Computational methods for chromosome-scale haplotype reconstruction

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 9,781 · see citing works

Occurrence of the potent mutagens 2- nitrobenzanthrone and 3-nitrobenzanthrone in fine airborne particles

Santos, A. G., da Rocha, G. O., & de Andrade, J. B. (2019) · Scientific Reports · doi:10.1038/s41598-018-37186-2 · Cited by 8,495 · see citing works

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint

Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,340 · see citing works

Assembly of long, error-prone reads using repeat graphs

Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986 · see citing works

metaSPAdes: a new versatile metagenomic assembler

Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496 · see citing works

Mash: fast genome and metagenome distance estimation using MinHash

(2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373 · see citing works

Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

Browning, S. R., & Browning, B. L. (2007) · The American Journal of Human Genetics · doi:10.1086/521987 · Cited by 3,138 · see citing works

Fast and accurate de novo genome assembly from long uncorrected readsPreprint

Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017) · Genome Research · doi:10.1101/gr.214270.116 · Cited by 3,059 · see citing works

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

Peng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts174 · Cited by 2,997 · see citing works

PacBio Sequencing and its Applications

Rhoads, A., & Au, K. F. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.08.002 · Cited by 2,338 · see citing works

RNA sequencing: the teenage years

Stark, R., Grzelak, M., & Hadfield, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0150-2 · Cited by 1,906 · see citing works

Reference-based phasing using the Haplotype Reference Consortium panel

Loh, P.-R., Danecek, P., Palamara, P. F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G. R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3679 · Cited by 1,894 · see citing works

Nanopore sequencing and assembly of a human genome with ultra-long reads

Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892 · see citing works

Phased diploid genome assembly with single-molecule real-time sequencing

Chin, C.-S., Peluso, P. S., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O’Malley, R. C., Figueroa-Balderas, R. E., Morales‐Cruz, A., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4035 · Cited by 1,847 · see citing works

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841 · see citing works

Fast and accurate long-read assembly with wtdbg2

Ruan, J., & Li, H. (2019) · Nature Methods · doi:10.1038/s41592-019-0669-3 · Cited by 1,314 · see citing works

Long-read human genome sequencing and its applications

Logsdon, G. A., Vollger, M. R., & Eichler, E. E. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0236-x · Cited by 1,222 · see citing works

Inference of Population Structure using Dense Haplotype Data

Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002453 · Cited by 1,188 · see citing works

Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population

Vignuzzi, M., Stone, J. K., Arnold, J. J., Cameron, C. E., & Andino, R. (2006) · Nature · doi:10.1038/nature04388 · Cited by 1,116 · see citing works

metaFlye: scalable long-read metagenome assembly using repeat graphs

Kolmogorov, M., Bickhart, D. M., Behsaz, B., Gurevich, A. A., Rayko, M., Shin, S. B., Kuhn, K. L., Yuan, J., Polevikov, E., Smith, T. P. L., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-00971-x · Cited by 1,087 · see citing works

Segmental Duplications and Copy-Number Variation in the Human Genome

Sharp, A. J., Locke, D. P., McGrath, S. D., Cheng, Z., Bailey, J. A., Vallente, R. U., Pertz, L. M., Clark, R. A., Schwartz, S., Segraves, R., et al. (2005) · The American Journal of Human Genetics · doi:10.1086/431652 · Cited by 973 · see citing works

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08148-z · Cited by 891 · see citing works

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4458 · Cited by 873 · see citing works

Direct determination of diploid genome sequences

Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M., & Jaffe, D. B. (2017) · Genome Research · doi:10.1101/gr.214874.116 · Cited by 803 · see citing works

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

Zook, J. M., Chapman, B., Wang, J., Mittelman, D., Hofmann, O., Hide, W., & Salit, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2835 · Cited by 800 · see citing works

Telomere-to-telomere assembly of a complete human X chromosome

Miga, K. H., Koren, S., Rhie, A., Vollger, M. R., Gershman, A., Bzikadze, A., Brooks, S., Howe, E., Porubsky, D., Logsdon, G. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2547-7 · Cited by 765 · see citing works

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long readsPreprint

Nurk, S., Walenz, B. P., Rhie, A., Vollger, M. R., Logsdon, G. A., Grothe, R., Miga, K. H., Eichler, E. E., Phillippy, A. M., & Koren, S. (2020) · Genome Research · doi:10.1101/gr.263566.120 · Cited by 709 · see citing works

GAGE: A critical evaluation of genome assemblies and assembly algorithmsPreprint

Salzberg, S. L., Phillippy, A. M., Zimin, A. V., Puiu, D., Magoč, T., Koren, S., Treangen, T. J., Schatz, M. C., Delcher, A. L., Roberts, M., et al. (2011) · Genome Research · doi:10.1101/gr.131383.111 · Cited by 680 · see citing works

How to apply de Bruijn graphs to genome assembly

Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011) · Nature Biotechnology · doi:10.1038/nbt.2023 · Cited by 673 · see citing works

Role of Telomeres and Telomerase in Aging and Cancer

Shay, J. W. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0062 · Cited by 668 · see citing works

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Bradnam, K. R., Fass, J., Alexandrov, A., Baranay, P., Bechner, M., Birol, İ., Boisvert, S., Chapman, J., Chapuis, G., Chikhi, R., et al. (2013) · GigaScience · doi:10.1186/2047-217x-2-10 · Cited by 658 · see citing works

Haplotype phasing: existing methods and new developments

Browning, S. R., & Browning, B. L. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3054 · Cited by 650 · see citing works

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0503-6 · Cited by 567 · see citing works

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

Scientists, G. 1. C. O. (2009) · Journal of Heredity · doi:10.1093/jhered/esp086 · Cited by 539 · see citing works

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.08.014 · Cited by 536 · see citing works

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0003-4 · Cited by 530 · see citing works

Assemblathon 1: A competitive assessment of de novo short read assembly methodsPreprint

Earl, D. A., Bradnam, K. R., John, J. S., Darling, A. E., Lin, D., Fass, J., Yu, H. O. K., Buffalo, V., Zerbino, D. R., Diekhans, M., et al. (2011) · Genome Research · doi:10.1101/gr.126599.111 · Cited by 503 · see citing works

De novo assembly of haplotype-resolved genomes with trio binning

Koren, S., Rhie, A., Walenz, B. P., Dilthey, A., Bickhart, D. M., Kingan, S. B., Hiendleder, S., Williams, J. L., Smith, T. P. L., & Phillippy, A. M. (2018) · Nature Biotechnology · doi:10.1038/nbt.4277 · Cited by 494 · see citing works

A first look at the Oxford Nanopore MinION sequencer

Mikheyev, A. S., & Tin, M. M. Y. (2014) · Molecular Ecology Resources · doi:10.1111/1755-0998.12324 · Cited by 483 · see citing works

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

Lloyd, K. G., Ladau, J., Steen, A. D., Yin, J., & Crosby, L. D. (2018) · mSystems · doi:10.1128/msystems.00055-18 · Cited by 461 · see citing works

WhatsHap: fast and accurate read-based phasingPreprint

Martin, M., Patterson, M., Garg, S., Fischer, S. O., Pisanti, N., Klau, G. W., Schönhuth, A., & Marschall, T. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/085050 · Cited by 454 · see citing works

W <scp>hats</scp> H <scp>ap</scp> : Weighted Haplotype Assembly for Future-Generation Sequencing Reads

Patterson, M., Marschall, T., Pisanti, N., van Iersel, L., Stougie, L., Klau, G. W., & Schönhuth, A. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2014.0157 · Cited by 453 · see citing works

