halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
Open accessAbstract
Background: Large-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production. Findings: halSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment. The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred–way, reference-free vertebrate alignments built with the Cactus system. Conclusions: halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments. The method is implemented in C++11 as a component of the halTools software and released under MIT license. The package is available at https://github.com/ComparativeGenomicsToolkit/hal/.
AI snapshot
Written from the paper’s full text.
TL;DR
halSynteny is a C++11 tool in halTools that constructs conserved synteny blocks directly from HAL multiple whole-genome alignments using a DAG-based heuristic, without requiring gene annotations. It reports high genome coverage and large speed gains over SatsumaSynteny2 in tested vertebrate and nematode datasets.
Key findings
- On cat (FelCat 8.0) vs dog (CanFam 3.1) with human outgroup, halSynteny blocks covered 99% of the cat genome; 81.7% agreed with chromosome painting, and discrepant regions on cat chromosomes A1, B1, and C1 comprised 3.5% of constructed synteny. Gene-level orthology via OMA Browser supported halSynteny’s assignments.
- In nematode comparisons, halSynteny achieved higher genome coverage than SatsumaSynteny2 for S. ratti (72.5% vs 55.6%), C. elegans (92.5% vs 20.0%), and C. briggsae (88.3% vs 18.7%); S. stercoralis was similar/slightly lower (55.5% vs 56.6%).
- Runtime was much lower for halSynteny after excluding alignment construction: S. ratti 18 min (+496 min Progressive Cactus alignment) vs 1,232 min for SatsumaSynteny2; C. elegans 74 min (+496) vs 547 min.
- The method uses alignment as the only required input and can be scaled to multiple genome comparison without loss of precision because a third genome’s alignment does not affect pairwise synteny.
Methods
- Algorithm: alignment blocks are vertices in a DAG; edges connect blocks that are on one chromosome, non-overlapping, same strand, and within dmax; weights are block sizes; topological traversal updates path weights, then maximal-weight paths are traced back and retained if at least bmin, removed, and repeated.
- Evaluation: cat/dog/human Progressive Cactus alignment for cat-dog synteny compared with chromosome painting and OMA Browser orthology; performance compared with SatsumaSynteny2 on C. elegans/C. briggsae and S. ratti/S. stercoralis, with halSynteny parameters –maxAnchorDistance 1000000 and –minBlockSize 100000 (S. ratti/S. stercoralis) or 1000000 (C. elegans/C. briggsae).
- Implementation: C++11 component of halTools, Linux, HAL API, MIT license.
Limitations
- The paper states that cat-dog discrepancies with chromosome painting may arise from the different nature of the approaches; chromosome painting can misclassify small insertions/translocations and can be laborious in complex rearrangements. It also notes that assembly qualities can be accommodated by adjusting resolution parameters, which may increase genome coverage.
- Evident from the text: there is no dedicated limitations section; evaluation is limited to cat-dog and two nematode species pairs, and the reported halSynteny runtimes exclude the 496-minute Progressive Cactus alignment construction, which is required input. S. stercoralis coverage was not higher than SatsumaSynteny2 (55.5% vs 56.6%).
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
11 of 21 cited sources checked · 5 supported · 1 flagged · accuracy not yet measured
- Premisecitation
Chromosomal painting tends to misclassify small insertions and small translocations.
“Although chromosomal painting provides an efficient technique to discover large-scale similarity of continuous homology, it tends to misclassify small insertions and small translocations [21].”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [21] Lee C, Gisselsson S, Jin C, et al. Limitations of chromosome classification by multicolor karyotyping. Am J Hum Genet. 2001; 68(4): 1043– 7. 11222105 PMC1275623 source
In “Limitations of Chromosome Classification by Multicolor Karyotyping” (page unavailable), the paper reports missed or misclassified small insertions and translocations with SKY/M-FISH. The claim is too broad if “chromosomal painting” includes conventional painting: the paper explicitly says conventional painting does not produce similar algorithmic misinterpretations and recommends it to check SKY/M-FISH results. (LLM, conf=0.88)
Experimental — accuracy not yet measured
- Findingcitation
Comparison of gene-level orthology between cat chromosomes A1, B1, C1 and dog chromosomes 28 and 25 using OMA Browser supports the conclusions of inference derived by halSynteny.
