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Items: 1 to 50 of 80

1.

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.

Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N.

mSystems. 2019 Sep 24;4(5). pii: e00375-19. doi: 10.1128/mSystems.00375-19.

2.

A framework for reviewing livestock disease reporting systems in high-risk areas: assessing performance and perceptions towards foot and mouth disease reporting in the Thrace region of Greece, Bulgaria and Turkey.

Motta P, Garner G, Hòvari M, Alexandrov T, Bulut A, Fragou IA, Sumption K.

Transbound Emerg Dis. 2019 May;66(3):1268-1279. doi: 10.1111/tbed.13143. Epub 2019 Mar 2.

PMID:
30734513
3.

Field observations and experiences gained from the implementation of control measures against lumpy skin disease in South-East Europe between 2015 and 2017.

Tuppurainen ESM, Antoniou SE, Tsiamadis E, Topkaridou M, Labus T, Debeljak Z, Plavšić B, Miteva A, Alexandrov T, Pite L, Boci J, Marojevic D, Kondratenko V, Atanasov Z, Murati B, Acinger-Rogic Z, Kohnle L, Calistri P, Broglia A.

Prev Vet Med. 2018 Dec 13. pii: S0167-5877(18)30548-8. doi: 10.1016/j.prevetmed.2018.12.006. [Epub ahead of print]

PMID:
30581092
4.

Neethling vaccine proved highly effective in controlling lumpy skin disease epidemics in the Balkans.

Klement E, Broglia A, Antoniou SE, Tsiamadis V, Plevraki E, Petrović T, Polaček V, Debeljak Z, Miteva A, Alexandrov T, Marojevic D, Pite L, Kondratenko V, Atanasov Z, Gubbins S, Stegeman A, Abrahantes JC.

Prev Vet Med. 2018 Dec 5. pii: S0167-5877(18)30537-3. doi: 10.1016/j.prevetmed.2018.12.001. [Epub ahead of print]

PMID:
30553537
5.

Data-Driven Rescoring of Metabolite Annotations Significantly Improves Sensitivity.

C Silva AS, Palmer A, Kovalev V, Tarasov A, Alexandrov T, Martens L, Degroeve S.

Anal Chem. 2018 Oct 2;90(19):11636-11642. doi: 10.1021/acs.analchem.8b03224. Epub 2018 Sep 21.

PMID:
30188119
6.

Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data.

Alexandrov T, Golyandina N, Holloway D, Shlemov A, Spirov A.

J Comput Biol. 2018 Nov;25(11):1220-1230. doi: 10.1089/cmb.2017.0063. Epub 2018 Aug 17.

PMID:
30117746
7.

Economic cost of lumpy skin disease outbreaks in three Balkan countries: Albania, Bulgaria and the Former Yugoslav Republic of Macedonia (2016-2017).

Casal J, Allepuz A, Miteva A, Pite L, Tabakovsky B, Terzievski D, Alexandrov T, Beltrán-Alcrudo D.

Transbound Emerg Dis. 2018 Dec;65(6):1680-1688. doi: 10.1111/tbed.12926. Epub 2018 Jul 10.

PMID:
29992738
8.

Suitability of group-level oral fluid sampling in ruminant populations for lumpy skin disease virus detection.

Dietze K, Moritz T, Alexandrov T, Krstevski K, Schlottau K, Milovanovic M, Hoffmann D, Hoffmann B.

Vet Microbiol. 2018 Jul;221:44-48. doi: 10.1016/j.vetmic.2018.05.022. Epub 2018 May 31.

PMID:
29981707
9.

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation.

Nothias LF, Nothias-Esposito M, da Silva R, Wang M, Protsyuk I, Zhang Z, Sarvepalli A, Leyssen P, Touboul D, Costa J, Paolini J, Alexandrov T, Litaudon M, Dorrestein PC.

J Nat Prod. 2018 Apr 27;81(4):758-767. doi: 10.1021/acs.jnatprod.7b00737. Epub 2018 Mar 2.

PMID:
29498278
10.

Creating a 3D microbial and chemical snapshot of a human habitat.

Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC.

Sci Rep. 2018 Feb 27;8(1):3669. doi: 10.1038/s41598-018-21541-4.

11.

3D molecular cartography using LC-MS facilitated by Optimus and 'ili software.

Protsyuk I, Melnik AV, Nothias LF, Rappez L, Phapale P, Aksenov AA, Bouslimani A, Ryazanov S, Dorrestein PC, Alexandrov T.

Nat Protoc. 2018 Jan;13(1):134-154. doi: 10.1038/nprot.2017.122. Epub 2017 Dec 21.

PMID:
29266099
12.

Curatr: a web application for creating, curating and sharing a mass spectral library.

Palmer A, Phapale P, Fay D, Alexandrov T.

