The DOI matches its Crossref record; 30 of the 32 references it cites were found in a registry or an index.
Fast and accurate short read alignment with Burrows-Wheeler transform
Open accessAbstract
MOTIVATION: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. RESULTS: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is approximately 10-20x faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. AVAILABILITY: http://maq.sourceforge.net.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“For example, Martiniano et al. [9] find that the more relaxed parameters -n 0.02 -l 1024 -o 2 work best for BWA aln [10]”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [10]
In the citing paper
“Allelic imbalance is commonly observed in a tissue-specific manner (51, 52).”
From Variation in the Oxytocin Receptor Gene Predicts Brain Region–Specific Expression and Social Attachment (2016) · cites this paper as [52]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citationUltrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
A Greedy Algorithm for Aligning DNA Sequences
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000) · Journal of Computational Biology · doi:10.1089/10665270050081478 · Cited by 5,459
Real-Time DNA Sequencing from Single Polymerase Molecules
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., et al. (2009) · Science · doi:10.1126/science.1162986 · Cited by 3,732
SOAP: Short oligonucleotide alignment program
Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638
Self-citationA Block-sorting Lossless Data Compression Algorithm
Burrows, M. T., & Wheeler, D. J. (1994) · Cited by 2,333
Flagged first, then by citations
2 of the 32 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 1,401–1,500 of 1,715
A Genome-wide Comparison of the Functional Properties of Rare and Common Genetic Variants in Humans
Zhu, Q., Ge, D., Maia, J. M., Zhu, M., Petrovski, S., Dickson, S. P., Heinzen, E. L., Shianna, K. V., & Goldstein, D. B. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.03.008 · Cited by 96
Genomic responses to selection for tame/aggressive behaviors in the silver fox ( Vulpes vulpes )
Wang, X., Pipes, L., Trut, L. N., Herbeck, Y., Vladimirova, A. V., Gulevich, R. G., Kharlamova, A. V., Johnson, J. L., Acland, G. M., Kukekova, A. V., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1800889115 · Cited by 100
Analytical tools and current challenges in the modern era of neuroepigenomics
Maze, I., Shen, L., Zhang, B., Garcia, B. A., Shao, N., Mitchell, A., Sun, H., Akbarian, S., Allis, C. D., & Nestler, E. J. (2014) · Nature Neuroscience · doi:10.1038/nn.3816 · Cited by 100
Mutant KRAS Circulating Tumor DNA Is an Accurate Tool for Pancreatic Cancer Monitoring
Perets, R., Greenberg, O., Shentzer, T., Semenisty, V., Epelbaum, R., Bick, T., Sarji, S., Ben-Izhak, O., Sabo, E., & Hershkovitz, D. (2018) · The Oncologist · doi:10.1634/theoncologist.2017-0467 · Cited by 100
Giri, D., Vignola, M. L., Gualtieri, A., Scagliotti, V., McNamara, P., Peak, M., Didi, M., Gaston-Massuet, C., & Senniappan, S. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx318 · Cited by 91
Reservoirs of antimicrobial resistance genes in retail raw milk
Liu, J., Zhu, Y., Jay-Russell, M., Lemay, D. G., & Mills, D. A. (2020) · Microbiome · doi:10.1186/s40168-020-00861-6 · Cited by 99
RNA‐seq Data: Challenges in and Recommendations for Experimental Design and Analysis