“Comparison of gene-level orthology performed between the cat chromosomes A1, B1, and C1 and dog chromosomes 28 and 25 [23] using OMA Browser [24,25] support the conclusions of inference derived by halSynteny.”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites [23] Krasheninnikova K, Diekhans M, Armstrong J, et al. Supporting data for ”halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments.”. GigaScience Database. 2020;. 10.5524/100740. PMC7254927 32463100 source
- cites [24] OMA Browser. https://omabrowser.org/. Accessed on 21 May 2020.
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites [25] Altenhoff AM, Glover N, Train CM, et al. The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. Nucleic Acids Res. 2018; 46(D1): D477– 85. 29106550 PMC5753216 source
- Findingown data
The regions of disagreement between halSynteny and chromosomal painting comprise 3.5% of the constructed synteny.
“These regions comprise 3.5% of the constructed synteny.”
Quote in the paperNot a substantial claim - Findingcitation
81.7% of the cat genome covered by synteny blocks agrees with the assignment of homologous chromosomes obtained by chromosomal painting.
“while 81.7% of that agrees with the assignment of homologous chromosomes obtained by the chromosomal painting approach [20]”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [20] Yang F, Graphodatsky A, O’Brien P, et al. Reciprocal chromosome painting illuminates the history of genome evolution of the domestic cat, dog and human. Chromosome Res. 2000; 8(5): 393– 404. 10997780 source
- Findingown data
halSynteny produced results different from chromosomal painting results in the red regions of cat chromosomes A1, B1, and C1.
“halSynteny produced results different from the chromosomal painting results in the red regions of the cat chromosomes A1, B1, and C1.”
Quote in the paperNot a substantial claim
- Findingreasoning
With halSynteny, the alignment is the only required input.
“With halSynteny, the alignment is the only required input.”
Quote in the paperSubstantial claim - Findingown data
The resulting synteny blocks cover 99% of the cat's genome.
“The resulting synteny blocks cover 99% of the cat’s genome”
Quote in the paperNot a substantial claim - Findingreasoning
In comparison with other modern alignment-based software, halSynteny allows for obtaining high-coverage results that follow from the definition of synteny.
“In comparison with the other modern alignment-based software, halSynteny allows for obtaining high-coverage results that follow from the definition of synteny.”
Quote in the paperSubstantial claim - Interpretationnone given
halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments.
“halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments.”
Quote in the paperNot a substantial claim - Interpretationreasoning
Discrepancies between halSynteny and chromosomal painting can stem from the different nature of the two approaches.
“Such discrepancies can stem from the different nature of the 2 approaches.”
Quote in the paperNot a substantial claim - Interpretationreasoning
The halSynteny approach can be scaled to the problem of multiple genome comparison without loss of precision.
“Thus our approach can be scaled to the problem of multiple genome comparison without loss of precision.”
Quote in the paperSubstantial claim- Rests on an assumption: Given an alignment of 2 genomes, information about their alignment with a third genome does not affect synteny between the original pair of genomes.
- May combine two claims. 7
- Classified as probably not a substantial claim. 12
May combine two claims.
FindingcitationhalSynteny implements a DAG-based algorithm for identification of synteny blocks directly from HAL alignment and reporting synteny blocks in PSL format.