Bioinformatics. 2018 Apr 15;34(8):1436-1438. doi: 10.1093/bioinformatics/btx786.

PMID:
29253079
13.

Meta-mass shift chemical profiling of metabolomes from coral reefs.

Hartmann AC, Petras D, Quinn RA, Protsyuk I, Archer FI, Ransome E, Williams GJ, Bailey BA, Vermeij MJA, Alexandrov T, Dorrestein PC, Rohwer FL.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11685-11690. doi: 10.1073/pnas.1710248114. Epub 2017 Oct 12.

14.

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung.

Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC.

Cell Host Microbe. 2017 Nov 8;22(5):705-716.e4. doi: 10.1016/j.chom.2017.10.001. Epub 2017 Oct 19.

15.

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples.

Melnik AV, da Silva RR, Hyde ER, Aksenov AA, Vargas F, Bouslimani A, Protsyuk I, Jarmusch AK, Tripathi A, Alexandrov T, Knight R, Dorrestein PC.

Anal Chem. 2017 Jul 18;89(14):7549-7559. doi: 10.1021/acs.analchem.7b01381. Epub 2017 Jul 6.

PMID:
28628333
16.

N-acyl Taurines and Acylcarnitines Cause an Imbalance in Insulin Synthesis and Secretion Provoking β Cell Dysfunction in Type 2 Diabetes.

Aichler M, Borgmann D, Krumsiek J, Buck A, MacDonald PE, Fox JEM, Lyon J, Light PE, Keipert S, Jastroch M, Feuchtinger A, Mueller NS, Sun N, Palmer A, Alexandrov T, Hrabe de Angelis M, Neschen S, Tschöp MH, Walch A.

Cell Metab. 2017 Jun 6;25(6):1334-1347.e4. doi: 10.1016/j.cmet.2017.04.012.

17.

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae.

Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC.

Elife. 2017 May 11;6. pii: e24214. doi: 10.7554/eLife.24214.

18.

Prediction of Pig Trade Movements in Different European Production Systems Using Exponential Random Graph Models.

Relun A, Grosbois V, Alexandrov T, Sánchez-Vizcaíno JM, Waret-Szkuta A, Molia S, Etter EM, Martínez-López B.

Front Vet Sci. 2017 Mar 3;4:27. doi: 10.3389/fvets.2017.00027. eCollection 2017.

19.

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen.

Garg N, Zeng Y, Edlund A, Melnik AV, Sanchez LM, Mohimani H, Gurevich A, Miao V, Schiffler S, Lim YW, Luzzatto-Knaan T, Cai S, Rohwer F, Pevzner PA, Cichewicz RH, Alexandrov T, Dorrestein PC.

mSystems. 2016 Dec 20;1(6). pii: e00139-16. doi: 10.1128/mSystems.00139-16. eCollection 2016 Nov-Dec.

20.

Lifestyle chemistries from phones for individual profiling.

Bouslimani A, Melnik AV, Xu Z, Amir A, da Silva RR, Wang M, Bandeira N, Alexandrov T, Knight R, Dorrestein PC.

Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7645-E7654. Epub 2016 Nov 14.

21.

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.

Palmer A, Phapale P, Chernyavsky I, Lavigne R, Fay D, Tarasov A, Kovalev V, Fuchser J, Nikolenko S, Pineau C, Becker M, Alexandrov T.

Nat Methods. 2017 Jan;14(1):57-60. doi: 10.1038/nmeth.4072. Epub 2016 Nov 14.

22.

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.

Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook V, Garg N, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling TJ, Luzzatto-Knaan T, McCall LI, McGrath AP, Meehan MJ, Merritt JK, Mills RH, Morton J, Podvin S, Protsyuk I, Purdy T, Satterfield K, Searles S, Shah S, Shires S, Steffen D, White M, Todoric J, Tuttle R, Wojnicz A, Sapp V, Vargas F, Yang J, Zhang C, Dorrestein PC.

Anal Chem. 2016 Nov 15;88(22):10775-10784. Epub 2016 Oct 24.

23.

Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques.

Burns JH, Alexandrov T, Ovchinnikova K, Gates RD, Takabayashi M.

Data Brief. 2016 Sep 19;9:460-462. eCollection 2016 Dec.

24.

Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition.

Lotz JM, Hoffmann F, Lotz J, Heldmann S, Trede D, Oetjen J, Becker M, Ernst G, Maas P, Alexandrov T, Guntinas-Lichius O, Thiele H, von Eggeling F.

Biochim Biophys Acta Proteins Proteom. 2017 Jul;1865(7):946-956. doi: 10.1016/j.bbapap.2016.08.018. Epub 2016 Sep 1.

PMID:
27594533
25.

Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework.

