Author details

Full Name

Arian F A Smit

Affiliation

ORCID

Career Start Year

1993

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37104599	Evolutionary constraint and innovation across hundreds of placental mammals.	Science	2023
37071810	Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.	Mol Biol Evol	2023
35357925	From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.	Science	2022
35591887	Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families.	NAR Genomics and Bioinformatics	2022
35456515	Methodologies for the Discovery of Transposable Element Families.	Genes	2022
35962045	Author Correction: Comparative and demographic analysis of orang-utan genomes.	Nature	2022
34749730	The transposable element-rich genome of the cereal pest Sitophilus oryzae.	BMC Biol	2021
34138525	Curation Guidelines for de novo Generated Transposable Element Families.	Current Protocols	2021
33436076	The Dfam community resource of transposable element families, sequence models, and genome annotations.	Mobile DNA	2021
32300014	RepeatModeler2 for automated genomic discovery of transposable element families.	Proc Natl Acad Sci U S A	2020
26612867	The Dfam database of repetitive DNA families.	Nucleic Acids Res	2016
25483050	Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs.	Cell Cycle	2016
26916108	Discovery of a new repeat family in the Callithrix jacchus genome.	Genome Res	2016
26244060	A call for benchmarking transposable element annotation methods.	Mob DNA	2015
25428374	The UCSC Genome Browser database: 2015 update.	Nucleic Acids Res	2015
25209798	Gibbon genome and the fast karyotype evolution of small apes.	Nature	2014
25504731	Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.	Science	2014
25503085	Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.	Genome Biol Evol	2014
25499090	Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes.	Retrovirology	2014
24727652	Multiscale representation of genomic signals.	Nat Methods	2014
24803667	Realistic artificial DNA sequences as negative controls for computational genomics.	Nucleic Acids Res	2014
23203985	Dfam: a database of repetitive DNA based on profile hidden Markov models.	Nucleic Acids Res	2013
22541534	Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers.	Mob DNA	2012
21855840	Chromosomal haplotypes by genetic phasing of human families.	Am J Hum Genet	2011
21270892	Comparative and demographic analysis of orang-utan genomes.	Nature	2011
20360741	The genome of a songbird.	Nature	2010
20220176	Analysis of genetic inheritance in a family quartet by whole-genome sequencing.	Science	2010
18502942	DupMasker: a tool for annotating primate segmental duplications.	Genome Res	2008
18464734	Genome analysis of the platypus reveals unique signatures of evolution.	Nature	2008
17431169	Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome.	Science	2007
17431167	Evolutionary and biomedical insights from the rhesus macaque genome.	Science	2007
16717141	Functional noncoding sequences derived from SINEs in the mammalian genome.	Genome Research	2006
16543943	A third approach to gene prediction suggests thousands of additional human transcribed regions.	PLoS Comput Biol	2006
16344559	Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates.	Genome Res	2006
15616140	A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).	Molecular Biology and Evolution	2005
15057822	Genome sequence of the Brown Norway rat yields insights into mammalian evolution.	Nature	2004
15060014	Aligning multiple genomic sequences with the threaded blockset aligner.	Genome Res	2004
15059992	Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.	Genome Res	2004
12824357	MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.	Nucleic Acids Res	2003
12529312	Human-mouse alignments with BLASTZ.	Genome Res	2003
12529302	Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.	Genome Res	2003
12917688	Comparative analyses of multi-species sequences from targeted genomic regions.	Nature	2003
12466850	Initial sequencing and comparative analysis of the mouse genome.	Nature	2002
11779833	Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor alpha/delta loci.	Genome Res	2002
12142439	Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.	Science	2002
11237011	Initial sequencing and analysis of the human genome.	Nature	2001
11567625	Comparative genomics of the human and mouse T cell receptor loci.	Immunity	2001
10779500	PipMaker--a web server for aligning two genomic DNA sequences.	Genome Res	2000
11042147	Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway.	Genome Res	2000
10525406	Ataxia in prion protein (PrP)-deficient mice is associated with upregulation of the novel PrP-like protein doppel.	J Mol Biol	1999