Williams, A. G., Thomas, S., Wyman, S. K., & Holloway, A. K. (2014) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1113s83 · Cited by 93
ABCA7 frameshift deletion associated with Alzheimer disease in African Americans
Cukier, H. N., Kunkle, B. W., Vardarajan, B. N., Rolati, S., Hamilton-Nelson, K. L., Kohli, M. A., Whitehead, P. L., Dombroski, B. A., Van Booven, D., Lang, R., et al. (2016) · Neurology Genetics · doi:10.1212/nxg.0000000000000079 · Cited by 100
COVID‐19 severity from Omicron and Delta SARS‐CoV‐2 variants
Wrenn, J. O., Pakala, S. B., Vestal, G., Shilts, M. H., Brown, H. M., Bowen, S. M., Strickland, B. A., Williams, T., Mallal, S. A., Jones, I. D., et al. (2022) · Influenza and Other Respiratory Viruses · doi:10.1111/irv.12982 · Cited by 99
Genetic Variants in SGLT1, Glucose Tolerance, and Cardiometabolic Risk
Seidelmann, S. B., Feofanova, E., Yu, B., Franceschini, N., Claggett, B., Kuokkanen, M., Puolijoki, H., Ebeling, T., Perola, M., Salomaa, V., et al. (2018) · Journal of the American College of Cardiology · doi:10.1016/j.jacc.2018.07.061 · Cited by 97
Targeting mutant KRAS with CRISPR-Cas9 controls tumor growth
Kim, W., Lee, S., Kim, H. S., Song, M., Cha, Y. H., Kim, Y.-H., Shin, J., Lee, E.-S., Joo, Y., Song, J. J., et al. (2018) · Genome Research · doi:10.1101/gr.223891.117 · Cited by 97
Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia
Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., et al. (2018) · Science · doi:10.1126/science.aar8486 · Cited by 97
Bossaert, M., Pipier, A., Riou, J.-F., Noirot, C., Nguyên, L.-T., Serre, R.-F., Bouchez, O., Defrancq, E., Calsou, P., Britton, S., et al. (2021) · eLife · doi:10.7554/elife.65184 · Cited by 97
Mak, A. C. Y., Pullinger, C. R., Tang, L. F., Wong, J. S., Deo, R. C., Schwarz, J.-M., Gugliucci, A., Movsesyan, I., Ishida, B. Y., Chu, C., et al. (2014) · JAMA Neurology · doi:10.1001/jamaneurol.2014.2011 · Cited by 94
Wei, S. C., Sharma, R., Anang, N.-A. A. S., Levine, J. H., Zhao, Y., Mancuso, J. J., Setty, M., Sharma, P., Wang, J., Pe’er, D., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.03.004 · Cited by 97
Genetic and Genomic Architecture of the Evolution of Resistance to Antifungal Drug Combinations
Hill, J. A., Ammar, R., Torti, D., Nislow, C., & Cowen, L. E. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003390 · Cited by 93
Hennig, T., Michalski, M., Rutkowski, A. J., Djakovic, L., Whisnant, A. W., Friedl, M.-S., Jha, B. A., Baptista, M. A. P., L’Hernault, A., Erhard, F., et al. (2018) · PLOS Pathogens · doi:10.1371/journal.ppat.1006954 · Cited by 95
Celik, H., Mallaney, C., Kothari, A., Ostrander, E. L., Eultgen, E., Martens, A., Miller, C. A., Hundal, J., Klco, J. M., & Challen, G. A. (2015) · Blood · doi:10.1182/blood-2014-08-594564 · Cited by 95
E2f8 mediates tumor suppression in postnatal liver development
Kent, L. N., Rakijas, J. B., Pandit, S. K., Westendorp, B., Chen, H.-Z., Huntington, J. T., Tang, X., Bae, S., Srivastava, A., Senapati, S., et al. (2016) · Journal of Clinical Investigation · doi:10.1172/jci85506 · Cited by 95
ATRX is a regulator of therapy induced senescence in human cells
Kovatcheva, M., Liao, W., Klein, M. E., Robine, N., Geiger, H., Crago, A. M., Dickson, M. A., Tap, W. D., Singer, S., & Koff, A. (2017) · Nature Communications · doi:10.1038/s41467-017-00540-5 · Cited by 89