Diversity within Species: Interpreting Strains in Microbiomes

Van Rossum, T., Ferretti, P., Maistrenko, O. M., & Bork, P. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0368-1 · Cited by 441 · see citing works

Long-Read Sequencing Emerging in Medical Genetics

Mantere, T., Kersten, S., & Hoischen, A. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00426 · Cited by 430 · see citing works

The fragment assembly string graph

Myers, E. W. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1114 · Cited by 424 · see citing works

A robust benchmark for detection of germline large deletions and insertions

Zook, J. M., Hansen, N. F., Olson, N. D., Chapman, L., Mullikin, J. C., Xiao, C., Sherry, S., Koren, S., Phillippy, A. M., Boutros, P. C., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0538-8 · Cited by 418 · see citing works

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

Smillie, C. S., Sauk, J. S., Gevers, D., Friedman, J., Sung, J., Youngster, I., Hohmann, E. L., Staley, C. M., Khoruts, A., Sadowsky, M. J., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.01.003 · Cited by 417 · see citing works

An open resource for accurately benchmarking small variant and reference calls

Zook, J. M., McDaniel, J., Olson, N. D., Wagner, J., Parikh, H. M., Heaton, H., Irvine, S. A., Trigg, L., Truty, R., McLean, C. Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0074-6 · Cited by 404 · see citing works

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Cretu-Stancu, M., van Roosmalen, M. J., Renkens, I., Nieboer, M. M., Middelkamp, S., de Ligt, J., Pregno, G., Giachino, D. F., Mandrile, G., Valle-Inclán, J. E., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01343-4 · Cited by 392 · see citing works

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologiesPreprint

Edge, P., Bafna, V., & Bansal, V. (2016) · Genome Research · doi:10.1101/gr.213462.116 · Cited by 379 · see citing works

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

Bertrand, D., Shaw, J., Kalathiyappan, M., Ng, A. H. Q., Kumar, M. S. B., Li, C., Dvorničić, M., Soldo, J. P., Koh, J. Y., Tong, C., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0191-2 · Cited by 379 · see citing works

Whole-genome molecular haplotyping of single cells

Fan, H. C., Wang, J., Potanina, A., & Quake, S. R. (2010) · Nature Biotechnology · doi:10.1038/nbt.1739 · Cited by 364 · see citing works

Pan-genomics in the human genome era

Sherman, R. M., & Salzberg, S. L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0210-7 · Cited by 364 · see citing works

ENSO-induced co-variability of Salinity, Plankton Biomass and Coastal Currents in the Northern Gulf of Mexico

Gomez, F. A., Lee, S., Hernandez, F. J., Chiaverano, L. M., Muller-Karger, F. E., Liu, Y., & Lamkin, J. T. (2019) · Scientific Reports · doi:10.1038/s41598-018-36655-y · Cited by 337 · see citing works

Long-read sequence assembly of the gorilla genome

Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science · doi:10.1126/science.aae0344 · Cited by 333 · see citing works

De novo assembly and phasing of a Korean human genome

Seo, J.-S., Rhie, A., Kim, J., Lee, S.-J., Sohn, M.-H., Kim, C.-U., Hastie, A., Cao, H., Yun, J.-Y., Kim, J., et al. (2016) · Nature · doi:10.1038/nature20098 · Cited by 312 · see citing works

Long walk to genomics: History and current approaches to genome sequencing and assembly

Giani, A. M., Gallo, G. R., Gianfranceschi, L., & Formenti, G. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.11.002 · Cited by 306 · see citing works

The importance of phase information for human genomics

Tewhey, R., Bansal, V., Torkamani, A., Topol, E. J., & Schork, N. J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2950 · Cited by 302 · see citing works

The Human Pseudoautosomal Region (PAR): Origin, Function and Future

Mangs, A. H., & Morris, B. J. (2007) · Current Genomics · doi:10.2174/138920207780368141 · Cited by 289 · see citing works

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

Selvaraj, S., Dixon, J. R., Bansal, V., & Ren, B. (2013) · Nature Biotechnology · doi:10.1038/nbt.2728 · Cited by 278 · see citing works

ConStrains identifies microbial strains in metagenomic datasets

Luo, C., Knight, R. D., Siljander, H., Knip, M., Xavier, R. J., & Gevers, D. (2015) · Nature Biotechnology · doi:10.1038/nbt.3319 · Cited by 267 · see citing works

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Nir, G., Farabella, I., Pérez Estrada, C., Ebeling, C. G., Beliveau, B. J., Sasaki, H. M., Lee, S. D., Nguyen, S. C., McCole, R. B., Chattoraj, S., et al. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007872 · Cited by 261 · see citing works

Long-read sequencing and de novo assembly of a Chinese genome

Shi, L., Guo, Y., Dong, C., Huddleston, J., Yang, H., Han, X., Fu, A., Li, Q., Li, N., Gong, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms12065 · Cited by 257 · see citing works

Recovering complete and draft population genomes from metagenome datasets

Sangwan, N., Xia, F., & Gilbert, J. A. (2016) · Microbiome · doi:10.1186/s40168-016-0154-5 · Cited by 255 · see citing works

Resolving the full spectrum of human genome variation using Linked-ReadsPreprint

Marks, P., Garcia, S., Barrio, Á. M., Belhocine, K., Bernate, J., Bharadwaj, R., Bjornson, K. P., Catalanotti, C., Delaney, J., Fehr, A. N., et al. (2019) · Genome Research · doi:10.1101/gr.234443.118 · Cited by 252 · see citing works

Comparing and evaluating metagenome assembly tools from a microbiologist's perspective - not only size matters!

Vollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240 · see citing works

Centromere reference models for human chromosomes X and Y satellite arraysPreprint

Miga, K. H., Newton, Y., Jain, M., Altemose, N., Willard, H. F., & Kent, W. J. (2014) · Genome Research · doi:10.1101/gr.159624.113 · Cited by 229 · see citing works

New approaches for metagenome assembly with short reads

Ayling, M., Clark, M. D., & Leggett, R. M. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz020 · Cited by 218 · see citing works

Long-read sequence and assembly of segmental duplications

Vollger, M. R., Dishuck, P. C., Sorensen, M., Welch, A. E., Dang, V., Dougherty, M. L., Graves-Lindsay, T. A., Wilson, R. K., Chaisson, M., & Eichler, E. E. (2018) · Nature Methods · doi:10.1038/s41592-018-0236-3 · Cited by 204 · see citing works

Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem

Lippert, R. A. (2002) · Briefings in Bioinformatics · doi:10.1093/bib/3.1.23 · Cited by 203 · see citing works

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Human Genome Structural Variation Consortium, Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., Marijon, P., Ebler, J., Munson, K. M., Sorensen, M., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0719-5 · Cited by 203 · see citing works

Early changes in hepatitis C viral quasispecies during interferon therapy predict the therapeutic outcome

Farci, P., Strazzera, R., Alter, H. J., Farci, S., Degioannis, D., Coiana, A., Peddis, G., Usai, F., Serra, G., Chessa, L., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052712599 · Cited by 200 · see citing works

Haplotype estimation for biobank-scale data sets

O’Connell, J., Sharp, K., Shrine, N. R. G., Wain, L. V., Hall, I. P., Tobin, M. D., Zagury, J., Delaneau, O., & Marchini, J. (2016) · Nature Genetics · doi:10.1038/ng.3583 · Cited by 200 · see citing works

