Alexandre Lomsadze

Molecular Biology · 2001–2023

A researcher in the Science corpus: 13 papers; trusts 47 researchers and is trusted by 34 researchers here, as inferred from the citation graph.

Subfields

• Molecular Biology — 184 citations into it; #964 of 17,773 by trust here, #3,494 by citations
• Genetics — 48 citations into it; #740 of 6,854 by trust here, #2,476 by citations
• Plant Science — 34 citations into it; #3,015 of 8,232 by trust here, #4,310 by citations
• Ecology — 22 citations into it; #3,005 of 10,717 by trust here, #3,573 by citations
• Computational Biology & Bioinformatics — 12 citations into it
• Cancer Research — 10 citations into it

Whom Alexandre Lomsadze trusts overall

Their strongest outbound trust, strongest first, inferred from their citations.

1. Ian Korf
2. Mario Stanke
3. John Besemer
4. Mark Borodovsky
5. Carson Holt
6. Lawrence R. Rabiner
7. Bernard Walter Silverman
8. Vardges Ter-Hovhannisyan
9. Genís Parra
10. W. James Kent

Who trusts Alexandre Lomsadze overall

1. Tomás Bruna
2. Mark Borodovsky
3. Katharina Jasmin Hoff
4. L. Gabriel
5. Vardges Ter-Hovhannisyan
6. Non Yok
7. Mark Yandell
8. Mario Stanke
9. Carson Holt
10. Shiyuyun Tang

Papers from Alexandre Lomsadze's perspective

Ordered by how strongly the researchers Alexandre Lomsadze trusts endorse each paper. Same corpus, a different order for every researcher.

1. Basic local alignment search tool.
2. Gene finding in novel genomes (BMC Bioinformatics)
3. Gene prediction with a hidden Markov model and a new intron submodel (European Conference on Computational Biology)
4. GeneID in Drosophila. (Genome Research)
5. BLAT--the BLAST-like alignment tool. (Genome Research)
6. A computational analysis of sequence features involved in recognition of short introns (Proceedings of the National Academy of Sciences of the United States of America)
7. Integrating genomic homology into gene structure prediction (Intelligent Systems in Molecular Biology)
8. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
9. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects (BMC Bioinformatics)
10. The generic genome browser: a building block for a model organism system database. (Genome Research)

Their papers

• GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. (2001) — 2,278 citations
• GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020) — 478 citations
• Gene identification in novel eukaryotic genomes by self-training algorithm (2005) — 947 citations
• BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS (2016) — 1,039 citations
• Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. (2008) — 894 citations
• Identification of protein coding regions in RNA transcripts (2014) — 429 citations
• Ab initio gene identification in metagenomic sequences (2010) — 1,616 citations
• BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020) — 1,454 citations
• NCBI prokaryotic genome annotation pipeline (2016) — 6,445 citations
• Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm (2014) — 518 citations
• Whole-Genome Annotation with BRAKER (2019) — 573 citations
• BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA (2023) — 587 citations
• Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication (2014) — 626 citations