The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts
Saini, N., Roberts, S. A., Klimczak, L. J., Chan, K., Grimm, S. A., Dai, S., Fargo, D. C., Boyer, J. C., Kaufmann, W. K., Taylor, J. A., et al. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006385 · Cited by 94
Karamboulas, C., Bruce, J. P., Hope, A. J., Meens, J., Huang, S. H., Erdmann, N., Hyatt, E., Pereira, K., Goldstein, D. P., Weinreb, I., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.10.004 · Cited by 94
IsdB-dependent hemoglobin binding is required for acquisition of heme by Staphylococcus aureus
Pishchany, G., Sheldon, J. R., Dickson, C. F., Alam, M. T., Read, T. D., Gell, D. A., Heinrichs, D. E., & Skaar, E. P. (2014) · The Journal of Infectious Diseases · doi:10.1093/infdis/jit817 · Cited by 88
Philippine Ayta possess the highest level of Denisovan ancestry in the world
Larena, M., McKenna, J., Sanchez-Quinto, F., Bernhardsson, C., Ebeo, C., Reyes, R., Casel, O., Huang, J.-Y., Hagada, K. P., Guilay, D., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.07.022 · Cited by 93
Tamburini, F. B., Maghini, D., Oduaran, O. H., Brewster, R., Hulley, M. R., Sahibdeen, V., Norris, S. A., Tollman, S., Kahn, K., Wagner, R. G., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27917-x · Cited by 88
Muñoz, J. F., Delorey, T., Ford, C. B., Li, B. Y., Thompson, D. A., Rao, R. P., & Cuomo, C. A. (2019) · Nature Communications · doi:10.1038/s41467-019-09599-8 · Cited by 89
Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans
Kaasinen, E., Kuismin, O., Rajamäki, K., Ristolainen, H., Aavikko, M., Kondelin, J., Saarinen, S., Berta, D. G., Katainen, R., Hirvonen, E. A. M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09198-7 · Cited by 92
Bioinformatics for the Human Microbiome Project
Gevers, D., Pop, M., Schloss, P. D., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002779 · Cited by 91
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms
Abyzov, A., Li, S., Kim, D. R., Mohiyuddin, M., Stütz, A. M., Parrish, N. F., Mu, X. J., Clark, W., Chen, K., Hurles, M., et al. (2015) · Nature Communications · doi:10.1038/ncomms8256 · Cited by 91
Santana, D. J., & O’Meara, T. R. (2021) · Nature Communications · doi:10.1038/s41467-021-27545-5 · Cited by 91
Tissue Culture-Induced Heritable Genomic Variation in Rice, and Their Phenotypic Implications
Zhang, D., Wang, Z., Wang, N., Gao, Y., Liu, Y., Wu, Y., Bai, Y., Zhang, Z., Lin, X., Dong, Y., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096879 · Cited by 90
Veatch, J. R., Jesernig, B. L., Kargl, J., Fitzgibbon, M., Lee, S. M., Baik, C., Martins, R., Houghton, A. M., & Riddell, S. R. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0402 · Cited by 89
Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer
Jäger, N., Schlesner, M., Jones, D. T. W., Raffel, S., Mallm, J.-P., Junge, K. M., Weichenhan, D., Bauer, T., Ishaque, N., Kool, M., et al. (2013) · Cell · doi:10.1016/j.cell.2013.09.042 · Cited by 90
ATP13A3 is a major component of the enigmatic mammalian polyamine transport system
Hamouda, N. N., Van den Haute, C., Vanhoutte, R., Sannerud, R., Azfar, M., Mayer, R., Cortés Calabuig, Á., Swinnen, J. V., Agostinis, P., Baekelandt, V., et al. (2021) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.013908 · Cited by 85