“Here we present halSynteny, a tool that implements a DAG-based algorithm for identification of synteny blocks directly from HAL alignment and reporting synteny blocks in PSL format [19].”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [19] Schlenoff CI, Gruninger M, Tissot F, et al. The Process Specification Language (PSL) overview and version 1.0 specification. NIST Interagency/Internal Report (NISTIR) - 6459 2004, doi: 10.6028/NIST.IR.6459. source
The cited paper’s Section 1.3 identifies PSL as a language for exchanging manufacturing process specifications, not a format for reporting genomic alignments. Its Appendix D defines the syntax of that process language. The citation therefore does not substantiate the sentence’s reference to synteny blocks in “PSL format”; the paper also says nothing about halSynteny or its algorithm. (LLM, conf=0.87)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
PremisecitationBy producing a single, reference-free multiple alignment, Cactus allows synteny block reconstruction between any 2 genomes without reference bias, directly from the HAL representation.
“By producing a single, reference-free multiple alignment, Cactus allows synteny block reconstruction between any 2 genomes without reference bias, directly from the HAL representation.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [17] Paten B, Earl D, Nguyen N, et al. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011; 21(9): 1512– 28. 21665927 PMC3166836
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites [18] Paten B, Diekhans M, Earl D, et al. Cactus graphs for genome comparisons. J Comput Biol. 2011; 18(3): 469– 81. 21385048 PMC8884192 source
The Overview and Abstract describe cactus graphs as representing comparisons of sets of genomes through homologous blocks and chains that can be visualized as multiple alignments. This supports the multiple-genome alignment aspect, but our copy does not describe synteny-block reconstruction between any two genomes, establish freedom from reference bias, or mention a HAL representation (searched: HAL, synteny, reference bias). (LLM, conf=0.88)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
PremisecitationProgressive Cactus produces reference-free all-to-all genome alignments.
“One of the state-of-the-art tools [14–16] is Progressive Cactus [17,18] which produces reference-free all-to-all genome alignments.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [17] Paten B, Earl D, Nguyen N, et al. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011; 21(9): 1512– 28. 21665927 PMC3166836
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites [18] Paten B, Diekhans M, Earl D, et al. Cactus graphs for genome comparisons. J Comput Biol. 2011; 18(3): 469– 81. 21385048 PMC8884192 source
Section 2 (Overview; page unavailable) describes aligning homologous segments between and within multiple genomes, supporting the general genome-alignment aspect. But the paper describes cactus graphs, not a tool called Progressive Cactus, and the passages do not establish that it produces reference-free, all-to-all genome alignments. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
FindingcitationThe results of SatsumaSynteny2 in terms of genome coverage are similar to the ones reported by the benchmark study for the older version of SatsumaSynteny.
“The results of SatsumaSynteny2 in terms of genome coverage are similar to the ones reported by the benchmark study [14] for the older version of the tool SatsumaSynteny [5].”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [14] Liu D, Hunt M, Tsai IJ Inferring synteny between genome assemblies: A systematic evaluation. BMC Bioinformatics. 2018; 19(1): 26. 29382321 PMC5791376 source
- cites [5] Grabherr MG, Russell P, Meyer M, et al. Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics. 2010; 26(9): 1145– 51. 20208069 PMC2859124 source
Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).
PremisecitationMulti-species genome alignments are a useful tool for analysis of species homology in large-scale comparative genomic projects.
“Multi-species genome alignments are a useful tool for analysis of species homology in large-scale comparative genomic projects [12,13].”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [12] Lilue J, Doran AG, Fiddes IT, et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet. 2018; 50(11): 1574– 83. 30275530 PMC6205630 source
Online Methods (Gene prediction and annotation; page unavailable) says whole-genome alignments were used to identify orthologs across mouse strains, supporting the usefulness of alignments for comparing related genomes. The Discussion (page unavailable) describes work with multiple rodent assemblies, but the paper does not establish the broader claim about species homology across large-scale comparative genomic projects generally. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [13] Zhang G, Li C, Li Q, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014; 346(6215): 1311– 20. 25504712 PMC4390078 source
May combine two claims.
FindingcitationThese results are closer to the results of anchor-based tools reported in the benchmark study, while halSynteny does not require an intermediate genome annotation step.
