User profiles for D. Portik

Daniel Portik

Staff Bioinformatics Scientist, PacBio
Verified email at pacificbiosciences.com
Cited by 2060

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

DM Bickhart, M Kolmogorov, E Tseng, DM Portik… - Nature …, 2022 - nature.com
… able to identify candidate hosts for assembled plasmid sequence (d) in the HiFi assembly. …
Porubsky, D. et al. Fully phased human genome assembly without parental data using single-…

A high-quality Ixodes scapularis genome advances tick science

S De, SB Kingan, C Kitsou, DM Portik, SD Foor… - Nature Genetics, 2023 - nature.com
Ixodes spp. and related ticks transmit prevalent infections, although knowledge of their
biology and development of anti-tick measures have been hindered by the lack of a high-quality …

Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection

DM Portik, AD Leaché, D Rivera, MF Barej… - Molecular …, 2017 - Wiley Online Library
The accumulation of biodiversity in tropical forests can occur through multiple allopatric and
parapatric models of diversification, including forest refugia, riverine barriers and ecological …

Metagenome assembly of high-fidelity long reads with hifiasm-meta

X Feng, H Cheng, D Portik, H Li - Nature methods, 2022 - nature.com
d, Phylogeny of human gut MAGs from the co-assembly. A colored clade corresponds to a
phylum inferred by GTDB-Tk 18,19 . A MAG is omnivore/vegan specific if 90% of reads in the …

Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation

…, RA Knapp, A Muñoz, DM Portik… - Proceedings of the …, 2019 - National Acad Sciences
Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way
that humans have triggered wildlife declines is by transporting disease-causing agents to …

[HTML][HTML] Genetics, Morphology, Advertisement Calls, and Historical Records Distinguish Six New Polyploid Species of African Clawed Frog (Xenopus, Pipidae) from …

…, DB Kelley, PJ McLaughlin, OSG Pauwels, DM Portik… - PloS one, 2015 - journals.plos.org
… known to be present in ZMB, (ZMB 8328A-D, including one tadpole in metamorphosis), ZMB
8329 (… D. Rungger (specimen from captive population originally housed in Laboratoire de …

An evaluation of transcriptome‐based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

DM Portik, LL Smith, K Bi - Molecular ecology resources, 2016 - Wiley Online Library
… Samples were pooled for capture reactions according to phylogenetic relatedness as
determined by 16S mtDNA data (DM Portik, unpublished data). Typical pools contained 5–6 …

[HTML][HTML] Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

DM Portik, CT Brown, NT Pierce-Ward - BMC bioinformatics, 2022 - Springer
Background Long-read shotgun metagenomic sequencing is gaining in popularity and
offers many advantages over short-read sequencing. The higher information content in long …

Redefining possible: combining phylogenomic and supersparse data in frogs

DM Portik, JW Streicher, DC Blackburn… - Molecular Biology …, 2023 - academic.oup.com
The data available for reconstructing molecular phylogenies have become wildly disparate.
Phylogenomic studies can generate data for thousands of genetic markers for dozens of …

Sexual dichromatism drives diversification within a major radiation of African amphibians

DM Portik, RC Bell, DC Blackburn, AM Bauer… - Systematic …, 2019 - academic.oup.com
Abstract Theory predicts that sexually dimorphic traits under strong sexual selection, particularly
those involved with intersexual signaling, can accelerate speciation and produce bursts …