-017-1350-7. Epub 2017 Sep 1.

PMID:
28865010
13.

Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA.

Alkam D, Wongsurawat T, Jenjaroenpun P, Connor S, Hobbs C, Wassenaar TM, Jun SR, Nookaew I, Ussery D.

Genome Announc. 2017 Aug 10;5(32). pii: e00555-17. doi: 10.1128/genomeA.00555-17.

14.

Metabolomics and Integrative Omics for the Development of Thai Traditional Medicine.

Khoomrung S, Wanichthanarak K, Nookaew I, Thamsermsang O, Seubnooch P, Laohapand T, Akarasereenont P.

Front Pharmacol. 2017 Jul 18;8:474. doi: 10.3389/fphar.2017.00474. eCollection 2017. Review.

15.

Assessment of genome annotation using gene function similarity within the gene neighborhood.

Jun SR, Nookaew I, Hauser L, Gorin A.

BMC Bioinformatics. 2017 Jul 19;18(1):345. doi: 10.1186/s12859-017-1761-2.

16.

In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis.

Thorell K, Bengtsson-Palme J, Liu OH, Palacios Gonzales RV, Nookaew I, Rabeneck L, Paszat L, Graham DY, Nielsen J, Lundin SB, Sjöling Å.

Infect Immun. 2017 Sep 20;85(10). pii: e00031-17. doi: 10.1128/IAI.00031-17. Print 2017 Oct.

17.

Network Proteomics: From Protein Structure to Protein-Protein Interaction.

Hu G, Di Paola L, Pullara F, Liang Z, Nookaew I.

Biomed Res Int. 2017;2017:8929613. doi: 10.1155/2017/8929613. Epub 2017 Feb 16. No abstract available.

18.

Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics.

Thankaswamy-Kosalai S, Sen P, Nookaew I.

Genomics. 2017 Jul;109(3-4):186-191. doi: 10.1016/j.ygeno.2017.03.001. Epub 2017 Mar 9.

PMID:
28286147
19.

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer.

Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I.

Sci Rep. 2017 Jan 19;7:40712. doi: 10.1038/srep40712.

20.

Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass.

Poudel S, Giannone RJ, Rodriguez M Jr, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL.

Biotechnol Biofuels. 2017 Jan 10;10:14. doi: 10.1186/s13068-016-0697-5. eCollection 2017.

21.

Splenic Immune Response Is Down-Regulated in C57BL/6J Mice Fed Eicosapentaenoic Acid and Docosahexaenoic Acid Enriched High Fat Diet.

Soni NK, Ross AB, Scheers N, Savolainen OI, Nookaew I, Gabrielsson BG, Sandberg AS.

Nutrients. 2017 Jan 10;9(1). pii: E50. doi: 10.3390/nu9010050.

22.

PanViz: interactive visualization of the structure of functionally annotated pangenomes.

Pedersen TL, Nookaew I, Wayne Ussery D, Månsson M.

Bioinformatics. 2017 Apr 1;33(7):1081-1082. doi: 10.1093/bioinformatics/btw761.

23.

Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants.

Olafsdottir TA, Lindqvist M, Nookaew I, Andersen P, Maertzdorf J, Persson J, Christensen D, Zhang Y, Anderson J, Khoomrung S, Sen P, Agger EM, Coler R, Carter D, Meinke A, Rappuoli R, Kaufmann SH, Reed SG, Harandi AM.

Sci Rep. 2016 Dec 13;6:39097. doi: 10.1038/srep39097.

24.

Comparative Analysis of Two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics.

Karlsson R, Thorell K, Hosseini S, Kenny D, Sihlbom C, Sjöling Å, Karlsson A, Nookaew I.

Front Microbiol. 2016 Nov 11;7:1757. eCollection 2016.

25.

Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome.

Thompson RA, Dahal S, Garcia S, Nookaew I, Trinh CT.

Biotechnol Biofuels. 2016 Sep 6;9(1):194. doi: 10.1186/s13068-016-0607-x. eCollection 2016.

26.