“These results are closer to the results of anchor-based tools reported in the benchmark study [14], while halSynteny does not require an intermediate genome annotation step.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [14] Liu D, Hunt M, Tsai IJ Inferring synteny between genome assemblies: A systematic evaluation. BMC Bioinformatics. 2018; 19(1): 26. 29382321 PMC5791376 source
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe alignment-based method SatsumaSynteny2 takes pairs of genome sequences as input and implements a dynamic programming algorithm for chaining the pairwise alignment blocks.
“The alignment-based method SatsumaSynteny2 takes pairs of genome sequences as input and implements a dynamic programming algorithm for chaining the pairwise alignment blocks.”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [5] Grabherr MG, Russell P, Meyer M, et al. Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics. 2010; 26(9): 1145– 51. 20208069 PMC2859124 source
The Introduction (p. 1) describes Satsuma comparing query and target genomic sequences, and the Synteny filter (p. 3) says it uses dynamic programming to chain alignment matches. The paper describes Satsuma, however, not a method named SatsumaSynteny2, so it does not establish that the named method has these features. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [26] Satsuma2. https://github.com/bioinfologics/satsuma2. Accessed 21st May 2020
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim: may not pass S4 (based).
Findingnone givenhalSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment.
“halSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe regions of disagreement between halSynteny and chromosomal painting on cat chromosomes A1, B1, and C1 were labeled as homologous to dog chromosome 28 with chromosome painting, while halSynteny revealed homology with chromosome 25.
“These regions were labeled as homologous to dog chromosome 28 with chromosome painting, while halSynteny revealed homology with chromosome 25.”
Quote in the paperNot a substantial claimMay combine two claims.
FindingreasoningWhen the performance of halSynteny is compared to that of alignment-based software, halSynteny produces much higher genome coverage, which agrees with the properties of the dataset.
“When the performance of halSynteny is compared to that of alignment-based software, halSynteny produces much higher genome coverage, which agrees with the properties of the dataset.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationIn cases of complex rearrangements, chromosomal painting can be laborious and requires confirmation.
“Also, it was reported that in cases of complex rearrangements chromosomal painting can be laborious and requires confirmation [22].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [22] Ried T, Schröck T, Ning Y, et al. Chromosome painting: a useful art. Hum Mol Genet. 1998; 7(10): 1619– 26. 9735383 source
Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Interpretationnone givenIt is possible to account for specific assembly qualities, such as the diverse size of assembly fragments, by adjusting the resolution parameters of halSynteny, which may result in an increase of genome coverage.
“It is possible to account for specific assembly qualities, such as the diverse size of assembly fragments, by adjusting the resolution parameters of halSynteny, which may result in an increase of genome coverage.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
Premisenone givenhalSynteny is targeted to build synteny blocks for multi-hundred-way, reference-free vertebrate alignments built with the Cactus system.
“The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred–way, reference-free vertebrate alignments built with the Cactus system.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Interpretationnone givenHere the authors first apply the DAG-based approach to whole-genome alignments.
“Here we first apply the DAG-based approach to whole-genome alignments.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationDAGchainer operates with homologous gene pairs found within complete genome sequences, combining them into chains of syntenic genes.
“It operates with homologous gene pairs found within complete genome sequences, combining them into chains of syntenic genes.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [4] Haas BJ, Delcher AL, Wortman JR, et al. DAGchainer: A tool for mining segmental genome duplications and synteny. Bioinformatics. 2004; 20(18): 3643– 6. 15247098 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe DAG-based method DAGchainer was previously implemented for constructing synteny from BLAST alignments of gene annotations.
“The DAG-based method DAGchainer [4] was previously implemented for constructing synteny from the BLAST [29] alignments of gene annotations.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [4] Haas BJ, Delcher AL, Wortman JR, et al. DAGchainer: A tool for mining segmental genome duplications and synteny. Bioinformatics. 2004; 20(18): 3643– 6. 15247098 source
- cites [29] Altschul SF, Gish W, Miller W, et al. Basic Local Alignment Search Tool. J Mol Biol. 1990; 215(3): 403– 10. 2231712 source
The paper relies on this without support.
The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments.
“The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments.”
The paper relies on this without support.
Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production.
“Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production.”
The paper relies on this without support.
With the increased availability of large-scale computing facilities, multiple-vertebrate whole-genome alignment is now tractable.
“With the increased availability of large-scale computing facilities, multiple-vertebrate whole-genome alignment is now tractable.”
The paper relies on this without support.
Given an alignment of 2 genomes, information about their alignment with a third genome does not affect synteny between the original pair of genomes.
“Given an alignment of 2 genomes, information about their alignment with a third genome does not affect synteny between the original pair of genomes.”
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400 · see citing works
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Wang, Y., Tang, H., DeBarry, J. D., Tan, X., Li, J., Wang, X., Lee, T., Jin, H., Marler, B. S., Guo, H., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1293 · Cited by 7,613 · see citing works
Comparative genomics reveals insights into avian genome evolution and adaptation
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., et al. (2014) · Science · doi:10.1126/science.1251385 · Cited by 1,055 · see citing works
Self-citationEvolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W., & Haussler, D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1932072100 · Cited by 850 · see citing works
Raney, B. J., Dreszer, T. R., Barber, G. P., Clawson, H., Fujita, P. A., Wang, T., Nguyen, N., Paten, B., Zweig, A., Karolchik, D., et al. (2013) · Bioinform. · doi:10.1093/bioinformatics/btt637 · Cited by 422 · see citing works
Self-citationDAGchainer: a tool for mining segmental genome duplications and synteny
Haas, B. J., Delcher, A. L., Wortman, J. R., & Salzberg, S. L. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth397 · Cited by 381 · see citing works
Genome rearrangements in mammalian evolution: lessons from human and mouse genomes
Pevzner, P., & Tesler, G. (2003) · Genome Research · doi:10.1101/gr.757503 · Cited by 369 · see citing works
SyMAP v3.4: a turnkey synteny system with application to plant genomes
Soderlund, C. A., Bomhoff, M., & Nelson, W. M. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr123 · Cited by 321 · see citing works
Genome-wide synteny through highly sensitive sequence alignment: <i>Satsuma</i>
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq102 · Cited by 287 · see citing works
HAL: a hierarchical format for storing and analyzing multiple genome alignments
Hickey, G., Paten, B., Earl, D., Zerbino, D., & Haussler, D. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt128 · Cited by 272 · see citing works
Self-citationLilue, J., Doran, A. G., Fiddes, I. T., Abrudan, M., Armstrong, J., Bennett, R., Chow, W., Collins, J., Collins, S., Czechanski, A., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0223-8 · Cited by 267 · see citing works
Self-citationCactus: Algorithms for genome multiple sequence alignment
Paten, B., Earl, D., Nguyen, N., Diekhans, M., Zerbino, D., & Haussler, D. (2011) · Genome Research · doi:10.1101/gr.123356.111 · Cited by 243 · see citing works
Self-citationi-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets
Proost, S., Fostier, J., Witte, D. D., Dhoedt, B., Demeester, P., de Peer, Y. V., & Vandepoele, K. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr955 · Cited by 226 · see citing works
Altenhoff, A. M., Glover, N. M., Train, C.-M., Kaleb, K., Warwick Vesztrocy, A., Dylus, D., de Farias, T. M., Zile, K., Stevenson, C., Long, J., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1019 · Cited by 221 · see citing works
Genomic legacy of the African cheetah, Acinonyx jubatus
