Jakub Truszkowski
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Explore the profile of Jakub Truszkowski including associated specialties, affiliations and a list of published articles.
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10
Citations
32
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Recent Articles
1.
Truszkowski J, Maor R, Yousuf R, Biswas S, Chater C, Gasson P, et al.
Ecol Appl
. 2025 Jan;
35(1):e3077.
PMID: 39835343
Determining the harvest location of timber is crucial to enforcing international regulations designed to protect natural resources and to tackle illegal logging and associated trade in forest products. Stable isotope...
2.
Mortier T, Truszkowski J, Norman M, Boner M, Buliga B, Chater C, et al.
Nat Plants
. 2024 Mar;
10(3):390-401.
PMID: 38467801
Scientific testing including stable isotope ratio analysis (SIRA) and trace element analysis (TEA) is critical for establishing plant origin, tackling deforestation and enforcing economic sanctions. Yet methods combining SIRA and...
3.
Truszkowski J, Perrigo A, Broman D, Ronquist F, Antonelli A
Syst Biol
. 2023 Jul;
72(5):1199-1206.
PMID: 37498209
Bayesian phylogenetics is now facing a critical point. Over the last 20 years, Bayesian methods have reshaped phylogenetic inference and gained widespread popularity due to their high accuracy, the ability...
4.
De Maio N, Alekseyenko A, Coleman-Smith W, Pardi F, Suchard M, Tamuri A, et al.
BMC Bioinformatics
. 2021 May;
22(1):285.
PMID: 34049487
Background: Many important applications in bioinformatics, including sequence alignment and protein family profiling, employ sequence weighting schemes to mitigate the effects of non-independence of homologous sequences and under- or over-representation...
5.
Truszkowski J, Scornavacca C, Pardi F
Theor Popul Biol
. 2020 Dec;
137:22-31.
PMID: 33333117
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between a gene tree and the species...
6.
Davila Felipe M, Domelevo Entfellner J, Lemoine F, Truszkowski J, Gascuel O
J Math Biol
. 2019 May;
79(2):485-508.
PMID: 31037350
The transfer distance (TD) was introduced in the classification framework and studied in the context of phylogenetic tree matching. Recently, Lemoine et al. (Nature 556(7702):452-456, 2018. https://doi.org/10.1038/s41586-018-0043-0 ) showed that...
7.
Truszkowski J, Goldman N
Syst Biol
. 2015 Nov;
65(2):328-33.
PMID: 26615177
We prove that maximum likelihood phylogenetic inference is consistent on gapped multiple sequence alignments (MSAs) as long as substitution rates across each edge are greater than zero, under mild assumptions...
8.
Brown D, Truszkowski J
Pac Symp Biocomput
. 2013 Feb;
:310-9.
PMID: 23424136
We consider the problem of phylogenetic placement, in which large numbers of sequences (often next-generation sequencing reads) are placed onto an existing phylogenetic tree. We adapt our recent work on...
9.
Truszkowski J, Hao Y, Brown D
Algorithms Mol Biol
. 2012 Nov;
7(1):32.
PMID: 23181935
: Recently, we have identified a randomized quartet phylogeny algorithm that has O(nlogn) runtime with high probability, which is asymptotically optimal. Our algorithm has high probability of returning the correct...
10.
Truszkowski J, Brown D
BMC Bioinformatics
. 2011 May;
12:168.
PMID: 21586147
Background: Identifying recombinations in HIV is important for studying the epidemiology of the virus and aids in the design of potential vaccines and treatments. The previous widely-used tool for this...