Billmyre, R. B., Croll, D., Li, W., Mieczkowski, P., Carter, D. A., Cuomo, C. A., Kronstad, J. W., & Heitman, J. (2014) · mBio · doi:10.1128/mbio.01494-14 · Cited by 90
Røssevold, A. H., Andresen, N. K., Bjerre, C. A., Gilje, B., Jakobsen, E. H., Raj, S. X., Falk, R. S., Russnes, H. G., Jahr, T., Mathiesen, R. R., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-02126-1 · Cited by 89
Zhang, Y., Amaral, M. L., Zhu, C., Grieco, S. F., Hou, X., Lin, L., Buchanan, J., Tong, L., Preissl, S., Xu, X., et al. (2022) · Cell Research · doi:10.1038/s41422-022-00719-6 · Cited by 89
Fan, J., Lu, F., Qin, T., Peng, W., Zhuang, X., Li, Y., Hou, X., Fang, Z., Yang, Y., Guo, E., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01570-0 · Cited by 93
Lorente-Galdos, B., Lao, O., Serra-Vidal, G., Santpere, G., Kuderna, L. F. K., Arauna, L. R., Fadhlaoui-Zid, K., Pimenoff, V. N., Soodyall, H., Zalloua, P., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1684-5 · Cited by 77
Green, M. R., Vicente-Dueñas, C., Romero-Camarero, I., Long Liu, C., Dai, B., González-Herrero, I., García-Ramírez, I., Alonso-Escudero, E., Iqbal, J., Chan, W. C., et al. (2014) · Nature Communications · doi:10.1038/ncomms4904 · Cited by 88
Biology and medicine in the landscape of quantum advantages
Cordier, B. A., Sawaya, N. P. D., Guerreschi, G. G., & McWeeney, S. K. (2022) · Journal of The Royal Society Interface · doi:10.1098/rsif.2022.0541 · Cited by 87
Li, M., Tian, S., Yeung, C. K. L., Meng, X., Tang, Q., Niu, L., Wang, X., Jin, L., Ma, J., Long, K., et al. (2014) · Scientific Reports · doi:10.1038/srep04678 · Cited by 87
Rivas, M. A., Avila, B. E., Koskela, J., Huang, H., Stevens, C., Pirinen, M., Haritunians, T., Neale, B. M., Kurki, M., Ganna, A., et al. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007329 · Cited by 87
Genome structures resolve the early diversification of teleost fishes
Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., et al. (2023) · Science · doi:10.1126/science.abq4257 · Cited by 87
Consensus molecular subtype classification of colorectal adenomas
Komor, M. A., Bosch, L. J., Bounova, G., Bolijn, A. S., Delis‐van Diemen, P. M., Rausch, C., Hoogstrate, Y., Stubbs, A. P., de Jong, M., Jenster, G., et al. (2018) · The Journal of Pathology · doi:10.1002/path.5129 · Cited by 86
Bing, J., Hu, T., Zheng, Q., Muñoz, J. F., Cuomo, C. A., & Huang, G. (2020) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01466-20 · Cited by 86
The Genomic History of the Bronze Age Southern Levant
Agranat-Tamir, L., Waldman, S., Martin, M. A. S., Gokhman, D., Mishol, N., Eshel, T., Cheronet, O., Rohland, N., Mallick, S., Adamski, N., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.024 · Cited by 80
Munger, S. C., Raghupathy, N., Choi, K., Simons, A. K., Gatti, D. M., Hinerfeld, D. A., Svenson, K. L., Keller, M. P., Attie, A. D., Hibbs, M. A., et al. (2014) · Genetics · doi:10.1534/genetics.114.165886 · Cited by 85
Yang, B., Li, X., Zhang, W., Fan, J., Zhou, Y., Li, W., Yin, J., Yang, X., Guo, E., Li, X., et al. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100856 · Cited by 84
Overexpression of PGC ‐1α in aging muscle enhances a subset of young‐like molecular patterns
Garcia, S., Nissanka, N., Mareco, E. A., Rossi, S., Peralta, S., Diaz, F., Rotundo, R. L., Carvalho, R. F., & Moraes, C. T. (2018) · Aging Cell · doi:10.1111/acel.12707 · Cited by 81