Eicosapentaenoic and Docosahexaenoic Acid-Enriched High Fat Diet Delays Skeletal Muscle Degradation in Mice.

Soni NK, Ross AB, Scheers N, Savolainen OI, Nookaew I, Gabrielsson BG, Sandberg AS.

Nutrients. 2016 Sep 3;8(9). pii: E543. doi: 10.3390/nu8090543.

27.

Adenine-induced chronic renal failure in rats decreases aortic relaxation rate and alters expression of proteins involved in vascular smooth muscle calcium handling.

Nguy L, Shubbar E, Jernås M, Nookaew I, Lundgren J, Olsson B, Nilsson H, Guron G.

Acta Physiol (Oxf). 2016 Dec;218(4):250-264. doi: 10.1111/apha.12724. Epub 2016 Jun 19.

PMID:
27239807
28.

Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System.

Timm CM, Pelletier DA, Jawdy SS, Gunter LE, Henning JA, Engle N, Aufrecht J, Gee E, Nookaew I, Yang Z, Lu TY, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Weston DJ.

Front Plant Sci. 2016 Apr 26;7:497. doi: 10.3389/fpls.2016.00497. eCollection 2016.

29.

Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.

Gatto F, Volpi N, Nilsson H, Nookaew I, Maruzzo M, Roma A, Johansson ME, Stierner U, Lundstam S, Basso U, Nielsen J.

Cell Rep. 2016 May 24;15(8):1822-36. doi: 10.1016/j.celrep.2016.04.056. Epub 2016 May 12.

30.

Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids.

Svahn SL, Väremo L, Gabrielsson BG, Peris E, Nookaew I, Grahnemo L, Sandberg AS, Wernstedt Asterholm I, Jansson JO, Nielsen J, Johansson ME.

PLoS One. 2016 May 11;11(5):e0155099. doi: 10.1371/journal.pone.0155099. eCollection 2016.

31.

Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua.

Thorell K, Hosseini S, Palacios Gonzáles RV, Chaotham C, Graham DY, Paszat L, Rabeneck L, Lundin SB, Nookaew I, Sjöling Å.

BMC Evol Biol. 2016 Feb 29;16:53. doi: 10.1186/s12862-016-0619-y.

32.

Voluntary Running Suppresses Tumor Growth through Epinephrine- and IL-6-Dependent NK Cell Mobilization and Redistribution.

Pedersen L, Idorn M, Olofsson GH, Lauenborg B, Nookaew I, Hansen RH, Johannesen HH, Becker JC, Pedersen KS, Dethlefsen C, Nielsen J, Gehl J, Pedersen BK, Thor Straten P, Hojman P.

Cell Metab. 2016 Mar 8;23(3):554-62. doi: 10.1016/j.cmet.2016.01.011. Epub 2016 Feb 16.

33.

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes.

Väremo L, Scheele C, Broholm C, Mardinoglu A, Kampf C, Asplund A, Nookaew I, Uhlén M, Pedersen BK, Nielsen J.

Cell Rep. 2016 Feb 16;14(6):1567. doi: 10.1016/j.celrep.2016.01.054. Epub 2016 Feb 16. No abstract available.

34.

Normalised immune expression in remission of paediatric ITP.

Jernås M, Strömberg Célind F, Nookaew I, Mellgren K, Wadenvik H, Olsson B.

Thromb Haemost. 2016 Jun 2;115(6):1229-30. doi: 10.1160/TH15-12-0976. Epub 2016 Feb 4. No abstract available.

PMID:
26843317
35.

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW.

Appl Environ Microbiol. 2015 Oct 30;82(1):375-83. doi: 10.1128/AEM.02612-15. Print 2016 Jan 1.

36.

Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa.

Abraham PE, Wang X, Ranjan P, Nookaew I, Zhang B, Tuskan GA, Hettich RL.

J Proteome Res. 2015 Dec 4;14(12):5318-26. doi: 10.1021/acs.jproteome.5b00823. Epub 2015 Oct 30.

PMID:
26483142
37.

Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization.