Burns JHR, Alexandrov T, Ovchinnikova E, Gates RD, Takabayashi M.

J Invertebr Pathol. 2016 Oct;140:51-57. doi: 10.1016/j.jip.2016.08.007. Epub 2016 Aug 20.

PMID:
27555383
26.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N.

Nat Biotechnol. 2016 Aug 9;34(8):828-837. doi: 10.1038/nbt.3597.

27.

An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments.

Oetjen J, Lachmund D, Palmer A, Alexandrov T, Becker M, Boskamp T, Maass P.

Anal Bioanal Chem. 2016 Sep;408(24):6729-40. doi: 10.1007/s00216-016-9793-4. Epub 2016 Aug 2.

PMID:
27485623
28.

Spatial and Functional Organization of Pig Trade in Different European Production Systems: Implications for Disease Prevention and Control.

Relun A, Grosbois V, Sánchez-Vizcaíno JM, Alexandrov T, Feliziani F, Waret-Szkuta A, Molia S, Etter EM, Martínez-López B.

Front Vet Sci. 2016 Feb 4;3:4. doi: 10.3389/fvets.2016.00004. eCollection 2016.

29.

Molecular and chemical dialogues in bacteria-protozoa interactions.

Song C, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM.

Sci Rep. 2015 Aug 6;5:12837. doi: 10.1038/srep12837.

30.

Using collective expert judgements to evaluate quality measures of mass spectrometry images.

Palmer A, Ovchinnikova E, Thuné M, Lavigne R, Guével B, Dyatlov A, Vitek O, Pineau C, Borén M, Alexandrov T.

Bioinformatics. 2015 Jun 15;31(12):i375-84. doi: 10.1093/bioinformatics/btv266.

31.

Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry.

Oetjen J, Veselkov K, Watrous J, McKenzie JS, Becker M, Hauberg-Lotte L, Kobarg JH, Strittmatter N, Mróz AK, Hoffmann F, Trede D, Palmer A, Schiffler S, Steinhorst K, Aichler M, Goldin R, Guntinas-Lichius O, von Eggeling F, Thiele H, Maedler K, Walch A, Maass P, Dorrestein PC, Takats Z, Alexandrov T.

Gigascience. 2015 May 4;4:20. doi: 10.1186/s13742-015-0059-4. eCollection 2015.

32.

Molecular cartography of the human skin surface in 3D.

Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Moeller Christensen GJ, Nakatsuji T, Zhang L, Borkowski AW, Meehan MJ, Dorrestein K, Gallo RL, Bandeira N, Knight R, Alexandrov T, Dorrestein PC.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2120-9. doi: 10.1073/pnas.1424409112. Epub 2015 Mar 30.

33.

Serial 3D imaging mass spectrometry at its tipping point.

Palmer AD, Alexandrov T.

Anal Chem. 2015 Apr 21;87(8):4055-62. doi: 10.1021/ac504604g. Epub 2015 Apr 7.

PMID:
25817912
34.

The community ecology of microbial molecules.

Quinn RA, Alexandrov T.

J Chem Ecol. 2014 Dec;40(11-12):1161-2. doi: 10.1007/s10886-014-0528-8. No abstract available.

35.

Spatial segmentation of MALDI FT-ICR MSI data: a powerful tool to explore the head and neck tumor in situ lipidome.

Krasny L, Hoffmann F, Ernst G, Trede D, Alexandrov T, Havlicek V, Guntinas-Lichius O, von Eggeling F, Crecelius AC.

J Am Soc Mass Spectrom. 2015 Jan;26(1):36-43. doi: 10.1007/s13361-014-1018-5. Epub 2014 Nov 6.

PMID:
25374335
36.

MALDI imaging mass spectrometry: discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures.

Klein O, Strohschein K, Nebrich G, Oetjen J, Trede D, Thiele H, Alexandrov T, Giavalisco P, Duda GN, von Roth P, Geissler S, Klose J, Winkler T.

Proteomics. 2014 Oct;14(20):2249-60. doi: 10.1002/pmic.201400088. Epub 2014 Aug 21. Erratum in: Proteomics. 2014 Nov;14(21-22):2630.

PMID:
25056804
37.

Progression from cirrhosis to cancer is associated with early ubiquitin post-translational modifications: identification of new biomarkers of cirrhosis at risk of malignancy.

Laouirem S, Le Faouder J, Alexandrov T, Mestivier D, Léger T, Baudin X, Mebarki M, Paradis V, Camadro JM, Bedossa P.

J Pathol. 2014 Dec;234(4):452-63. doi: 10.1002/path.4398. Epub 2014 Sep 12.

PMID:
24979321
38.

Histomolecular interpretation of pleomorphic adenomas of the salivary gland by matrix-assisted laser desorption ionization imaging and spatial segmentation.