Edlund, A., Yang, Y., Yooseph, S., Hall, A. P., Nguyen, D. D., Dorrestein, P. C., Nelson, K. E., He, X., Lux, R., Shi, W., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.72 · Cited by 84
Initiative, F. T. A. D. N., Ridge, P. G., Karch, C. M., Hsu, S., Arano, I., Teerlink, C. C., Ebbert, M. T. W., Gonzalez Murcia, J. D., Farnham, J. M., Damato, A. R., et al. (2017) · Genome Medicine · doi:10.1186/s13073-017-0486-1 · Cited by 83
Human T-cell leukemia virus type 1 infects multiple lineage hematopoietic cells in vivo
Furuta, R., Yasunaga, J.-I., Miura, M., Sugata, K., Saito, A., Akari, H., Ueno, T., Takenouchi, N., Fujisawa, J.-I., Koh, K.-R., et al. (2017) · PLOS Pathogens · doi:10.1371/journal.ppat.1006722 · Cited by 83
Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver
Bochkis, I. M., Przybylski, D., Chen, J., & Regev, A. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.09.048 · Cited by 78
Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer
Wyatt, A. W., Mo, F., Wang, K., McConeghy, B., Brahmbhatt, S., Jong, L., Mitchell, D. M., Johnston, R. L., Haegert, A., Li, E., et al. (2014) · Genome Biology · doi:10.1186/s13059-014-0426-y · Cited by 82
Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe
Peyrégne, S., Slon, V., Mafessoni, F., de Filippo, C., Hajdinjak, M., Nagel, S., Nickel, B., Essel, E., Le Cabec, A., Wehrberger, K., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw5873 · Cited by 82
Cajigas, I., Chakraborty, A., Swyter, K. R., Luo, H., Bastidas, M., Nigro, M., Morris, E. R., Chen, S., VanGompel, M. J. W., Leib, D., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.07.024 · Cited by 82
Gene duplicates cause hybrid lethality between sympatric species of Mimulus
Zuellig, M. P., & Sweigart, A. L. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007130 · Cited by 82
Ozaki, K., Doi, H., Mitsui, J., Sato, N., Iikuni, Y., Majima, T., Yamane, K., Irioka, T., Ishiura, H., Doi, K., et al. (2015) · JAMA Neurology · doi:10.1001/jamaneurol.2015.0610 · Cited by 81
Barøy, T., Koster, J., Strømme, P., Ebberink, M. S., Misceo, D., Ferdinandusse, S., Holmgren, A., Hughes, T., Merckoll, E., Westvik, J., et al. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv305 · Cited by 81
Guide Swap enables genome-scale pooled CRISPR-Cas9 screening in human primary cells
Ting, P. Y., Parker, A. E., Lee, J. S., Trussell, C., Sharif, O., Luna, F., Federe, G., Barnes, S. W., Walker, J. R., Vance, J., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0149-1 · Cited by 80
Billmyre, R. B., Clancey, S. A., & Heitman, J. (2017) · eLife · doi:10.7554/elife.28802 · Cited by 79
Camacho, J., Truong, L., Kurt, Z., Chen, Y.-W., Morselli, M., Gutierrez, G., Pellegrini, M., Yang, X., & Allard, P. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.04.078 · Cited by 72
Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus
Ozga, A. T., Nieves‐Colón, M. A., Honap, T. P., Sankaranarayanan, K., Hofman, C. A., Milner, G. R., Lewis, C. M., Stone, A. C., & Warinner, C. (2016) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22960 · Cited by 79
Cai, N., Gomez-Duran, A., Yonova-Doing, E., Kundu, K., Burgess, A. I., Golder, Z. J., Calabrese, C., Bonder, M. J., Camacho, M., Lawson, R. A., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01441-3 · Cited by 73
Colonization of the human gut by bovine bacteria present in Parmesan cheese
