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List of works by Mihaela Pertea

A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding

article

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.

scientific article

Abdominal wall actinomycosis associated with prolonged use of an intrauterine device: a case report and review of the literature.

scientific article

Abstracts of Beyond the Genome: The true gene count, human evolution and disease genomics. Boston, Massachusetts, USA. October 11-13, 2010

article

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

scientific article (publication date: 11 January 2008)

Between a chicken and a grape: estimating the number of human genes

scientific article

Between a chicken and a grape: estimating the number of human genes

Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations

scientific article published on 7 January 2015

Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum

scientific article (publication date: 6 November 1998)

Computational gene finding in plants

scientific article

Computational gene finding in plants

article

Computational gene prediction using multiple sources of evidence

scientific article

DIAMUND: direct comparison of genomes to detect mutations

scientific article

Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape.

scientific article

Detection of lineage-specific evolutionary changes among primate species

scientific article published on 4 July 2011

Do-it-yourself genetic testing ⬇️

scientific article published on October 7, 2010

Draft genome of the filarial nematode parasite Brugia malayi

scientific article

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

scientific article

Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments

scientific article published on 23 December 2020

Efficient decoding algorithms for generalized hidden Markov model gene finders

scientific article

Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.

scientific article published on 2 February 2005

Erratum: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

scientific article published in Nature

GFF Utilities: GffRead and GffCompare

scientific article published on 28 April 2020

GeneSplicer: a new computational method for splice site prediction

scientific article

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

scientific article

Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article

Genome sequence of the human malaria parasite Plasmodium falciparum

scientific article

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

scientific article

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

scientific article

Genomics of Theileria Parva

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders

scientific article

Human contamination in bacterial genomes has created thousands of spurious proteins

scientific article published on 07 May 2019

Improved transcriptome assembly using a hybrid of long and short reads with StringTie

scientific article published on 01 June 2022

Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster

scientific article published on April 2004

Interpolated Markov models for eukaryotic gene finding.

scientific article

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions

scientific article published on 7 August 2006

OperonDB: a comprehensive database of predicted operons in microbial genomes

scientific article

Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

scientific article published on 21 September 2020

Searching for genes and biologically related signals in DNA sequences

article

Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14

scientific article (publication date: 3 October 2002)

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species

scientific article

Sim4cc: a cross-species spliced alignment program

scientific article published on 08 May 2009

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

scientific article

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans

scientific article

The genome of the blood fluke Schistosoma mansoni

scientific article

The human transcriptome: an unfinished story

scientific article (publication date: September 2012)

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders

scientific article published on 14 May 2004

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

scientific article published on 11 August 2016

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

scientific article published on 16 December 2019

Using GlimmerM to find genes in eukaryotic genomes

scientific article published in November 2002

Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding

article

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