Centrifuge: rapid and sensitive classification of metagenomic sequences von Kim, Daehwan, Song, Li, Breitwieser, Florian P, Salzberg, Steven L

Volltext

A review of methods and databases for metagenomic classification and assembly von Breitwieser, Florian P, Lu, Jennifer, Salzberg, Steven L

Volltext

Bracken: estimating species abundance in metagenomics data von Lu, Jennifer, Breitwieser, Florian P, Thielen, Peter, Salzberg, Steven L

Volltext

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise von Pertea, Mihaela, Shumate, Alaina, Pertea, Geo, Varabyou, Ales, Breitwieser, Florian P, Chang, Yu-Chi, Madugundu, Anil K, Pandey, Akhilesh, Salzberg, Steven L

Volltext

Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification von Breitwieser, Florian P, Salzberg, Steven L

Volltext

Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics von Simner, Patricia J, Miller, Heather B, Breitwieser, Florian P, Pinilla Monsalve, Gabriel, Pardo, Carlos A, Salzberg, Steven L, Sears, Cynthia L, Thomas, David L, Eberhart, Charles G, Carroll, Karen C

Volltext

Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing von Li, Zhigang, Breitwieser, Florian P, Lu, Jennifer, Jun, Albert S, Asnaghi, Laura, Salzberg, Steven L, Eberhart, Charles G

Volltext

The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity von Heinz, Leonhard X., Baumann, Christoph L., Köberlin, Marielle S., Snijder, Berend, Gawish, Riem, Shui, Guanghou, Sharif, Omar, Aspalter, Irene M., Müller, André C., Kandasamy, Richard K., Breitwieser, Florian P., Pichlmair, Andreas, Bruckner, Manuela, Rebsamen, Manuele, Blüml, Stephan, Karonitsch, Thomas, Fauster, Astrid, Colinge, Jacques, Bennett, Keiryn L., Knapp, Sylvia, Wenk, Markus R., Superti-Furga, Giulio

Volltext

Statistical analysis of co-occurrence patterns in microbial presence-absence datasets von Mainali, Kumar P, Bewick, Sharon, Thielen, Peter, Mehoke, Thomas, Breitwieser, Florian P, Paudel, Shishir, Adhikari, Arjun, Wolfe, Joshua, Slud, Eric V, Karig, David, Fagan, William F

Volltext

Metagenome analysis using the Kraken software suite von Lu, Jennifer, Rincon, Natalia, Wood, Derrick E., Breitwieser, Florian P., Pockrandt, Christopher, Langmead, Ben, Salzberg, Steven L., Steinegger, Martin

Volltext

A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN von Mazouzi, Abdelghani, Stukalov, Alexey, Müller, André C., Chen, Doris, Wiedner, Marc, Prochazkova, Jana, Chiang, Shih-Chieh, Schuster, Michael, Breitwieser, Florian P., Pichlmair, Andreas, El-Khamisy, Sherif F., Bock, Christoph, Kralovics, Robert, Colinge, Jacques, Bennett, Keiryn L., Loizou, Joanna I.

Volltext

General Statistical Modeling of Data from Protein Relative Expression Isobaric Tags von Breitwieser, Florian P, Müller, André, Dayon, Loïc, Köcher, Thomas, Hainard, Alexandre, Pichler, Peter, Schmidt-Erfurth, Ursula, Superti-Furga, Giulio, Sanchez, Jean-Charles, Mechtler, Karl, Bennett, Keiryn L, Colinge, Jacques

Volltext

Human contamination in bacterial genomes has created thousands of spurious proteins von Breitwieser, Florian P, Pertea, Mihaela, Zimin, Aleksey V, Salzberg, Steven L

Volltext

Deconvoluting virome-wide antibody epitope reactivity profiles von Monaco, Daniel R., Kottapalli, Sanjay V., Breitwieser, Florian P., Anderson, Danielle E., Wijaya, Limin, Tan, Kevin, Chia, Wan Ni, Kammers, Kai, Caturegli, Patrizio, Waugh, Kathleen, Roederer, Mario, Petri, Michelle, Goldman, Daniel W., Rewers, Marian, Wang, Lin-Fa, Larman, H. Benjamin

Volltext

Identification of kinase inhibitor targets in the lung cancer microenvironment by chemical and phosphoproteomics von Gridling, Manuela, Ficarro, Scott B, Breitwieser, Florian P, Song, Lanxi, Parapatics, Katja, Colinge, Jacques, Haura, Eric B, Marto, Jarrod A, Superti-Furga, Giulio, Bennett, Keiryn L, Rix, Uwe

Volltext

Author Correction: Metagenome analysis using the Kraken software suite von Lu, Jennifer, Rincon, Natalia, Wood, Derrick E, Breitwieser, Florian P, Pockrandt, Christopher, Langmead, Ben, Salzberg, Steven L, Steinegger, Martin

Volltext

A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib von Burkard, Thomas R, Rix, Uwe, Breitwieser, Florian P, Superti-Furga, Giulio, Colinge, Jacques

Volltext

Building and exploring an integrated human kinase network: Global organization and medical entry points von Colinge, Jacques, César-Razquin, Adrián, Huber, Kilian, Breitwieser, Florian P., Májek, Peter, Superti-Furga, Giulio

Volltext

Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection von Breitwieser, Florian P., Pardo, Carlos A., Salzberg, Steven L.

Volltext

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms von Yee, Rebecca, Breitwieser, Florian P., Hao, Stephanie, Opene, Belita N.A., Workman, Rachael E., Tamma, Pranita D., Dien-Bard, Jennifer, Timp, Winston, Simner, Patricia J.

Volltext