Dobrynin, P., Liu, S., Tamazian, G., Xiong, Z., Yurchenko, A. A., Krasheninnikova, K., Kliver, S., Schmidt-Küntzel, A., Koepfli, K.-P., Johnson, W., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0837-4 · Cited by 204 · see citing works
Self-citationChromosome painting: a useful art
Ried, T. (1998) · Human Molecular Genetics · doi:10.1093/hmg/7.10.1619 · Cited by 154 · see citing works
Inferring synteny between genome assemblies: a systematic evaluation
Liu, D., Hunt, M., & Tsai, I. J. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2026-4 · Cited by 147 · see citing works
The Process Specification Language (PSL) overview and version 1.0 specification
Schlenoff, C., Gruninger, M., Tissot, F., Valois, J., & Lee, J. (2000) · doi:10.6028/nist.ir.6459 · Cited by 141 · see citing works
Pangolin genomes and the evolution of mammalian scales and immunityPreprint
Choo, S. W., Rayko, M., Tan, T. K., Hari, R., Komissarov, A. S., Wee, W. Y., Yurchenko, A. A., Kliver, S. F., Tamazian, G., Antunes, A., et al. (2016) · Genome Research · doi:10.1101/gr.203521.115 · Cited by 130 · see citing works
Self-citationDrillon, G., Carbone, A., & Fischer, G. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092621 · Cited by 118 · see citing works
Yang, F., Graphodatsky, A. S., O'Brien, P. C. M., Colabella, A., Solanky, N., Squire, M., Sargan, D. R., & Ferguson-Smith, M. A. (2000) · Chromosome Research · doi:10.1023/a:1009210803123 · Cited by 112 · see citing works
Cactus Graphs for Genome Comparisons
Paten, B., Diekhans, M., Earl, D., John, J. S., Ma, J., Suh, B., & Haussler, D. (2011) · Journal of Computational Biology · doi:10.1089/cmb.2010.0252 · Cited by 102 · see citing works
Self-citationDRIMM-Synteny: decomposing genomes into evolutionary conserved segments
Pham, S., & Pevzner, P. A. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq465 · Cited by 97 · see citing works
Limitations of Chromosome Classification by Multicolor Karyotyping
Lee, C., Gisselsson, D., Jin, C., Nordgren, A., Ferguson, D. O., Blennow, E., Fletcher, J. A., & Morton, C. C. (2001) · The American Journal of Human Genetics · doi:10.1086/319503 · Cited by 82 · see citing works
CYNTENATOR: Progressive Gene Order Alignment of 17 Vertebrate Genomes
Rödelsperger, C., & Dieterich, C. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008861 · Cited by 61 · see citing works
Krasheninnikova, K., Diekhans, M., Armstrong, J., Dievskii, A., Paten, B., & O’Brien, S. (2020) · GigaScience Database · doi:10.5524/100740
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Segmental duplications and their variation in a complete human genome
Vollger, M. R., Guitart, X., Dishuck, P. C., Mercuri, L., Harvey, W. T., Gershman, A., Diekhans, M., Sulovari, A., Munson, K. M., Lewis, A. P., et al. (2022) · Science · doi:10.1126/science.abj6965 · Cited by 350 · see citing works
Self-citationComplex evolutionary processes maintain an ancient chromosomal inversion
Nosil, P., Soria‐Carrasco, V., Villoutreix, R., De‐la‐Mora, M., de Carvalho, C. F., Parchman, T. L., Feder, J. L., & Gompert, Z. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2300673120 · Cited by 43 · see citing works
Adaptation repeatedly uses complex structural genomic variation
Gompert, Z., Feder, J. L., Parchman, T. L., Planidin, N. P., Whiting, F. J. H., & Nosil, P. (2025) · Science · doi:10.1126/science.adp3745 · Cited by 33 · see citing works
Multi-genome synteny detection using minimizer graph mappingsPreprint
Coombe, L., Kazemi, P., Wong, J., Birol, İ., & Warren, R. L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.07.579356 · Cited by 30 · see citing works
NGSEP 4: Efficient and accurate identification of orthogroups and whole‐genome alignment