SNPs Problems, Complexity, and Algorithms

Lancia, G., Bafna, V., Istrail, S., Lippert, R. A., & Schwartz, R. S. (2001) · Lecture notes in computer science · doi:10.1007/3-540-44676-1_15 · Cited by 199 · see citing works

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

Falconer, E., Hills, M., Naumann, U., Poon, S. S. S., Chavez, E. A., Sanders, A. D., Zhao, Y., Hirst, M., & Lansdorp, P. M. (2012) · Nature Methods · doi:10.1038/nmeth.2206 · Cited by 199 · see citing works

Chromosome-specific subsets of human alpha satellite DNA: Analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat

Willard, H. F., & Waye, J. S. (1987) · Journal of Molecular Evolution · doi:10.1007/bf02100014 · Cited by 198 · see citing works

Haplotype-resolved genome analyses of a heterozygous diploid potato

Zhou, Q., Tang, D., Huang, W., Yang, Z., Zhang, Y., Hamilton, J., Visser, R., Bachem, C., Buell, C. R., Zhang, Z.-H., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0699-x · Cited by 196 · see citing works

Haplotype-resolved genome sequencing: experimental methods and applications

Snyder, M. W., Adey, A., Kitzman, J. O., & Shendure, J. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3903 · Cited by 189 · see citing works

Chromosome-scale, haplotype-resolved assembly of human genomes

Garg, S., Fungtammasan, A., Carroll, A. W., Chou, M., Schmitt, A. D., Zhou, X., Mac, S., Peluso, P. S., Hatas, E., Ghurye, J., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0711-0 · Cited by 177 · see citing works

DESMAN: a new tool for de novo extraction of strains from metagenomes

Quince, C., Delmont, T., Raguideau, S., Alneberg, J., Darling, A., Collins, G., & Eren, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1309-9 · Cited by 175 · see citing works

Managing, Analysing, and Integrating Big Data in Medical Bioinformatics: Open Problems and Future Perspectives

Merelli, I., Pérez‐Sánchez, H., Gesing, S., & D’Agostino, D. (2014) · BioMed Research International · doi:10.1155/2014/134023 · Cited by 172 · see citing works

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

Dilthey, A., Jain, C., Koren, S., & Phillippy, A. M. (2019) · Nature Communications · doi:10.1038/s41467-019-10934-2 · Cited by 170 · see citing works

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Kronenberg, Z. N., Rhie, A., Koren, S., Concepcion, G. T., Peluso, P. S., Munson, K. M., Porubskỳ, D., Kuhn, K. L., Mueller, K. A., Low, W. Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20536-y · Cited by 169 · see citing works

Visualizing genomes: techniques and challenges

Nielsen, C. B., Cantor, M., Dubchak, I. L., Gordon, D., & Wang, T. (2010) · Nature Methods · doi:10.1038/nmeth.1422 · Cited by 167 · see citing works

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity

Low, W. Y., Tearle, R. G., Bickhart, D. M., Rosen, B. D., Kingan, S. B., Swale, T., Thibaud‐Nissen, F., Murphy, T. D., Young, R. A., Lefèvre, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08260-0 · Cited by 165 · see citing works

Centromere Repeats: Hidden Gems of the Genome

Hartley, G. A., & O'Neill, R. J. W. (2019) · Genes · doi:10.3390/genes10030223 · Cited by 163 · see citing works

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

Zaccaria, S., & Raphael, B. J. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0661-6 · Cited by 159 · see citing works

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint

Koren, S., Walenz, B. P., Berlin, K., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/071282 · Cited by 157 · see citing works

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

Yaffe, E., & Relman, D. A. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0625-0 · Cited by 157 · see citing works

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

Olson, N. D., Treangen, T. J., Hill, C. M., Cepeda-Espinoza, V. P., Ghurye, J., Koren, S., & Pop, M. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx098 · Cited by 156 · see citing works

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

Cleary, B., Brito, I., Huang, K. H., Gevers, D., Shea, T., Young, S., & Alm, E. J. (2015) · Nature Biotechnology · doi:10.1038/nbt.3329 · Cited by 151 · see citing works

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

Beitel, C. W., Froenicke, L., Lang, J., Korf, I. F., Michelmore, R. W., Eisen, J. A., & Darling, A. E. (2014) · PeerJ · doi:10.7717/peerj.415 · Cited by 131 · see citing works

Human-specific tandem repeat expansion and differential gene expression during primate evolution

Sulovari, A., Li, R., Audano, P. A., Porubskỳ, D., Vollger, M. R., Logsdon, G. A., Warren, W. C., Pollen, A. A., Chaisson, M., Eichler, E. E., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912175116 · Cited by 131 · see citing works

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

Sanders, A. D., Falconer, E., Hills, M., Spierings, D. C. J., & Lansdorp, P. M. (2017) · Nature Protocols · doi:10.1038/nprot.2017.029 · Cited by 125 · see citing works

Tasks, Techniques, and Tools for Genomic Data Visualization

Nusrat, S., Harbig, T. A., & Gehlenborg, N. (2019) · Computer Graphics Forum · doi:10.1111/cgf.13727 · Cited by 125 · see citing works

Telomere-to-telomere assembly of a complete human X chromosomePreprint

Miga, K. H., Koren, S., Rhie, A., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/735928 · Cited by 117 · see citing works

A haplotype-led approach to increase the precision of wheat breeding

Brinton, J., Ramirez-Gonzalez, R. H., Simmonds, J., Wingen, L. U., Orford, S., Griffiths, S., 10 Wheat Genome Project, Haberer, G., Spannagl, M., Walkowiak, S., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-01413-2 · Cited by 113 · see citing works

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

DeMaere, M. Z., & Darling, A. E. (2019) · Genome biology · doi:10.1186/s13059-019-1643-1 · Cited by 109 · see citing works

Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions

Press, M. O., Wiser, A. H., Kronenberg, Z. N., Langford, K. W., Shakya, M., Lo, C.-C., Mueller, K. A., Sullivan, S. T., Chain, P. S. G., & Liachko, I. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/198713 · Cited by 103 · see citing works

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implicationsPreprint

Weissensteiner, M. H., Pang, A. W. C., Bunikis, I., Höijer, I., Pettersson, O. V., Suh, A., & Wolf, J. B. W. (2017) · Genome Research · doi:10.1101/gr.215095.116 · Cited by 99 · see citing works

Human Genome Assembly in 100 MinutesPreprint

Chin, C.-S., & Khalak, A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/705616 · Cited by 97 · see citing works

Dense and accurate whole-chromosome haplotyping of individual genomes

Porubskỳ, D., Garg, S., Sanders, A. D., Korbel, J. O., Guryev, V., Lansdorp, P. M., & Marschall, T. (2017) · Nature Communications · doi:10.1038/s41467-017-01389-4 · Cited by 95 · see citing works

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

Berger, E., Yörükoğlu, D., Peng, J., & Berger, B. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-05269-4_2 · Cited by 93 · see citing works

Haplotype-aware graph indexes

Sirén, J., Garrison, E., Novak, A. M., Paten, B., & Durbin, R. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz575 · Cited by 92 · see citing works

Keeping ribosomal DNA intact: a repeating challenge

Warmerdam, D. O., & Wolthuis, R. M. F. (2018) · Chromosome Research · doi:10.1007/s10577-018-9594-z · Cited by 91 · see citing works

