Safa Jammali
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View article: CBFA2T3::GLIS2 pediatric acute megakaryoblastic leukemia is sensitive to BCL-XL inhibition by navitoclax and DT2216
CBFA2T3::GLIS2 pediatric acute megakaryoblastic leukemia is sensitive to BCL-XL inhibition by navitoclax and DT2216 Open
Acute megakaryoblastic leukemia (AMKL) is a rare, developmentally restricted, and highly lethal cancer of early childhood. The paucity and hypocellularity (due to myelofibrosis) of primary patient samples hamper the discovery of cell- and …
View article: Potential of L- and C- Bands Polarimetric SAR Data for Monitoring Soil Moisture over Forested Sites
Potential of L- and C- Bands Polarimetric SAR Data for Monitoring Soil Moisture over Forested Sites Open
This study investigates the potential of L- and C- bands Polarimetric Synthetic Aperture Radar (PolSAR) data to monitor soil moisture over the forested sites of SMAP Validation Experiment 2012 (SMAPVEX12). The optimal backscattering coeffi…
View article: From pairwise to multiple spliced alignment
From pairwise to multiple spliced alignment Open
Motivation Alternative splicing is a ubiquitous process in eukaryotes that allows distinct transcripts to be produced from the same gene. Yet, the study of transcript evolution within a gene family is still in its infancy. One prerequisite…
View article: SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution
SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution Open
Background It is now well established that eukaryotic coding genes have the ability to produce more than one type of transcript thanks to the mechanisms of alternative splicing and alternative transcription. Because of the lack of gold sta…
View article: SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups
SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups Open
Motivation The inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene structures in genomes. Spliced alignment that consists in aligning a spliced…
View article: Improving spliced alignment for identification of ortholog groups and multiple CDS alignment
Improving spliced alignment for identification of ortholog groups and multiple CDS alignment Open
The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures i…
View article: MOESM5 of Aligning coding sequences with frameshift extension penalties
MOESM5 of Aligning coding sequences with frameshift extension penalties Open
Additional file 5: Pairwise alignments for the 21-CDS dataset. Zip file containing the sequence file and the pairwise alignment files at the fasta format for the 21-CDS benchmarkconsidered in the “Results” section, for each of the five met…
View article: MOESM2 of Aligning coding sequences with frameshift extension penalties
MOESM2 of Aligning coding sequences with frameshift extension penalties Open
Additional file 2: CDS of the ten gene families. Zip file containing the CDS files at the fasta format for each of the ten gene families considered in the “Results” section.
View article: MOESM4 of Aligning coding sequences with frameshift extension penalties
MOESM4 of Aligning coding sequences with frameshift extension penalties Open
Additional file 4: Pairwise alignments for the 3-CDS benchmark. Zip file containing the sequence file and the pairwise alignment files at the fasta format for the manually-built3-CDS benchmark considered in the “Results” section, for each …