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Items: 33


Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification.

Breitwieser FP, Salzberg SL.

Bioinformatics. 2019 Sep 25. pii: btz715. doi: 10.1093/bioinformatics/btz715. [Epub ahead of print]


Human contamination in bacterial genomes has created thousands of spurious proteins.

Breitwieser FP, Pertea M, Zimin AV, Salzberg SL.

Genome Res. 2019 Jun;29(6):954-960. doi: 10.1101/gr.245373.118. Epub 2019 May 7.


CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.

Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL.

Genome Biol. 2018 Nov 28;19(1):208. doi: 10.1186/s13059-018-1590-2.


KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.

Breitwieser FP, Baker DN, Salzberg SL.

Genome Biol. 2018 Nov 16;19(1):198. doi: 10.1186/s13059-018-1568-0.


Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics.

Simner PJ, Miller HB, Breitwieser FP, Pinilla Monsalve G, Pardo CA, Salzberg SL, Sears CL, Thomas DL, Eberhart CG, Carroll KC.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00472-18. doi: 10.1128/JCM.00472-18. Print 2018 Sep.


Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.

Li Z, Breitwieser FP, Lu J, Jun AS, Asnaghi L, Salzberg SL, Eberhart CG.

Invest Ophthalmol Vis Sci. 2018 Jan 1;59(1):280-288. doi: 10.1167/iovs.17-21617.


Statistical analysis of co-occurrence patterns in microbial presence-absence datasets.

Mainali KP, Bewick S, Thielen P, Mehoke T, Breitwieser FP, Paudel S, Adhikari A, Wolfe J, Slud EV, Karig D, Fagan WF.

PLoS One. 2017 Nov 16;12(11):e0187132. doi: 10.1371/journal.pone.0187132. eCollection 2017.


A review of methods and databases for metagenomic classification and assembly.

Breitwieser FP, Lu J, Salzberg SL.

Brief Bioinform. 2019 Jul 19;20(4):1125-1136. doi: 10.1093/bib/bbx120.


Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs.

Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A.

Ann Intern Med. 2017 Jul 4;167(1):1-7. doi: 10.7326/M17-0085. Epub 2017 Jun 6.


Intracellular HIV-1 RNA and CD4+ T-cell activation in patients starting antiretrovirals.

El-Diwany R, Breitwieser FP, Soliman M, Skaist AM, Srikrishna G, Blankson JN, Ray SC, Wheelan SJ, Thomas DL, Balagopal A.

AIDS. 2017 Jun 19;31(10):1405-1414. doi: 10.1097/QAD.0000000000001480.


Centrifuge: rapid and sensitive classification of metagenomic sequences.

Kim D, Song L, Breitwieser FP, Salzberg SL.

Genome Res. 2016 Dec;26(12):1721-1729. Epub 2016 Oct 17.


Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system.

Salzberg SL, Breitwieser FP, Kumar A, Hao H, Burger P, Rodriguez FJ, Lim M, Quiñones-Hinojosa A, Gallia GL, Tornheim JA, Melia MT, Sears CL, Pardo CA.

Neurol Neuroimmunol Neuroinflamm. 2016 Jun 13;3(4):e251. doi: 10.1212/NXI.0000000000000251. eCollection 2016 Aug.


A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN.

Mazouzi A, Stukalov A, Müller AC, Chen D, Wiedner M, Prochazkova J, Chiang SC, Schuster M, Breitwieser FP, Pichlmair A, El-Khamisy SF, Bock C, Kralovics R, Colinge J, Bennett KL, Loizou JI.

Cell Rep. 2016 Apr 26;15(4):893-908. doi: 10.1016/j.celrep.2016.03.077. Epub 2016 Apr 14.


Germline RBBP6 mutations in familial myeloproliferative neoplasms.