A Review on Viral Metagenomics in Extreme Environments

Dávila‐Ramos, S., Castelán-Sánchez, H. G., Martínez-Ávila, L., Sánchez‐Carbente, M. D. R., Peralta, R., Hernández-Mendoza, A., Dobson, A. D. W., González, R. A., Pastor, N., & Batista‐García, R. A. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02403 · Cited by 89 · see citing works

Unzipping haplotypes in diploid and polyploid genomes

Zhang, X., Wu, R., Wang, Y., Yu, J., & Tang, H. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.11.011 · Cited by 88 · see citing works

Haplotype threading: accurate polyploid phasing from long reads

Schrinner, S. D., Mari, R. S., Ebler, J., Rautiainen, M., Seillier, L., Reimer, J. J., Usadel, B., Marschall, T., & Klau, G. W. (2020) · Genome biology · doi:10.1186/s13059-020-02158-1 · Cited by 88 · see citing works

Whole-genome haplotyping approaches and genomic medicine

Glusman, G., Cox, H. C., & Roach, J. C. (2014) · Genome Medicine · doi:10.1186/s13073-014-0073-7 · Cited by 84 · see citing works

Automated assembly of centromeres from ultra-long error-prone reads

Bzikadze, A. V., & Pevzner, P. A. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0582-4 · Cited by 79 · see citing works

SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming

Das, S., & Vikalo, H. (2015) · BMC Genomics · doi:10.1186/s12864-015-1408-5 · Cited by 76 · see citing works

De novo assembly of a haplotype-resolved human genome

Cao, H., Wu, H., Luo, R., Huang, S., Sun, Y., Tong, X., Xie, Y., Liu, B., Yang, H., Zheng, H., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3200 · Cited by 65 · see citing works

Centromere studies in the era of ‘telomere-to-telomere’ genomics

Miga, K. H. (2020) · Experimental Cell Research · doi:10.1016/j.yexcr.2020.112127 · Cited by 63 · see citing works

H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids

Xie, M., Wu, Q., Wang, J., & Jiang, T. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw537 · Cited by 61 · see citing works

Probabilistic single-individual haplotyping

Kuleshov, V. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu484 · Cited by 60 · see citing works

Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study

Motazedi, E., Finkers, R., Maliepaard, C. A., & de Ridder, D. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw126 · Cited by 60 · see citing works

Computational analysis of next generation sequencing data and its applications in clinical oncology

Wadapurkar, R. M., & Vyas, R. (2018) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2018.05.003 · Cited by 57 · see citing works

Assembly and annotation of an Ashkenazi human reference genome

Shumate, A., Zimin, A. V., Sherman, R. M., Puiu, D., Wagner, J., Olson, N. D., Pertea, M., Salit, M., Zook, J. M., & Salzberg, S. L. (2020) · Genome biology · doi:10.1186/s13059-020-02047-7 · Cited by 57 · see citing works

Read-based phasing of related individuals

Garg, S., Martin, M., & Marschall, T. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw276 · Cited by 54 · see citing works

Direct chromosome-length haplotyping by single-cell sequencingPreprint

Porubskỳ, D., Sanders, A. D., van Wietmarschen, N., Falconer, E., Hills, M., Spierings, D. C. J., Bevova, M. R., Guryev, V., & Lansdorp, P. M. (2016) · Genome Research · doi:10.1101/gr.209841.116 · Cited by 51 · see citing works

The string decomposition problem and its applications to centromere analysis and assembly

Dvorkina, T., Bzikadze, A. V., & Pevzner, P. A. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa454 · Cited by 46 · see citing works

Linked read technology for assembling large complex and polyploid genomes

Ott, A., Schnable, J. C., Yeh, C., Wu, L., Liu, C., Hu, H.-C., Dalgard, C. L., Sarkar, S., & Schnable, P. S. (2018) · BMC Genomics · doi:10.1186/s12864-018-5040-z · Cited by 44 · see citing works

New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes

Liu, R., Low, W. Y., Tearle, R. G., Koren, S., Ghurye, J., Rhie, A., Phillippy, A. M., Rosen, B. D., Bickhart, D. M., Smith, T. P. L., et al. (2019) · BMC Genomics · doi:10.1186/s12864-019-6364-z · Cited by 43 · see citing works

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

Hoehe, M. R., Church, G. M., Lehrach, H. R., Kroslak, T., Palczewski, S., Nowick, K., Schulz, S., Suk, E.-K., & Huebsch, T. (2014) · Nature Communications · doi:10.1038/ncomms6569 · Cited by 31 · see citing works

Next generation sequencing technologies

Jarvie, T. P. (2005) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2005.08.003 · Cited by 30 · see citing works

Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26

Gudmundsson, S., Wilbe, M., Ekvall, S., Ameur, A., Cahill, N., Alexandrov, L. B., Virtanen, M., Pigg, M. H., Vahlquist, A., Törmä, H., et al. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx017 · Cited by 30 · see citing works

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals

Motazedi, E., de Ridder, D., Finkers, R., Baldwin, S. J., Thomson, S. J., Monaghan, K. S., & Maliepaard, C. A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty442 · Cited by 30 · see citing works

A haplotype-aware de novo assembly of related individuals using pedigree sequence graph

Garg, S., Aach, J., Li, H., Sebenius, I., Durbin, R. M., & Church, G. M. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz942 · Cited by 29 · see citing works

Next Generation Sequencing and Sequence Assembly

Masoudi‐Nejad, A., Narimani, Z., & Hosseinkhan, N. (2013) · SpringerBriefs in systems biology · doi:10.1007/978-1-4614-7726-6 · Cited by 27 · see citing works

Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes

Bansal, V. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz329 · Cited by 25 · see citing works

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samplesPreprint

Aganezov, S. S., & Raphael, B. J. (2020) · Genome Research · doi:10.1101/gr.256701.119 · Cited by 23 · see citing works

Centromere 17 copy number gain reflects chromosomal instability in breast cancer

Lee, K., Kim, H. J., Jang, M. H., Lee, S., Ahn, S., & Park, S. Y. (2019) · Scientific Reports · doi:10.1038/s41598-019-54471-w · Cited by 22 · see citing works

Overlap graph-based generation of haplotigs for diploids and polyploids

Baaijens, J. A., & Schönhuth, A. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz255 · Cited by 20 · see citing works

InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strainsPreprint

Olm, M. R., Crits‐Christoph, A., Bouma‐Gregson, K., Firek, B., Morowitz, M. J., & Banfield, J. F. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.22.915579 · Cited by 20 · see citing works

On the complexity of haplotyping a microbial community

Nicholls, S. M., Aubrey, W., Grave, K. D., Schietgat, L., Creevey, C. J., & Clare, A. J. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa977 · Cited by 20 · see citing works

A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations

King, D. J., Freimanis, G., Lasecka‐Dykes, L., Asfor, A. S., Ribeca, P., Waters, R. A., King, D. P., & Laing, E. (2020) · Viruses · doi:10.3390/v12101187 · Cited by 19 · see citing works

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads

Majidian, S., Kahaei, M. H., & de Ridder, D. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03584-5 · Cited by 18 · see citing works

Haplotype phasing in single-cell DNA-sequencing data

Satas, G., & Raphael, B. J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty286 · Cited by 17 · see citing works

Haplotype Threading: Accurate Polyploid Phasing from Long ReadsPreprint

Schrinner, S. D., Mari, R. S., Ebler, J., Rautiainen, M., Seillier, L., Reimer, J. J., Usadel, B., Marschall, T., & Klau, G. W. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.04.933523 · Cited by 17 · see citing works

SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencingPreprint

Heller, D., Vingron, M., Church, G. M., Li, H., & Garg, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.25.964445 · Cited by 14 · see citing works

Towards a More Accurate Error Model for BioNano Optical Maps

Li, M., Mak, A. C. Y., Lam, E. T., Kwok, P., Xiao, M., Yip, K. Y.-L., Chan, T., & Yiu, S. (2016) · Lecture notes in computer science · doi:10.1007/978-3-319-38782-6_6 · Cited by 13 · see citing works

Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing

Nagasaki, M., Kuroki, Y., Shibata, T. F., Katsuoka, F., Mimori, T., Kawai, Y., Minegishi, N., Hozawa, A., Kuriyama, S., Suzuki, Y., et al. (2019) · Human Genome Variation · doi:10.1038/s41439-019-0057-7 · Cited by 13 · see citing works

HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data

Berger, E., Yörükoğlu, D., & Berger, B. (2015) · Lecture notes in computer science · doi:10.1007/978-3-319-16706-0_4 · Cited by 10 · see citing works

Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity

Bankevich, A., & Pevzner, P. A. (2018) · Cell Systems · doi:10.1016/j.cels.2018.06.009 · Cited by 10 · see citing works

A Guided Tour to Computational Haplotyping

Klau, G. W., & Marschall, T. (2017) · Lecture notes in computer science · doi:10.1007/978-3-319-58741-7_6 · Cited by 9 · see citing works

Sex chromosome evolution: life, death and repetitive DNA

Deshpande, N., & Meller, V. H. (2014) · Fly · doi:10.1080/19336934.2015.1024395 · Cited by 8 · see citing works

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samplesPreprint

Aganezov, S. S., & Raphael, B. J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/560839 · Cited by 8 · see citing works

Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communitiesPreprint

Nicholls, S. M., Aubrey, W., Edwards, A., Grave, K. D., Huws, S., Schietgat, L., Soares, A., Creevey, C. J., & Clare, A. J. (2018) · Research Portal (Queen's University Belfast) · doi:10.1101/223404 · Cited by 7 · see citing works

The haplotypes of various TNF related genes associated with scleritis in Chinese Han

Gao, Y., Du, L., Li, F., Ding, J., Geng, L., Cao, Q., Li, N., Su, G., Kijlstra, A., & Yang, P. (2020) · Human Genomics · doi:10.1186/s40246-020-00296-y · Cited by 6 · see citing works

Scalable Genomic Data Management System on the Cloud

Kaitoua, A., Gulino, A., Masseroli, M., Pinoli, P., & Ceri, S. (2017) · International Conference on High Performance Computing & Simulation (HPCS) · doi:10.1109/hpcs.2017.19 · Cited by 5 · see citing works

De novo and haplotype assembly of polyploid genomes

Moeinzadeh, M. (2019) · Refubium (Universitätsbibliothek der Freien Universität Berlin) · doi:10.17169/refubium-2712 · Cited by 4 · see citing works

Moving Towards Third‐Generation Sequencing Technologies

Janitz, K., & Janitz, M. (2011) · doi:10.1002/9783527644582.ch20 · Cited by 3 · see citing works

Human nuclear mitochondrial sequences (NumtS)

Attimonelli, M., & Calabrese, F. M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819656-4.00006-1 · Cited by 2 · see citing works

A QPTAS for Gapless MECPreprint

Garg, S., & Mömke, T. (2018) · arXiv (Cornell University) · doi:10.4230/lipics.esa.2018.34 · Cited by 1 · see citing works

A draft human pangenome reference.

Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works

Semi-automated assembly of high-quality diploid human reference genomes

Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., et al. (2022) · Nature · doi:10.1038/s41586-022-05325-5 · Cited by 209 · see citing works

Features and applications of haplotypes in crop breeding

Bhat, J. A., Yu, D., Bohra, A., Ganie, S. A., & Varshney, R. K. (2021) · Communications Biology · doi:10.1038/s42003-021-02782-y · Cited by 182 · see citing works

LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants

Lin, J.-H., Chen, L.-C., Shu-chi, Y., & Huang, Y. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac058 · Cited by 86 · see citing works

Analysis of metagenomic data

Liu, S., Rodriguez, J. S., Munteanu, V., Ronkowski, C., Sharma, N. K., Alser, M., Andreace, F., Blekhman, R., Błaszczyk, D., Chikhi, R., et al. (2025) · Nature Reviews Methods Primers · doi:10.1038/s43586-024-00376-6 · Cited by 92 · see citing works

Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction, and haploweb calculation

Vences, M., Patmanidis, S., Schmidt, J.-C., Matschiner, M., Miralles, A., & Renner, S. S. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae083 · Cited by 65 · see citing works

Genomics‐assisted breeding for designing salinity‐smart future crops

Raza, A., Zaman, Q. U., Shabala, S. N., Tester, M. A., Munns, R., Hu, Z., & Varshney, R. K. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.70104 · Cited by 66 · see citing works

Genomic and modern biotechnological strategies for enhancing salt tolerance in crops

Yuan, J., Cao, H., Qin, W., Yang, S., Zhang, D., Zhu, L., Song, H., & Zhang, Q. (2024) · New Crops · doi:10.1016/j.ncrops.2024.100057 · Cited by 60 · see citing works

A Draft Human Pangenome ReferencePreprint

Liao, W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J., Monlong, J., Abel, H., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.09.499321 · Cited by 58 · see citing works

Current advancements in fungal engineering technologies for Sustainable Development Goals

Garg, S., Kim, M., & Romero-Suárez, D. (2024) · Trends in Microbiology · doi:10.1016/j.tim.2024.11.001 · Cited by 62 · see citing works

Genomics-assisted speed breeding for crop improvement: present and future

Ćeran, M., Miladinović, D., Đorđević, V., Trkulja, D., Radanović, A., Glogovac, S., & Kondić‐Špika, A. (2024) · Frontiers in Sustainable Food Systems · doi:10.3389/fsufs.2024.1383302 · Cited by 54 · see citing works

Strain Identification and Quantitative Analysis in Microbial Communities

Ghazi, A. R., Münch, P. C., Chen, D., Jensen, J., & Huttenhower, C. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167582 · Cited by 43 · see citing works

Haplotype-based breeding: A new insight in crop improvement

Sivabharathi, R. C., Rajagopalan, V. R., Suresh, R., Sudha, M., KARTHIKEYAN, G., Jayakanthan, M., & Raveendran, M. (2024) · Plant Science · doi:10.1016/j.plantsci.2024.112129 · Cited by 47 · see citing works

Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

Masset, H., Ding, J., Dimitriadou, E., Ardeshirdavani, A., Debrock, S., Tšuiko, O., Smits, K., Peeraer, K., Moreau, Y., Voet, T., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac134 · Cited by 39 · see citing works

Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat

Alemu, A., Batista, L. G., Singh, P. K., Ceplitis, A., & Chawade, A. (2023) · Theoretical and Applied Genetics · doi:10.1007/s00122-023-04352-8 · Cited by 41 · see citing works

Strainline: full-length de novo viral haplotype reconstruction from noisy long reads

Luo, X., Kang, X., & Schönhuth, A. (2022) · Genome biology · doi:10.1186/s13059-021-02587-6 · Cited by 36 · see citing works

Complex genome assembly based on long-read sequencing

Zhang, T., Zhou, J., Gao, W., Jia, Y., Wei, Y., & Wang, G. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac305 · Cited by 35 · see citing works