Milani, C., Duranti, S., Napoli, S., Alessandri, G., Mancabelli, L., Anzalone, R., Longhi, G., Viappiani, A., Mangifesta, M., Lugli, G. A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09303-w · Cited by 78
Lethal Disorder of Mitochondrial Fission Caused by Mutations in DNM1L
Yoon, G., Malam, Z., Paton, T., Marshall, C. R., Hyatt, E., Ivakine, Z., Scherer, S. W., Lee, K.-S., Hawkins, C., Cohn, R. D., et al. (2016) · The Journal of Pediatrics · doi:10.1016/j.jpeds.2015.12.060 · Cited by 78
Suzuki, S., Ishii, S., Hoshino, T., Rietze, A., Tenney, A., Morrill, P. L., Inagaki, F., Kuenen, J. G., & Nealson, K. H. (2017) · The ISME Journal · doi:10.1038/ismej.2017.111 · Cited by 78
In vivo reprogramming drives Kras-induced cancer development
Shibata, H., Komura, S., Yamada, Y., Sankoda, N., Tanaka, A., Ukai, T., Kabata, M., Sakurai, S., Kuze, B., Woltjen, K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04449-5 · Cited by 76
Baumann, D., Hägele, T., Mochayedi, J., Drebant, J., Vent, C., Blobner, S., Noll, J. H., Nickel, I., Schumacher, C., Boos, S. L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15979-2 · Cited by 76
DNA damage contributes to neurotoxic inflammation in Aicardi-Goutières syndrome astrocytes
Giordano, A. M. S., Luciani, M., Gatto, F., Abou Alezz, M., Beghè, C., Della Volpe, L., Migliara, A., Valsoni, S., Genua, M., Dzieciatkowska, M., et al. (2022) · Journal of Experimental Medicine · doi:10.1084/jem.20211121 · Cited by 76
TBR1 regulates autism risk genes in the developing neocortex
Notwell, J. H., Heavner, W. E., Darbandi, S. F., Katzman, S., McKenna, W. L., Ortiz-Londono, C. F., Tastad, D., Eckler, M. J., Rubenstein, J. L. R., McConnell, S. K., et al. (2016) · Genome Research · doi:10.1101/gr.203612.115 · Cited by 74
A macrophage-hepatocyte glucocorticoid receptor axis coordinates fasting ketogenesis
Loft, A., Schmidt, S. F., Caratti, G., Stifel, U., Havelund, J., Sekar, R., Kwon, Y., Sulaj, A., Chow, K. K., Alfaro, A. J., et al. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.01.004 · Cited by 76
Reproductive isolation and introgression between sympatric Mimulus species
Kenney, A. M., & Sweigart, A. L. (2016) · Molecular Ecology · doi:10.1111/mec.13630 · Cited by 76
Pyle, A., Hudson, G., Wilson, I. J., Coxhead, J., Smertenko, T., Herbert, M., Santibanez-Koref, M., & Chinnery, P. F. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005040 · Cited by 77
iPSC Modeling of RBM20-Deficient DCM Identifies Upregulation of RBM20 as a Therapeutic Strategy
Briganti, F., Sun, H., Wei, W., Wu, J., Zhu, C., Liss, M., Karakikes, I., Rego, S., Cipriano, A., Snyder, M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108117 · Cited by 68
Kloth, M., Ruesseler, V., Engel, C., Koenig, K., Peifer, M., Mariotti, E., Kuenstlinger, H., Florin, A., Rommerscheidt-Fuss, U., Koitzsch, U., et al. (2016) · Gut · doi:10.1136/gutjnl-2014-309026 · Cited by 73
Deleterious ABCA7 mutations and transcript rescue mechanisms in early onset Alzheimer’s disease
On behalf of the European Early-Onset Dementia (EU EOD) consortium, De Roeck, A., Van den Bossche, T., van der Zee, J., Verheijen, J., De Coster, W., Van Dongen, J., Dillen, L., Baradaran-Heravi, Y., Heeman, B., et al. (2017) · Acta Neuropathologica · doi:10.1007/s00401-017-1714-x · Cited by 74
Next-generation data filtering in the genomics era