Tello, D., González-García, L. N., Gomez, J., Zuluaga‐Monares, J. C., Garcia, R., Angel, R., Mahecha, D., Duarte, E., Leon, M. D. R., Reyes, F., et al. (2022) · Molecular Ecology Resources · doi:10.1111/1755-0998.13737 · Cited by 29 · see citing works
Evolution repeats itself in replicate long-term studies in the wild
Nosil, P., de Carvalho, C. F., Villoutreix, R., Zamorano, L. S., Sinclair‐Waters, M., Planidin, N. P., Parchman, T. L., Feder, J. L., & Gompert, Z. (2024) · Science Advances · doi:10.1126/sciadv.adl3149 · Cited by 24 · see citing works
ntSynt-viz: visualizing synteny patterns across multiple genomes
Coombe, L., Warren, R. L., & Birol, İ. (2026) · Journal of Evolutionary Biology · doi:10.1093/jeb/voag079 · Cited by 23 · see citing works
Wang, T., Gong, G., Li, Z., Niu, J.-S., Du, W., Wang, Z., Wang, Y., Zhou, L., Zhang, X., Lian, Z., et al. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae169 · Cited by 22 · see citing works
Yakupova, A. R., Tomarovsky, A. A., Totikov, A., Beklemisheva, V. R., Logacheva, M. D., Perelman, P. L., Komissarov, A. S., Dobrynin, P. V., Krasheninnikova, K., Tamazian, G., et al. (2023) · Genes · doi:10.3390/genes14030619 · Cited by 17 · see citing works
Self-citationThom, G., Moreira, L. R., Batista, R., Gehara, M., Aleixo, A. L. P., & Smith, B. T. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae002 · Cited by 15 · see citing works
DeWeese, K., Molano, G., Calhoun, S., Lipzen, A., Jenkins, J., Williams, M. E., Plott, C., Talag, J., Grimwood, J., Jannink, J., et al. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1494480 · Cited by 12 · see citing works
ntSynt: multi-genome synteny detection using minimizer graph mappings
Coombe, L., Kazemi, P., Wong, J., Birol, İ., & Warren, R. L. (2025) · BMC Biology · doi:10.1186/s12915-025-02455-w · Cited by 41 · see citing works
Huang, Y.-Q., Zhang, X., Bian, C., Jiao, K.-Z., Zhang, L., Huang, Y. S., Yang, W., Li, Y., Shi, G., Huang, Y., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-08056-1 · Cited by 11 · see citing works
Kliver, S. F., Houck, M. L., Perelman, P. L., Totikov, A., Tomarovsky, A. A., Dudchenko, O., Omer, A. D., Colaric, Z., Weisz, D., Aiden, E. L., et al. (2023) · Journal of Heredity · doi:10.1093/jhered/esad035 · Cited by 9 · see citing works
Insights into the Evolution of Ancient Shark and Ray Sex ChromosomesPreprint
Lee, S.-H., Fedrigo, O. D., Soler-Clavel, L., Humble, E., Lesturgie, P., Balacco, J., O’Toole, B., Mountcastle, J., Haase, B., Brajuka, N., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.26.637739 · Cited by 8 · see citing works
A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus)
Kliver, S. F., Kovacic, I., Mak, S. S. T., Sinding, M. S., Stagegaard, J., Petersen, B., Nesme, J., & Gilbert, M. T. P. (2024) · Journal of Heredity · doi:10.1093/jhered/esae052 · Cited by 6 · see citing works
An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements
Moshe, A., Wygoda, E., Ecker, N., Loewenthal, G., Avram, O., Israeli, O., Hazkani‐Covo, E., Pe’er, I., & Pupko, T. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac231 · Cited by 6 · see citing works
Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora)
Totikov, A., Tomarovsky, A. A., Perelman, P. L., Bulyonkova, T., Serdyukova, N. A., Yakupova, A. R., Mohr, D. W., Förster, D. W., Grau, J., Beklemisheva, V. R., et al. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag014 · Cited by 4 · see citing works
Self-citationTomarovsky, A. A., Khan, R., Dudchenko, O., Totikov, A., Serdyukova, N. A., Weisz, D., Vorobieva, N. V., Bulyonkova, T., Abramov, A. V., Nie, W., et al. (2025) · Journal of Heredity · doi:10.1093/jhered/esaf001 · Cited by 4 · see citing works
Leone, M. J., van de Weerd, R., Brown, A. R., Noh, M., Phan, B. N., Wang, A. Z., Corrigan, K. A., Yeramosu, D., Sestili, H. H., Arokiaraj, C. M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.20.660790 · Cited by 4 · see citing works