Sequencing and Assembly of Polyploid Genomes

Wang, Y., Yu, J., Jiang, M., Lei, W., Zhang, X., & Tang, H. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-2561-3_23 · Cited by 33 · see citing works

Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffoldingPreprint

Antipov, D., Rautiainen, M., Nurk, S., Walenz, B. P., Solar, S. J., Phillippy, A. M., & Koren, S. (2025) · Genome Research · doi:10.1101/gr.280383.124 · Cited by 32 · see citing works

Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube

Li, K., Chen, R., Abudoukayoumu, A., Wei, Q., Ma, Z., Wang, Z., Hao, Q., & Huang, J. (2024) · Horticulture Research · doi:10.1093/hr/uhae071 · Cited by 30 · see citing works

Wheat Drought Tolerance: Unveiling a Synergistic Future with Conventional and Molecular Breeding Strategies

Singh, C., Yadav, S., Khare, V., Gupta, V., Patial, M., Kumar, S., V, Mishra, C. N., Tyagi, B. S., Gupta, A. K., Sharma, A. K., et al. (2025) · Plants · doi:10.3390/plants14071053 · Cited by 30 · see citing works

Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics

Garg, S. (2023) · Nature Communications · doi:10.1038/s41467-023-36689-5 · Cited by 27 · see citing works

Genotype error biases trio-based estimates of haplotype phase accuracy

Browning, B. L., & Browning, S. R. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.04.019 · Cited by 24 · see citing works

Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora

Jang, M., Cho, H. J., Park, Y.-S., Lee, H., Bae, E., Jung, S., Jin, H., Woo, J., Park, E., Kim, S.-J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01944-y · Cited by 23 · see citing works

Long-read-based single sperm genome sequencing for chromosome-wide haplotype phasing of both SNPs and SVs

Xie, H., Li, W., Guo, Y., Su, X., Chen, K., Wen, L., & Tang, F. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad532 · Cited by 21 · see citing works

Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes

Ramos, L., & Antunes, A. (2022) · Genomics · doi:10.1016/j.ygeno.2022.110277 · Cited by 20 · see citing works

Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references

Lou, H., Gao, Y., Xie, B., Wang, Y., Zhang, H., Shi, M., Ma, S., Zhang, X., Liu, C., & Xu, S. (2022) · Cell Systems · doi:10.1016/j.cels.2022.01.006 · Cited by 20 · see citing works

Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries

Lino, F. S. D. O., Garg, S., Li, S. S., Misiakou, M.-A., Kang, K., da Costa, B. L. V., Beyer-Pedersen, T. S.-A., Giacon, T. G., Basso, T. O., Panagiotou, G., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49683-2 · Cited by 24 · see citing works

The importance of fungal biotechnology for sustainable applications

Garg, S. (2025) · Trends in biotechnology · doi:10.1016/j.tibtech.2025.06.010 · Cited by 19 · see citing works

Chromosome-scale haplotype-resolved pangenomics

Garg, S., Balboa, R. F., & Kuja, J. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.06.011 · Cited by 18 · see citing works

Genetics of Wool and Cashmere Fibre: Progress, Challenges, and Future Research

Zhou, H., Bai, L., Li, S., Li, W., Wang, J., Tao, J., & Hickford, J. G. H. (2024) · Animals · doi:10.3390/ani14223228 · Cited by 19 · see citing works

Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide

Schell, T., Greve, C., & Podsiadłowski, L. (2025) · Frontiers in Zoology · doi:10.1186/s12983-025-00561-7 · Cited by 20 · see citing works

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Léger, A., Brettell, I., Monahan, J., Barton, C., Wolf, N., Kusminski, N., Herder, C., Aadepu, N., Becker, C., Gierten, J., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02602-4 · Cited by 16 · see citing works

TopoQual polishes circular consensus sequencing data and accurately predicts quality scores

Weerakoon, M., Lee, S., Mitchell, E., & Heaton, H. (2025) · BMC Bioinformatics · doi:10.1186/s12859-024-06020-0 · Cited by 15 · see citing works

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Szakállas, N., Barták, B. K., Valcz, G., Nagy, Z. B., Takács, I., & Molnar, B. A. (2024) · Pathology & Oncology Research · doi:10.3389/pore.2024.1611676 · Cited by 14 · see citing works

A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes

Marone, M. P., Singh, H. C., Pozniak, C. J., & Mascher, M. (2022) · Plant Methods · doi:10.1186/s13007-022-00964-1 · Cited by 14 · see citing works

PAnno: A pharmacogenomics annotation tool for clinical genomic testing

Liu, Y., Lin, Z., Chen, Q., Chen, Q., Sang, L., Wang, Y., Shi, L. M., Guo, L. J., & Yu, Y. (2023) · Frontiers in Pharmacology · doi:10.3389/fphar.2023.1008330 · Cited by 13 · see citing works

New developments in biotechnology applied to microorganisms

(GMO), E. P. O. G. M. O., Mullins, E. D., Bresson, J., Dewhurst, I. C., Epstein, M. M., Firbank, L. G., Guerche, P., Hejátko, J., Moreno, F. J., Naegeli, H., et al. (2024) · EFSA Journal · doi:10.2903/j.efsa.2024.8895 · Cited by 13 · see citing works

Empirical versus estimated accuracy of imputation: optimising filtering thresholds for sequence imputation

Nguyen, T. V., Bolormaa, S., Reich, C. M., Chamberlain, A. J., Jagt, C. J. V., Daetwyler, H. D., & MacLeod, I. M. (2024) · Genetics Selection Evolution · doi:10.1186/s12711-024-00942-2 · Cited by 13 · see citing works

A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake

Nachtigall, P. G., Nystrom, G. S., Broussard, E. M., Wray, K. P., Junqueira-de-Azevedo, I. L. M., Parkinson, C. L., Margres, M. J., & Rokyta, D. R. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf058 · Cited by 12 · see citing works

Geometric deep learning framework for de novo genome assemblyPreprint

Vrček, L., Bresson, X., Laurent, T., Schmitz, M., Kawaguchi, K., & Šikić, M. (2024) · Genome Research · doi:10.1101/gr.279307.124 · Cited by 14 · see citing works

Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds

Barani, S., Nejati‐Javaremi, A., Moradi, M. H., Moradi-Sharbabak, M., Gholizadeh, M., & Esfandyari, H. (2023) · PLoS ONE · doi:10.1371/journal.pone.0286463 · Cited by 11 · see citing works

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Brainard, S. H., Sanders, D., Brůna, T., Shu, S., & Dawson, J. C. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14199 · Cited by 11 · see citing works

Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing

Henglin, M., Ghareghani, M., Harvey, W. T., Porubskỳ, D., Koren, S., Eichler, E. E., Ebert, P., & Marschall, T. (2024) · Genome biology · doi:10.1186/s13059-024-03409-1 · Cited by 11 · see citing works

StrainXpress: strain aware metagenome assembly from short reads

Kang, X., Luo, X. L., & Schönhuth, A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac543 · Cited by 11 · see citing works

Editorial: Long-read sequencing—Pitfalls, benefits and success stories

Wohlers, I., Garg, S., & Hehir‐Kwa, J. Y. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2022.1114542 · Cited by 11 · see citing works

Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity

Ortigas-Vásquez, A., & SZPARA, M. L. (2024) · Annual Review of Virology · doi:10.1146/annurev-virology-100422-010336 · Cited by 10 · see citing works

