MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

por Koslicki, David, Falush, Daniel
Publicado 2016

CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices

por Liu, Shaopeng, Koslicki, David
Publicado 2022

Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac

por Wei, Wei, Millward, Andrew, Koslicki, David
Publicado 2023

WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification

por Koslicki, David, Foucart, Simon, Rosen, Gail
Publicado 2014

Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac

por Wei, Wei, Millward, Andrew, Koslicki, David
Publicado 2023

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample

por Koslicki, David, White, Stephen, Ma, Chunyu, Novikov, Alexei
Publicado 2023

KGML-xDTD: a knowledge graph–based machine learning framework for drug treatment prediction and mechanism description

por Ma, Chunyu, Zhou, Zhihan, Liu, Han, Koslicki, David
Publicado 2023

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles

por Sarwal, Varuni, Brito, Jaqueline, Mangul, Serghei, Koslicki, David
Publicado 2023

Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash

por Rahman Hera, Mahmudur, Pierce-Ward, N. Tessa, Koslicki, David
Publicado 2023

The minimizer Jaccard estimator is biased and inconsistent

por Belbasi, Mahdi, Blanca, Antonio, Harris, Robert S, Koslicki, David, Medvedev, Paul
Publicado 2022

Metalign: efficient alignment-based metagenomic profiling via containment min hash

por LaPierre, Nathan, Alser, Mohammed, Eskin, Eleazar, Koslicki, David, Mangul, Serghei
Publicado 2020

Improving the usability and comprehensiveness of microbial databases

por Loeffler, Caitlin, Karlsberg, Aaron, Martin, Lana S., Eskin, Eleazar, Koslicki, David, Mangul, Serghei
Publicado 2020

Correction to: Improving the usability and comprehensiveness of microbial databases

por Loeffler, Caitlin, Karlsberg, Aaron, Martin, Lana S., Eskin, Eleazar, Koslicki, David, Mangul, Serghei
Publicado 2020

Assessing taxonomic metagenome profilers with OPAL

por Meyer, Fernando, Bremges, Andreas, Belmann, Peter, Janssen, Stefan, McHardy, Alice C., Koslicki, David
Publicado 2019

MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples

por LaPierre, Nathan, Mangul, Serghei, Alser, Mohammed, Mandric, Igor, Wu, Nicholas C., Koslicki, David, Eskin, Eleazar
Publicado 2019

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

por Koslicki, David, Chatterjee, Saikat, Shahrivar, Damon, Walker, Alan W., Francis, Suzanna C., Fraser, Louise J., Vehkaperä, Mikko, Lan, Yueheng, Corander, Jukka
Publicado 2015

Application of MCAT questions as a testing tool and evaluation metric for knowledge graph–based reasoning systems

por Fecho, Karamarie, Balhoff, James, Bizon, Chris, Byrd, William E., Hang, Sui, Koslicki, David, Rensi, Stefano E., Schmitt, Patrick L., Wawer, Mathias J., Williams, Mark, Ahalt, Stanley C.
Publicado 2021

ARAX: a graph-based modular reasoning tool for translational biomedicine

por Glen, Amy K, Ma, Chunyu, Mendoza, Luis, Womack, Finn, Wood, E C, Sinha, Meghamala, Acevedo, Liliana, Kvarfordt, Lindsey G, Peene, Ross C, Liu, Shaopeng, Hoffman, Andrew S, Roach, Jared C, Deutsch, Eric W, Ramsey, Stephen A, Koslicki, David
Publicado 2023

Technology dictates algorithms: recent developments in read alignment

por Alser, Mohammed, Rotman, Jeremy, Deshpande, Dhrithi, Taraszka, Kodi, Shi, Huwenbo, Baykal, Pelin Icer, Yang, Harry Taegyun, Xue, Victor, Knyazev, Sergey, Singer, Benjamin D., Balliu, Brunilda, Koslicki, David, Skums, Pavel, Zelikovsky, Alex, Alkan, Can, Mutlu, Onur, Mangul, Serghei
Publicado 2021

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

por Olde Loohuis, Loes M., Mangul, Serghei, Ori, Anil P. S., Jospin, Guillaume, Koslicki, David, Yang, Harry Taegyun, Wu, Timothy, Boks, Marco P., Lomen-Hoerth, Catherine, Wiedau-Pazos, Martina, Cantor, Rita M., de Vos, Willem M., Kahn, René S., Eskin, Eleazar, Ophoff, Roel A.
Publicado 2018