Mihaela Pertea
@elapertea
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Joined February 2015
📢📢Dear friends, our new software, Splam, a deep learning-based splice junction predictor, is now officially released🎉If you do RNA-Seq data analysis or need a reliable tool to evaluate splice junctions/introns, Splam is the perfect fit for you 🔗 https://t.co/R345pehx5l (1/10)
github.com
✂️ Deep learning-based splice site predictor that improves spliced alignments - Kuanhao-Chao/splam
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I am also going to present our newly published first gapless, reference-quality, fully annotated Southern Han Chinese genome at poster B-068. Come to chat with me about genome assembly and annotation! @AlekseyZimin5 @StevenSalzberg1 @elapertea
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a 3rd #ISMBECCB2023 poster B-071 on Tuesday, presented by @elapertea, "Efficient and robust transcriptome reconstruction from hybrid RNA-seq data" on the latest StringTie2 RNA-seq assembly methods using long+short reads together 3/3
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Are you at #ISMBECCB2023? I am thrilled to share our new highly accurate splice junction recognition model - Splam! Come chat with me at poster B-258 about RNA-Seq, machine learning, and more. Splam preprint will be available soon, so stay tuned! @StevenSalzberg1 @elapertea
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Our paper describing our new, greatly improved human genome annotation is just out in preprint form, by @av_sparrow @elapertea @markusjsommer @ErdogduBeril @IliaMinkin @KuanHaoChao @JakobHeinz9 @alaina_shumate @thesteinegger @park_sukhwan et al.
biorxiv.org
The original CHESS database of human genes was assembled from nearly 10,000 RNA sequencing experiments in 53 human body sites produced by the Genotype-Tissue Expression (GTEx) project, and then...
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Congratulations to @samkovaka for defending his thesis on Computational Methods for Genomic, Transcriptomic, and Epi-Omic Analysis with Long-Read Sequencing! @timp0, @elapertea and I are so proud! @nanopore @PacBio @JHUCompSci @HopkinsEngineer
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New paper by @av_sparrow and @elapertea describes a surprising result: simulated data widely used to test RNA sequencing methods are *too* clean, hiding built-in biases in the methods
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New @biorxivpreprint paper from Ales Varabyou, @pocki91, and @elapertea describes an elegant, efficient way to find recombinant #COVID19 viruses from >85,000 genomes. We found 225 potential recombinants, some appearing in multiple patients
biorxiv.org
The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing...
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Happy we have a paper describing the useful GFF tools developed by @geo_pertea. GFF Utilities: GffRead and GffCompare. Pertea G and Pertea M, published by @F1000Research,
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Research goes on: see our newest paper on the first-ever human reference genome of an Ashkenazi individual, just out on @biorxiv:
biorxiv.org
Here we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more...
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Congratulations to @StevenSalzberg1 for winning the ISCB Senior Scientist Award!
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StringTie2 paper is out: more accurate than any other RNA-seq assembler, even faster than before, and now able to handle ONT and PacBio reads, where it's significantly more accurate and 80 times faster than the next-best method. s/o @elapertea @samkovaka
link.springer.com
Genome Biology - RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly...
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Well done Mihai Pop; junior scientists should not have to fear attacks when they improve upon others' work.
Mihai Pop with strong words for @lpachter .. power differential + impact on junior scientists in field. https://t.co/TaUKyAAmnA
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Thks for all the support! In case is not obvious, the accusations regarding Salmon are false, see detailed response:
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Scientists: let's all agree to refuse to review for any Elsevier journals until they abandon this patent.
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https://t.co/qhjw9KLhcX
#researchparasites discover major error in Science paper on first African genome @dataparasite @phylogenomics
nature.com
Nature - Finding that much of Africa has Eurasian ancestry was mistaken.
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https://t.co/bGD6JCaJdn New year begins with new release of our RNA-seq assembler, StringTie v1.2, with major new features
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We just released version 1.1.0 of StringTie: more accurate and with major memory usage improvements. Check it out at
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