Harutyunyan AS, Giambruno R, Krendl C, Stukalov A, Klampfl T, Berg T, Chen D, Milosevic Feenstra JD, Jäger R, Gisslinger B, Gisslinger H, Rumi E, Passamonti F, Pietra D, Müller AC, Parapatics K, Breitwieser FP, Herrmann R, Colinge J, Bennett KL, Superti-Furga G, Cazzola M, Hammond E, Kralovics R.

Blood. 2016 Jan 21;127(3):362-5. doi: 10.1182/blood-2015-09-668673. Epub 2015 Nov 16. No abstract available.


Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection.

Breitwieser FP, Pardo CA, Salzberg SL.

Version 2. F1000Res. 2015 Jul 2 [revised 2015 Jan 1];4:180. doi: 10.12688/f1000research.6743.2. eCollection 2015.


The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity.

Heinz LX, Baumann CL, Köberlin MS, Snijder B, Gawish R, Shui G, Sharif O, Aspalter IM, Müller AC, Kandasamy RK, Breitwieser FP, Pichlmair A, Bruckner M, Rebsamen M, Blüml S, Karonitsch T, Fauster A, Colinge J, Bennett KL, Knapp S, Wenk MR, Superti-Furga G.

Cell Rep. 2015 Jun 30;11(12):1919-28. doi: 10.1016/j.celrep.2015.05.006. Epub 2015 Jun 18.


Identification of kinase inhibitor targets in the lung cancer microenvironment by chemical and phosphoproteomics.

Gridling M, Ficarro SB, Breitwieser FP, Song L, Parapatics K, Colinge J, Haura EB, Marto JA, Superti-Furga G, Bennett KL, Rix U.

Mol Cancer Ther. 2014 Nov;13(11):2751-62. doi: 10.1158/1535-7163.MCT-14-0152. Epub 2014 Sep 4.


Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma.

Maurer M, Müller AC, Parapatics K, Pickl WF, Wagner C, Rudashevskaya EL, Breitwieser FP, Colinge J, Garg K, Griss J, Bennett KL, Wagner SN.

J Proteome Res. 2014 Jun 6;13(6):2830-45. doi: 10.1021/pr401270y. Epub 2014 May 6.


Building and exploring an integrated human kinase network: global organization and medical entry points.

Colinge J, César-Razquin A, Huber K, Breitwieser FP, Májek P, Superti-Furga G.

J Proteomics. 2014 Jul 31;107:113-27. doi: 10.1016/j.jprot.2014.03.028. Epub 2014 Apr 3.


CD4(+) T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2.

Boucheron N, Tschismarov R, Goeschl L, Moser MA, Lagger S, Sakaguchi S, Winter M, Lenz F, Vitko D, Breitwieser FP, Müller L, Hassan H, Bennett KL, Colinge J, Schreiner W, Egawa T, Taniuchi I, Matthias P, Seiser C, Ellmeier W.

Nat Immunol. 2014 May;15(5):439-448. doi: 10.1038/ni.2864. Epub 2014 Mar 30. Erratum in: Nat Immunol. 2014 Sep;15(9):894. Goeschl, Lisa [corrected to Göschl, Lisa].


A chemical biology approach identifies AMPK as a modulator of melanoma oncogene MITF.

Borgdorff V, Rix U, Winter GE, Gridling M, Müller AC, Breitwieser FP, Wagner C, Colinge J, Bennett KL, Superti-Furga G, Wagner SN.

Oncogene. 2014 May 8;33(19):2531-9. doi: 10.1038/onc.2013.185. Epub 2013 Jun 3.


Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins.

Breitwieser FP, Colinge J.

J Proteomics. 2013 Sep 2;90:77-84. doi: 10.1016/j.jprot.2013.02.022. Epub 2013 Mar 5.


Multiple and sequential data acquisition method: an improved method for fragmentation and detection of cross-linked peptides on a hybrid linear trap quadrupole Orbitrap Velos mass spectrometer.

Rudashevskaya EL, Breitwieser FP, Huber ML, Colinge J, Müller AC, Bennett KL.

Anal Chem. 2013 Feb 5;85(3):1454-61. doi: 10.1021/ac302251f. Epub 2013 Jan 23.