Zurawski JV, Conway JM, Lee LL, Simpson HJ, Izquierdo JA, Blumer-Schuette S, Nookaew I, Adams MW, Kelly RM.

Appl Environ Microbiol. 2015 Oct;81(20):7159-70. doi: 10.1128/AEM.01622-15. Epub 2015 Aug 7.

38.

Human metabolic atlas: an online resource for human metabolism.

Pornputtapong N, Nookaew I, Nielsen J.

Database (Oxford). 2015 Jul 24;2015:bav068. doi: 10.1093/database/bav068. Print 2015.

39.

Eicosapentaenoic and docosahexaenoic acid-enriched high fat diet delays the development of fatty liver in mice.

Soni NK, Nookaew I, Sandberg AS, Gabrielsson BG.

Lipids Health Dis. 2015 Jul 22;14:74. doi: 10.1186/s12944-015-0072-8.

40.

Ebolavirus comparative genomics.

Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW.

FEMS Microbiol Rev. 2015 Sep;39(5):764-78. doi: 10.1093/femsre/fuv031. Epub 2015 Jul 14. Review.

41.

Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes.

Väremo L, Scheele C, Broholm C, Mardinoglu A, Kampf C, Asplund A, Nookaew I, Uhlén M, Pedersen BK, Nielsen J.

Cell Rep. 2015 May 12;11(6):921-933. doi: 10.1016/j.celrep.2015.04.010. Epub 2015 Apr 30. Erratum in: Cell Rep. 2016 Feb 16;14(6):1567.

42.

Site-specific programming of the host epithelial transcriptome by the gut microbiota.

Sommer F, Nookaew I, Sommer N, Fogelstrand P, Bäckhed F.

Genome Biol. 2015 Mar 28;16:62. doi: 10.1186/s13059-015-0614-4.

43.

Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival.

Goossens KV, Ielasi FS, Nookaew I, Stals I, Alonso-Sarduy L, Daenen L, Van Mulders SE, Stassen C, van Eijsden RG, Siewers V, Delvaux FR, Kasas S, Nielsen J, Devreese B, Willaert RG.

MBio. 2015 Apr 14;6(2). pii: e00427-15. doi: 10.1128/mBio.00427-15.

44.

Insights from 20 years of bacterial genome sequencing.

Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW.

Funct Integr Genomics. 2015 Mar;15(2):141-61. doi: 10.1007/s10142-015-0433-4. Epub 2015 Feb 27. Review.

45.

Dietary polyunsaturated fatty acids increase survival and decrease bacterial load during septic Staphylococcus aureus infection and improve neutrophil function in mice.

Svahn SL, Grahnemo L, Pálsdóttir V, Nookaew I, Wendt K, Gabrielsson B, Schéle E, Benrick A, Andersson N, Nilsson S, Johansson ME, Jansson JO.

Infect Immun. 2015 Feb;83(2):514-21. doi: 10.1128/IAI.02349-14. Epub 2014 Nov 17.

46.

A dedicated database system for handling multi-level data in systems biology.

Pornputtapong N, Wanichthanarak K, Nilsson A, Nookaew I, Nielsen J.

Source Code Biol Med. 2014 Jul 10;9:17. doi: 10.1186/1751-0473-9-17. eCollection 2014.

47.

yStreX: yeast stress expression database.

Wanichthanarak K, Nookaew I, Petranovic D.

Database (Oxford). 2014 Jul 14;2014. pii: bau068. doi: 10.1093/database/bau068. Print 2014.

48.

Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue.

Karlsson FH, Nookaew I, Nielsen J.

PLoS Comput Biol. 2014 Jul 10;10(7):e1003706. doi: 10.1371/journal.pcbi.1003706. eCollection 2014 Jul.

49.

Veillonella, Firmicutes: Microbes disguised as Gram negatives.

Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.

Stand Genomic Sci. 2013 Dec 15;9(2):431-48. doi: 10.4056/sigs.2981345. eCollection 2013 Dec 20.

50.

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.

Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, Väremo L, Nookaew I, Nielsen J.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371. Epub 2014 May 3.

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