Romanenko, S. A., Kliver, S. F., Serdyukova, N. A., Perelman, P. L., Trifonov, V. A., Seluanov, A., Gorbunova, V. A., Azpurua, J., Pereira, J. C., Ferguson-Smith, M. A., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-46595-x · Cited by 4 · see citing works
Tomarovsky, A. A., Khan, R., Dudchenko, O., Beklemisheva, V. R., Perelman, P. L., Totikov, A., Serdyukova, N. A., Bulyonkova, T., Pobedintseva, M. A., Abramov, A. V., et al. (2025) · Journal of Heredity · doi:10.1093/jhered/esaf101 · Cited by 2 · see citing works
Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome
Stanek, T. J., Leung, W., Shaffer, C. D., Partnership, T. G. E., Kleinschmit, A. J., Mix, J., Starkey, J. M., Ogden, S., Robic, S., Roman, D., et al. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf304 · Cited by 2 · see citing works
Wright, K. M., Sood, P., Zemlemerova, E. D., Kostin, D. S., Fong, N. L., Yi, N., Ireland, A. T., Lam, I., Hardell, K. N. L., Smith, M., et al. (2025) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2025.1689079 · Cited by 2 · see citing works
GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions
Zhang, Z., Gupta, I., & Pevzner, P. A. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf058 · Cited by 1 · see citing works
On Deriving Synteny Blocks by Compacting Elements
Bohnenkämper, L., Parmigiani, L., Hepak, K., Chauve, C., & Stoye, J. (2026) · Journal of Computational Biology · doi:10.1177/15578666261491605 · Cited by 1 · see citing works
Evolution repeats itself in replicate long-term studies in the wildPreprint
Gompert, Z., Nosil, P., de Carvalho, C. F., Villoutreix, R., Zamorano, L. S., Sinclair‐Waters, M., Planidin, N., Parchman, T. L., & Feder, J. L. (2023) · Research Square · doi:10.21203/rs.3.rs-3390078/v1
Quantifying structural variants in chromosomes using landmark-based disparityPreprint
Mohan, A. V., Goswami, A., & Streicher, J. W. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.30.620815
Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteusPreprint
Sinding, M. S., Gargano, M., Li, Z., Trucchi, E., Arnold, P., Daly, K. G., Mattiangeli, V., Kliver, S. F., Duchêne, D. A., Wegmann, D., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.13.724764
- Authors
- Krasheninnikova, K., Diekhans, M., Armstrong, J., Dievskii, A., Paten, B., & O'Brien, S.
- Affiliations
- ITMO University (RU)
- University of California, Santa Cruz (US)
- Wellcome Trust (GB)
- Computer Technologies Laboratory, School of Translational Information Technologies, ITMO University , 49 Kronverkskiy Pr., St. Petersburg 197101, St. Petersburg,
- Corresponding author
- Krasheninnikova, Ksenia
- Venue
- GigaScience
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-05-28
- Volume
- 9
- Issue
- 6
- ISSN
- 2047-217X (ISSN-L)
- PMC
- PMC7254927
- OpenAlex
- W3029174313
- Semantic Scholar
- 1c532c9489012f6dc3b71a2838df9faac609f560
- Cited by
- 30
- References
- 27
- Citations by year
- 2026: 4 · 2025: 11 · 2024: 6 · 2023: 5 · 2022: 3 · 2020: 1
- FWCI
- 1.31
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- GigaScience (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- NSUWorks (Nova Southeastern University) (submittedVersion)
- Funders
- Korea National Institute of Health (R01HG008742)
- Russian Foundation for Basic Research
- Russian Science Foundation (17-14-01138)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- chromosomal rearrangements, comparative genomics, vertebrate genomes
- MeSH terms
- Algorithms, Software, Reproducibility of Results, Sequence Alignment, Computational Biology, Genomics, Synteny
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-11-02.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-11-02.
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