Ernst G, Guntinas-Lichius O, Hauberg-Lotte L, Trede D, Becker M, Alexandrov T, von Eggeling F.

Head Neck. 2015 Jul;37(7):1014-21. doi: 10.1002/hed.23713. Epub 2014 Jul 11.

PMID:
24942285
39.

Assessing the potential spread and maintenance of foot-and-mouth disease virus infection in wild ungulates: general principles and application to a specific scenario in Thrace.

Dhollander S, Belsham GJ, Lange M, Willgert K, Alexandrov T, Chondrokouki E, Depner K, Khomenko S, Özyörük F, Salman M, Thulke HH, Bøtner A.

Transbound Emerg Dis. 2016 Apr;63(2):165-74. doi: 10.1111/tbed.12240. Epub 2014 Jun 6.

PMID:
24903641
40.

Evaluation of the spatial patterns and risk factors, including backyard pigs, for classical swine fever occurrence in Bulgaria using a Bayesian model.

Martínez-López B, Alexandrov T, Mur L, Sánchez-Vizcaíno F, Sánchez-Vizcaíno JM.

Geospat Health. 2014 May;8(2):489-501.

41.

Early clinical and radiographic results of minimally invasive anterior approach hip arthroplasty.

Alexandrov T, Ahlmann ER, Menendez LR.

Adv Orthop. 2014;2014:954208. doi: 10.1155/2014/954208. Epub 2014 Mar 2.

42.

Tumoral heterogeneity of hepatic cholangiocarcinomas revealed by MALDI imaging mass spectrometry.

Le Faouder J, Laouirem S, Alexandrov T, Ben-Harzallah S, Léger T, Albuquerque M, Bedossa P, Paradis V.

Proteomics. 2014 Apr;14(7-8):965-72. doi: 10.1002/pmic.201300463.

PMID:
24678008
43.

Phenalenone-type phytoalexins mediate resistance of banana plants (Musa spp.) to the burrowing nematode Radopholus similis.

Hölscher D, Dhakshinamoorthy S, Alexandrov T, Becker M, Bretschneider T, Buerkert A, Crecelius AC, De Waele D, Elsen A, Heckel DG, Heklau H, Hertweck C, Kai M, Knop K, Krafft C, Maddula RK, Matthäus C, Popp J, Schneider B, Schubert US, Sikora RA, Svatoš A, Swennen RL.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):105-10. doi: 10.1073/pnas.1314168110. Epub 2013 Dec 9.

44.

The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

de Ridder J, Bromberg Y, Michaut M, Satagopam VP, Corpas M, MacIntyre G, Alexandrov T.

PLoS Comput Biol. 2013;9(11):e1003350. doi: 10.1371/journal.pcbi.1003350. Epub 2013 Nov 7. No abstract available.

45.

Learning how to run a lab: interviews with principal investigators.

Alexandrov T, Bourne PE.

PLoS Comput Biol. 2013;9(11):e1003349. doi: 10.1371/journal.pcbi.1003349. Epub 2013 Nov 7. No abstract available.

46.

Analysis and interpretation of imaging mass spectrometry data by clustering mass-to-charge images according to their spatial similarity.

Alexandrov T, Chernyavsky I, Becker M, von Eggeling F, Nikolenko S.

Anal Chem. 2013 Dec 3;85(23):11189-95. doi: 10.1021/ac401420z. Epub 2013 Nov 15.

PMID:
24180335
47.

Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry.

Watrous J, Roach P, Heath B, Alexandrov T, Laskin J, Dorrestein PC.

Anal Chem. 2013 Nov 5;85(21):10385-91. doi: 10.1021/ac4023154. Epub 2013 Oct 14.

48.

Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome.

Traxler MF, Watrous JD, Alexandrov T, Dorrestein PC, Kolter R.

MBio. 2013 Aug 20;4(4). pii: e00459-13. doi: 10.1128/mBio.00459-13.

49.

Testing for presence of known and unknown molecules in imaging mass spectrometry.

Alexandrov T, Bartels A.

Bioinformatics. 2013 Sep 15;29(18):2335-42. doi: 10.1093/bioinformatics/btt388. Epub 2013 Jul 19.

PMID:
23873892
50.

Surveillance of foot-and-mouth disease (FMD) in susceptible wildlife and domestic ungulates in Southeast of Bulgaria following a FMD case in wild boar.

Alexandrov T, Stefanov D, Kamenov P, Miteva A, Khomenko S, Sumption K, Meyer-Gerbaulet H, Depner K.

Vet Microbiol. 2013 Sep 27;166(1-2):84-90. doi: 10.1016/j.vetmic.2013.05.016. Epub 2013 Jun 14.

PMID:
23830685

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