Mark Chaisson

92.9k total citations · 3 hit papers
30 papers, 32.3k citations indexed

About

Mark Chaisson is a scholar working on Molecular Biology, Genetics and Plant Science. According to data from OpenAlex, Mark Chaisson has authored 30 papers receiving a total of 32.3k indexed citations (citations by other indexed papers that have themselves been cited), including 27 papers in Molecular Biology, 10 papers in Genetics and 10 papers in Plant Science. Recurrent topics in Mark Chaisson's work include Genomics and Phylogenetic Studies (23 papers), RNA and protein synthesis mechanisms (15 papers) and Chromosomal and Genetic Variations (10 papers). Mark Chaisson is often cited by papers focused on Genomics and Phylogenetic Studies (23 papers), RNA and protein synthesis mechanisms (15 papers) and Chromosomal and Genetic Variations (10 papers). Mark Chaisson collaborates with scholars based in United States, Italy and Türkiye. Mark Chaisson's co-authors include T Gingeras, Alexander Dobin, Carrie Davis, Philippe Batut, Felix Schlesinger, Jörg Drenkow, Chris Zaleski, Sonali Jha, Glenn Tesler and Pavel A. Pevzner and has published in prestigious journals such as Nature, Science and Proceedings of the National Academy of Sciences.

In The Last Decade

Mark Chaisson

29 papers receiving 32.1k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

STAR: ultrafast universal RNA-seq aligner

2012 28.9k citations Mark Chaisson et al. Bioinformatics profile →
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

2012 827 citations Mark Chaisson, Glenn Tesler BMC Bioinformatics profile →
Resolving the complexity of the human genome using single-molecule sequencing

2014 499 citations Mark Chaisson, John Huddleston et al. Nature profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Mark Chaisson United States	19	20.3k	4.6k	4.6k	4.4k	4.3k	30	32.3k
Felix Schlesinger United States	8	19.4k 1.0×	5.0k 1.1×	3.8k 0.8×	4.4k 1.0×	4.3k 1.0×	10	31.3k
Philippe Batut United States	6	18.0k 0.9×	4.4k 1.0×	3.6k 0.8×	4.3k 1.0×	3.4k 0.8×	7	29.4k
Carrie Davis United States	17	20.7k 1.0×	5.3k 1.2×	3.7k 0.8×	4.5k 1.0×	3.9k 0.9×	22	32.7k
Chris Zaleski United States	3	17.6k 0.9×	4.4k 1.0×	3.5k 0.8×	4.3k 1.0×	3.4k 0.8×	3	28.9k
Davis J. McCarthy Australia	20	21.0k 1.0×	6.2k 1.3×	5.6k 1.2×	4.6k 1.0×	4.1k 0.9×	40	35.2k
Alexander Dobin United States	25	19.1k 0.9×	4.9k 1.1×	3.8k 0.8×	4.6k 1.0×	3.8k 0.9×	53	32.3k
Jörg Drenkow United States	14	20.9k 1.0×	5.5k 1.2×	3.8k 0.8×	4.8k 1.1×	3.9k 0.9×	20	33.2k
Sonali Jha United Kingdom	4	17.6k 0.9×	4.4k 1.0×	3.5k 0.8×	4.3k 1.0×	3.4k 0.8×	7	29.0k
Jaime Huerta‐Cepas Spain	35	19.3k 1.0×	3.3k 0.7×	3.8k 0.8×	2.6k 0.6×	3.1k 0.7×	59	30.8k
Vladimı́r Beneš Germany	65	18.9k 0.9×	4.6k 1.0×	3.2k 0.7×	2.6k 0.6×	4.1k 1.0×	268	30.7k

Countries citing papers authored by Mark Chaisson

Since Specialization

Citations

This map shows the geographic impact of Mark Chaisson's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Mark Chaisson with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Mark Chaisson more than expected).

Fields of papers citing papers by Mark Chaisson

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Mark Chaisson. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Mark Chaisson. The network helps show where Mark Chaisson may publish in the future.