Haplotype breeding: fast-track the crop improvements

Meena, V. K., Thribhuvan, R., Dinkar, V., Bhatt, A., Pandey, S., Abhinav, A., Ahmad, D., Kumar, A., & Singh, A. K. (2025) · Planta · doi:10.1007/s00425-025-04622-3 · Cited by 10 · see citing works

A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms

Groza, C., Bourque, G., & Goubert, C. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2883-6_5 · Cited by 7 · see citing works

GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C

Ouchi, S., Kajitani, R., & Itoh, T. (2023) · Genome biology · doi:10.1186/s13059-023-03006-8 · Cited by 9 · see citing works

Bioinformatics for Plant Genetics and Breeding Research

Naik, Y. D., Zhao, C., Channale, S., Nayak, S. N., Bhutia, K. L., Gautam, A., Kumar, R., Niranjan, V., Shah, T. M., Mott, R., et al. (2024) · Sustainability Sciences in Asia and Africa · doi:10.1007/978-981-99-4673-0_3 · Cited by 10 · see citing works

Advances in haplotype phasing and genotype imputation

Sun, Q., & Li, Y. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00895-2 · Cited by 10 · see citing works

trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios

Miller, D. B., & Piccolo, S. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04470-4 · Cited by 8 · see citing works

Improving lab-of-origin prediction of genetically engineered plasmids via deep metric learning

Soares, I. M., Camargo, F. H. F., Marques, A., & Crook, O. M. (2022) · Nature Computational Science · doi:10.1038/s43588-022-00234-z · Cited by 8 · see citing works

Identification and characterization of extrachromosomal circular DNA in alcohol induced osteonecrosis of femoral head

Zhou, T., Ma, S., Zhao, Y., Guo, D., Wang, H., Kuang, M., & Li, X. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.918379 · Cited by 8 · see citing works

Targeted sequencing and iterative assembly of near-complete genomes

Gamaarachchi, H., Stevanovski, I., Hammond, J. W., Reis, A. L. M., Rapadas, M., Jayasooriya, K., Russell, T., Yeow, D., Hort, Y., Patel, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65410-x · Cited by 7 · see citing works

A haplotype‐resolved genome for Rhododendron × pulchrum and the expression analysis of heat shock genes

Shen, J., Lan, L., Kan, S., Cheng, H., Peng, D., Wan, Z., Hu, Y., Huang, X., Li, X., Ye, Y., et al. (2023) · Journal of Systematics and Evolution · doi:10.1111/jse.13007 · Cited by 7 · see citing works

Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffoldingPreprint

Antipov, D., Rautiainen, M., Nurk, S., Walenz, B. P., Solar, S. J., Phillippy, A. M., & Koren, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.20.629807 · Cited by 7 · see citing works

GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs

Pimenta-Zanon, M. H., Kashiwabara, A. Y., Vanzela, A. L. L., & Lopes, F. M. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06037-z · Cited by 6 · see citing works

KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost

Zhou, Q., Ji, F., Lin, D., Liu, X., Zhu, Z., & Ruan, J. (2024) · Nature Communications · doi:10.1038/s41467-024-47562-4 · Cited by 6 · see citing works

Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars

Cull, A., & Joly, D. L. (2025) · BMC Genomics · doi:10.1186/s12864-025-11263-z · Cited by 6 · see citing works

Genetic variation in the OPN gene affects milk composition in Chinese Holstein cows

Raza, S. H. A., Khan, R., Pant, S. D., Shah, M. A., Quan, G., Long, F., Cheng, G., Gui, L., & Zan, L. (2021) · Animal Biotechnology · doi:10.1080/10495398.2021.2001343 · Cited by 6 · see citing works

A complete pedigree-based graph workflow for rare candidate variant analysisPreprint

Markello, C., Huang, C., Rodríguez, Á., Carroll, A. W., Chang, P.-C., Eizenga, J. M., Markello, T. C., Haussler, D. H., & Paten, B. (2022) · Genome Research · doi:10.1101/gr.276387.121 · Cited by 5 · see citing works

Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors

Navarro, A. T., Bourke, P. M., Weg, E. W. V. D., Clot, C. R., Arens, P. F. P., Finkers, R., & Maliepaard, C. A. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1049988 · Cited by 5 · see citing works

Automated filtering of genome-wide large deletions through an ensemble deep learning framework

Hu, Y., Mangal, S., Zhang, L., & Zhou, X. (2022) · Methods · doi:10.1016/j.ymeth.2022.08.001 · Cited by 4 · see citing works

The Telomere-Telomerase System Is Detrimental to Health at High-Altitude

Pasha, Q., Rain, M., Tasnim, S., Hema, K., Thinlas, T., & Mohammad, G. (2023) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph20031935 · Cited by 4 · see citing works

SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs

Tolstoganov, I., Chen, Z., Pevzner, P. A., & Korobeynikov, A. (2024) · PeerJ · doi:10.7717/peerj.18050 · Cited by 3 · see citing works

Near telomere-to-telomere nuclear phased chromosomes of the dikaryotic wheat fungus Rhizoctonia cerealisPreprint

Zeng, Q., Cao, W., Li, W. L., Wu, J., Figueroa, M., Liu, H., Qin, G., Wang, Q., Yang, L., Zhou, Y., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.18.484966 · Cited by 4 · see citing works

Genomics-Assisted Breeding for Fodder Quality Improvement in Forage Sorghum

Behera, P. P., & Sarma, R. N. (2025) · Springer eBooks · doi:10.1007/978-3-032-04527-0_3 · Cited by 3 · see citing works

An integrated platform for concurrent structural and single-nucleotide variants improves copy-number detection and reveals pathogenic alleles in undiagnosed Mendelian families

Du, H., Lun, M. Y., Gagarina, L., Bengtsson, J. D., Grochowski, C. M., Mehaffey, M. G., Hwang, J. P., Jhangiani, S. N., Bhamidipati, S. V., Muzny, D. M., et al. (2025) · Genome Medicine · doi:10.1186/s13073-025-01593-8 · Cited by 3 · see citing works

Pan-genomics of polyploid crops: from complexity to breeding

Naik, Y. D., Thudi, M., Kamal, N. M., Egan, A. N., Janga, M. R., & Puppala, N. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2026.1800432 · Cited by 3 · see citing works

Characteristics and potential functional effects of long insertions in Asian butternuts

Chen, Y., Miao, Y., Bai, W., Lin, K., & Pang, E. (2022) · BMC Genomics · doi:10.1186/s12864-022-08961-3 · Cited by 3 · see citing works

Statistical and Computational Methods for Microbial Strain Analysis

Ma, S., & Li, H. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2986-4_11 · Cited by 2 · see citing works

BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies

Höjer, P., Frick, T., Siga, H., Pourbozorgi, P. L., Aghelpasand, H., Martin, M., & Ahmadian, A. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1010 · Cited by 3 · see citing works

Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points

Zhang, W., Tariq, A., Jia, X., Yan, J., Fernie, A. R., Usadel, B., & Wen, W. (2024) · Nature Protocols · doi:10.1038/s41596-024-01063-2 · Cited by 3 · see citing works

VPrimer: A Method of Designing and Updating Primer and Probe With High Variant Coverage for RNA Virus Detection

Jeon, H., Bae, J., Kim, H., & Kim, M. (2021) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2021.3138145 · Cited by 3 · see citing works

Revisiting the Genomic Approaches in the Cereals and the Path Forward

Kaur, I., Relan, A., Saini, D. K., Kaur, G., Biswas, A., Singh, L., Kaur, S., & Sandhu, K. S. (2023) · Springer eBooks · doi:10.1007/978-981-19-8218-7_1 · Cited by 3 · see citing works

