Mark Borodovsky
Molecular Biology · 2001–2023
A researcher in the Science corpus: 18 papers; trusts 66 researchers and is trusted by 50 researchers here, as inferred from the citation graph.
Subfields
- Molecular Biology — 241 citations into it; #676 of 17,773 by trust here, #2,422 by citations
- Genetics — 57 citations into it; #741 of 6,854 by trust here, #2,476 by citations
- Plant Science — 49 citations into it; #3,038 of 8,232 by trust here, #3,014 by citations
- Computational Biology & Bioinformatics — 26 citations into it
- Ecology — 25 citations into it; #2,245 of 10,717 by trust here, #3,102 by citations
- Cancer Research — 10 citations into it
- Materials Chemistry — 7 citations into it
- Algorithms & Complexity — 6 citations into it
Whom Mark Borodovsky trusts overall
Their strongest outbound trust, strongest first, inferred from their citations.
- Alexandre Lomsadze
- Mario Stanke
- Ian Korf
- John Besemer
- Carson Holt
- Burkhard Rost
- Lawrence R. Rabiner
- Stephen F. Altschul
- Katharina Jasmin Hoff
- James A. Cuff
Who trusts Mark Borodovsky overall
- Alexandre Lomsadze
- Martin J. Wainwright
- Mukund Deshpande
- Tomás Bruna
- L. Gabriel
- Katharina Jasmin Hoff
- Chuong B. Do
- Non Yok
- Stephan Waack
- Michael I. Jordan
Papers from Mark Borodovsky's perspective
Ordered by how strongly the researchers Mark Borodovsky trusts endorse each paper. Same corpus, a different order for every researcher.
- Basic local alignment search tool.
- Gene finding in novel genomes (BMC Bioinformatics)
- Gene prediction with a hidden Markov model and a new intron submodel (European Conference on Computational Biology)
- MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects (BMC Bioinformatics)
- GeneID in Drosophila. (Genome Research)
- Integrating genomic homology into gene structure prediction (Intelligent Systems in Molecular Biology)
- 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)
- AUGUSTUS: a web server for gene finding in eukaryotes (Nucleic Acids Res.)
- Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
- BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics (bioRxiv)
Their papers
- Protein secondary structure prediction for a single-sequence using hidden semi-Markov models (2006) — 118 citations
- 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
- The genome of woodland strawberry (Fragaria vesca) (2010) — 1,158 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
- GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses (2005) — 1,146 citations
- Ab initio gene identification in metagenomic sequences (2010) — 1,616 citations
- Problems and Solutions in Biological Sequence Analysis (2006) — 621 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
- TSEBRA: transcript selector for BRAKER (2021) — 294 citations
- Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication (2014) — 626 citations