Quantitative proteomics of aqueous and vitreous fluid from patients with idiopathic epiretinal membranes.

Pollreisz A, Funk M, Breitwieser FP, Parapatics K, Sacu S, Georgopoulos M, Dunavoelgyi R, Zlabinger GJ, Colinge J, Bennett KL, Schmidt-Erfurth U.

Exp Eye Res. 2013 Mar;108:48-58. doi: 10.1016/j.exer.2012.11.010. Epub 2012 Nov 29.


Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML.

Winter GE, Rix U, Carlson SM, Gleixner KV, Grebien F, Gridling M, Müller AC, Breitwieser FP, Bilban M, Colinge J, Valent P, Bennett KL, White FM, Superti-Furga G.

Nat Chem Biol. 2012 Nov;8(11):905-912. doi: 10.1038/nchembio.1085. Epub 2012 Sep 30.


A comparative proteomic study of human skin suction blister fluid from healthy individuals using immunodepletion and iTRAQ labeling.

Müller AC, Breitwieser FP, Fischer H, Schuster C, Brandt O, Colinge J, Superti-Furga G, Stingl G, Elbe-Bürger A, Bennett KL.

J Proteome Res. 2012 Jul 6;11(7):3715-27. doi: 10.1021/pr3002035. Epub 2012 May 31.


General statistical modeling of data from protein relative expression isobaric tags.

Breitwieser FP, Müller A, Dayon L, Köcher T, Hainard A, Pichler P, Schmidt-Erfurth U, Superti-Furga G, Sanchez JC, Mechtler K, Bennett KL, Colinge J.

J Proteome Res. 2011 Jun 3;10(6):2758-66. doi: 10.1021/pr1012784. Epub 2011 May 11.


Initial characterization of the human central proteome.

Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, Bürckstümmer T, Bennett KL, Superti-Furga G, Colinge J.

BMC Syst Biol. 2011 Jan 26;5:17. doi: 10.1186/1752-0509-5-17.


A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib.

Burkard TR, Rix U, Breitwieser FP, Superti-Furga G, Colinge J.

PLoS Comput Biol. 2010 Nov 18;6(11):e1001001. doi: 10.1371/journal.pcbi.1001001.


Using iTRAQ combined with tandem affinity purification to enhance low-abundance proteins associated with somatically mutated EGFR core complexes in lung cancer.

Haura EB, Müller A, Breitwieser FP, Li J, Grebien F, Colinge J, Bennett KL.

J Proteome Res. 2011 Jan 7;10(1):182-90. doi: 10.1021/pr100863f. Epub 2010 Nov 9.


Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ®-labelled specimens.

Bennett KL, Funk M, Tschernutter M, Breitwieser FP, Planyavsky M, Ubaida Mohien C, Müller A, Trajanoski Z, Colinge J, Superti-Furga G, Schmidt-Erfurth U.

J Proteomics. 2011 Feb 1;74(2):151-66. doi: 10.1016/j.jprot.2010.10.002. Epub 2010 Oct 16.


A comprehensive target selectivity survey of the BCR-ABL kinase inhibitor INNO-406 by kinase profiling and chemical proteomics in chronic myeloid leukemia cells.

Rix U, Remsing Rix LL, Terker AS, Fernbach NV, Hantschel O, Planyavsky M, Breitwieser FP, Herrmann H, Colinge J, Bennett KL, Augustin M, Till JH, Heinrich MC, Valent P, Superti-Furga G.

Leukemia. 2010 Jan;24(1):44-50. doi: 10.1038/leu.2009.228. Epub 2009 Nov 5.


Acid elution and one-dimensional shotgun analysis on an Orbitrap mass spectrometer: an application to drug affinity chromatography.

Fernbach NV, Planyavsky M, Müller A, Breitwieser FP, Colinge J, Rix U, Bennett KL.

J Proteome Res. 2009 Oct;8(10):4753-65. doi: 10.1021/pr900455x.


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