Haplotype-Assisted Breeding in Rice

Sagar, U. S. S. V., Pushpam, R., Raveendran, M., Kulkarni, V., & Rajanna, B. (2024) · Springer eBooks · doi:10.1007/978-981-97-7098-4_7 · Cited by 3 · see citing works

HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences

Fruzangohar, M., Timmins, W. A., Kravchuk, O. Y., & Taylor, J. (2022) · GigaScience · doi:10.1093/gigascience/giac038 · Cited by 3 · see citing works

Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

Huang, B., Wei, G., Wang, B., Ju, F., Zhong, Y., Shi, Z., Sun, S., & Bu, D. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04448-2 · Cited by 3 · see citing works

Potential and prospects of novel molecular breeding techniques for yield improvment in soybean (Glycine max)

Kumari, J., Kumari, V., Thakur, R., Kapoor, R., Priyanka, Kumari, S., & Chaturvedi, V. D. (2025) · Australian Journal of Agricultural Research · doi:10.1071/cp24139 · Cited by 2 · see citing works

Haplotype characterization of phosphorus homeostasis gene, SPX-MFS3 under combination of low nitrogen and phosphorus conditions in indica rice at seedling stage

Muduli, B. C., Selvaraj, S., Sahu, S., Dhall, S., Swain, N., Parameswaran, C., Meher, J., Pradhan, C., Chatterjee, D., Mohanty, S., et al. (2025) · 3 Biotech · doi:10.1007/s13205-025-04350-1 · Cited by 2 · see citing works

Smooth Descent: a Ploidy-Aware Algorithm To Improve Linkage Mapping In The Presence of Genotyping ErrorsPreprint

Navarro, A. T., Bourke, P. M., Weg, E. W. V. D., Arens, P. F. P., Finkers, R., & Maliepaard, C. A. (2022) · Research Square · doi:10.21203/rs.3.rs-1165750/v1 · Cited by 2 · see citing works

Review on Advancement of AI in Cell Engineering and Molecular Biology

Swargiary, D., Saikia, A., Basumatary, D., & Borah, J. C. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4690-8_10 · Cited by 1 · see citing works

Exploring standing genetic variation for barley leaf rust resistance in Australian breeding panel

Pandit, M., Dracatos, P. M., Periyannan, S. K., Lam, Y., Brunner, S. M., Honse, T., Tong, J., Dinglasan, E. G., Ganesalingam, A., Moody, D. B., et al. (2026) · Theoretical and Applied Genetics · doi:10.1007/s00122-025-05122-4 · Cited by 1 · see citing works

Trait Discovery in the Post-NGS Era

Rathore, M., Jan, F., Aggarwal, N., Bashir, M., Prasad, S. H., Khan, M. A., Sofi, P. A., Chitikineni, A., Saini, D. K., & Mir, R. R. (2026) · Sustainability Sciences in Asia and Africa · doi:10.1007/978-981-95-5109-5_12 · Cited by 1 · see citing works

HAT: haplotype assembly tool using short and error-prone long reads

Zade, R. S. H., Urhan, A., de Souza, A. A., Singh, A., & Abeel, T. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac702 · Cited by 1 · see citing works

GCphase: an SNP phasing method using a graph partition and error correction algorithm

Luo, J., Wang, J., Zhai, H., & Wang, J. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05901-8 · Cited by 1 · see citing works

Molecular Characterization of Maturase K Gene and Protein Prediction of Vanda spathulata (L.) - An Ayurinformatics Approaches

Jeline Rani, J., & Nandagopalan, V. (2023) · International Journal of Pharmaceutical Sciences and Drug Research · doi:10.25004/ijpsdr.2023.150319 · Cited by 1 · see citing works

Harvesting data from polyploid plants : developing tools for genetic analysis in strawberry / Alejandro Therese Navarro

Navarro, A. T. (2023) · doi:10.18174/630278 · Cited by 1 · see citing works

Smooth Descent: a ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errorsPreprint

Navarro, A. T., Bourke, P. M., Weg, E. W. V. D., Clot, C. R., Arens, P. F. P., Finkers, R., & Maliepaard, C. A. (2022) · Research Square · doi:10.21203/rs.3.rs-1165750/v2

Pairwise comparative analysis of six haplotype assembly methods based on users’ experience

Sun, S., Cheng, F., Han, D., Wei, S., Zhong, A., Massoudian, S., & Johnson, A. B. (2023) · BMC Genomic Data · doi:10.1186/s12863-023-01134-5

AsmMix: an efficient haplotype-resolved hybrid de novo genome assembling pipeline

Liu, C., Wu, P., Wu, X., Zhao, X., Chen, F., Cheng, X., Zhu, H., Wang, O., & Xu, M. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1421565

Comprehensive structural variant haplotype panel of 943 Han Chinese from long-read whole-genome sequencingPreprint

Gong, T., Zhou, Y., Huang, Y., Zhao, J., Gong, J., Li, J., Peng, Q., Wang, S., Li, J., & Fan, S. (2024) · Research Square · doi:10.21203/rs.3.rs-5343403/v1

A Long-read based Haplotype Panel Enhances Imputation and Discovery of Functional Small and Structural VariantsPreprint

Fan, S., Gong, T., Zhou, Y., Zhao, J., Huang, Y., Gong, J., Li, J., Peng, Q., Chang, H., Yuan, L., et al. (2025) · Research Square · doi:10.21203/rs.3.rs-6312842/v1

Genomics-Assisted Breeding: A Revolutionary Approach for Sugarcane Development

Naik, Y. D., Keshari, A. K., Kurhade, A. K., Patil, V. S., Veerendrakumar, H. V., Jadhav, M. P., & Upadhayay, V. K. (2025) · Springer eBooks · doi:10.1007/978-981-96-6871-7_15

Methods for Chromosome-Scale Haplotype Reconstruction

Garg, S. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4702-8_2

Direct inference of haplotypes from sequencing data

Zhang, Z., Zhu, B., Luo, Y., Shi, J., Lian, S., Hao, J., Hu, T., Ishibashi, T., Wang, D., Wang, S., et al. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf195

Local Haplotyping Analysis for Flowering Time in Soybean Using Crosshap

Mohamedikbal, S., Upadhyaya, S. R., Bestry, M., Marsh, J. I., & Edwards, D. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4820-9_6

From Genotype to Phased Haplotype: Multiplex Digital PCR-Based Haplotyping at the APOE Locus in Alzheimer’s DiseasePreprint

Chen, S., Lee, E.-G., Leong, L., Tulloch, J., & Yu, C. (2025) · Research Square · doi:10.21203/rs.3.rs-7634101/v1

Methods for Chromosome-Scale Haplotype Reconstruction

Garg, S. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4702-8_2

Additional file 1 of Computational methods for chromosome-scale haplotype reconstruction

Garg, S. (2021) · Figshare · doi:10.6084/m9.figshare.14404376

HAT: haplotype assembly tool using short and error-prone long reads

Zade, R. S. H., Urhan, A., de Souza, A. A., Singh, A., & Abeel, T. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac702 · Cited by 1 · see citing works

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

Selvaraj, S., Dixon, J. R., Bansal, V., & Ren, B. (2013) · Nature Biotechnology · doi:10.1038/nbt.2728 · Cited by 278 · see citing works

Statistical and computational methods for haplotype reconstruction

Pierre, U., & Curie, M. (2015)