Co-authorship network of co-authors of Mark Chaisson

This figure shows the co-authorship network connecting the top 25 collaborators of Mark Chaisson. A scholar is included among the top collaborators of Mark Chaisson based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Mark Chaisson. Mark Chaisson is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

English, Adam C., Egor Dolzhenko, Sean K. McKenzie, et al.. (2024). Analysis and benchmarking of small and large genomic variants across tandem repeats. Nature Biotechnology. 43(3). 431–442. 24 indexed citations

Diggavi, Suhas, et al.. (2023). HQAlign: aligning nanopore reads for SV detection using current-level modeling. Bioinformatics. 39(10). 2 indexed citations

Ren, Jingwen, et al.. (2023). vamos: variable-number tandem repeats annotation using efficient motif sets. Genome biology. 24(1). 175–175. 16 indexed citations

Chaisson, Mark, Arvis Sulovari, Paul N. Valdmanis, Danny E. Miller, & Evan E. Eichler. (2023). Advances in the discovery and analyses of human tandem repeats. Emerging Topics in Life Sciences. 7(3). 361–381. 16 indexed citations

Lu, Tsung-Yu, et al.. (2023). The motif composition of variable number tandem repeats impacts gene expression. Genome Research. 33(4). 511–524. 19 indexed citations

Chaisson, Mark, et al.. (2022). TT-Mars: structural variants assessment based on haplotype-resolved assemblies. Genome biology. 23(1). 110–110. 8 indexed citations

Lu, Tsung-Yu, Katherine M. Munson, Alexandra P. Lewis, et al.. (2021). Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs. Nature Communications. 12(1). 4250–4250. 27 indexed citations

Hoekstra, Jake G., Chiu-Hui Huang, Mark Chaisson, et al.. (2018). Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ. PLoS Genetics. 14(11). e1007805–e1007805. 29 indexed citations

Chaisson, Mark, Sudipto Mukherjee, Sreeram Kannan, & Evan E. Eichler. (2017). Resolving Multicopy Duplications de novo Using Polyploid Phasing. Lecture notes in computer science. 10229. 117–133. 16 indexed citations

10.

Fan, Xian, Mark Chaisson, Luay Nakhleh, & Ken Chen. (2017). HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies. Genome Research. 27(5). 793–800. 16 indexed citations

11.

Gordon, David, John Huddleston, Mark Chaisson, et al.. (2016). Long-read sequence assembly of the gorilla genome. Science. 352(6281). aae0344–aae0344. 218 indexed citations

12.

Lin, Yu, Jeffrey Yuan, Mikhail Kolmogorov, et al.. (2016). Assembly of long error-prone reads using de Bruijn graphs. Proceedings of the National Academy of Sciences. 113(52). E8396–E8405. 209 indexed citations

13.

Huddleston, John, Mark Chaisson, Karyn Meltz Steinberg, et al.. (2016). Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Research. 27(5). 677–685. 235 indexed citations

14.

Chaisson, Mark, John Huddleston, Megan Y. Dennis, et al.. (2014). Resolving the complexity of the human genome using single-molecule sequencing. Nature. 517(7536). 608–611. 499 indexed citations breakdown →

15.

Huddleston, John, Swati Ranade, Maika Malig, et al.. (2014). Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research. 24(4). 688–696. 179 indexed citations

16.

Chaisson, Mark & Glenn Tesler. (2012). Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics. 13(1). 238–238. 827 indexed citations breakdown →

17.

Medvedev, Paul, Son Pham, Mark Chaisson, Glenn Tesler, & Pavel A. Pevzner. (2011). Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. Journal of Computational Biology. 18(11). 1625–1634. 37 indexed citations

18.

Chaisson, Mark, Dumitru Brinza, & Pavel A. Pevzner. (2008). De novo fragment assembly with short mate-paired reads: Does the read length matter?. Genome Research. 19(2). 336–346. 174 indexed citations

19.

Chaisson, Mark & Pavel A. Pevzner. (2007). Short read fragment assembly of bacterial genomes. Genome Research. 18(2). 324–330. 297 indexed citations

20.

Chaisson, Mark, Pavel A. Pevzner, & Haixu Tang. (2004). Fragment assembly with short reads. Bioinformatics. 20(13). 2067–2074. 126 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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