Hemstrom, W., Grummer, J. A., Luikart, G., & Christie, M. R. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00738-6 · Cited by 77
Xu, F., Jerlström-Hultqvist, J., Einarsson, E., Ástvaldsson, Á., Svärd, S. G., & Andersson, J. O. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004053 · Cited by 74
Hope, W., Stone, N. R. H., Johnson, A., McEntee, L., Farrington, N., Santoro-Castelazo, A., Liu, X., Lucaci, A., Hughes, M., Oliver, J. D., et al. (2019) · mBio · doi:10.1128/mbio.02575-19 · Cited by 70
Metabolic mechanism of colistin resistance and its reverting in Vibrio alginolyticus
Li, L., Su, Y., Peng, B., Peng, X., & Li, H. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15021 · Cited by 74
Self-citationContribution of pks+ E. coli mutations to colorectal carcinogenesis
Chen, B., Ramazzotti, D., Heide, T., Spiteri, I., Fernandez-Mateos, J., James, C., Magnani, L., Graham, T. A., & Sottoriva, A. (2023) · Nature Communications · doi:10.1038/s41467-023-43329-5 · Cited by 74
Daniel, B., Nagy, G., Horvath, A., Czimmerer, Z., Cuaranta-Monroy, I., Poliska, S., Hays, T. T., Sauer, S., Francois-Deleuze, J., & Nagy, L. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky157 · Cited by 73
Mutations in HECW2 are associated with intellectual disability and epilepsy
Halvardson, J., Zhao, J. J., Zaghlool, A., Wentzel, C., Georgii-Hemming, P., Månsson, E., Ederth Sävmarker, H., Brandberg, G., Soussi Zander, C., Thuresson, A.-C., et al. (2016) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2016-103814 · Cited by 71
Cappi, C., Brentani, H., Lima, L., Sanders, S. J., Zai, G., Diniz, B. J., Reis, V. N. S., Hounie, A. G., Conceição do Rosário, M., Mariani, D., et al. (2016) · Translational Psychiatry · doi:10.1038/tp.2016.30 · Cited by 71
Rapid evolution of an adaptive multicellular morphology of Candida auris during systemic infection
Bing, J., Guan, Z., Zheng, T., Ennis, C. L., Nobile, C. J., Chen, C., Chu, H., & Huang, G. (2024) · Nature Communications · doi:10.1038/s41467-024-46786-8 · Cited by 74
Sala Frigerio, C., Lau, P., Troakes, C., Deramecourt, V., Gele, P., Van Loo, P., Voet, T., & De Strooper, B. (2015) · Alzheimer's & Dementia · doi:10.1016/j.jalz.2015.02.007 · Cited by 71
Kiezun, A., Pulit, S. L., Francioli, L. C., van Dijk, F., Swertz, M., Boomsma, D. I., van Duijn, C. M., Slagboom, P. E., van Ommen, G. J. B., Wijmenga, C., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003301 · Cited by 72
Tsai, A. P., Dong, C., Lin, P. B.-C., Oblak, A. L., Viana Di Prisco, G., Wang, N., Hajicek, N., Carr, A. J., Lendy, E. K., Hahn, O., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.08.008 · Cited by 71
Decatransin, a novel natural product inhibiting protein translocation at the Sec61/SecY translocon
Junne, T., Wong, J., Studer, C., Aust, T., Bauer, B. W., Beibel, M., Bhullar, B., Bruccoleri, R., Eichenberger, J., Estoppey, D., et al. (2015) · Journal of Cell Science · doi:10.1242/jcs.165746 · Cited by 67
Potent effect of the MDM2 inhibitor AMG232 on suppression of glioblastoma stem cells
Her, N.-G., Oh, J.-W., Oh, Y. J., Han, S., Cho, H. J., Lee, Y., Ryu, G. H., & Nam, D.-H. (2018) · Cell Death & Disease · doi:10.1038/s41419-018-0825-1 · Cited by 68
ABCA7 rare variants and Alzheimer disease risk
Le Guennec, K., Nicolas, G., Quenez, O., Charbonnier, C., Wallon, D., Bellenguez, C., Grenier-Boley, B., Rousseau, S., Richard, A.-C., Rovelet-Lecrux, A., et al. (2016) · Neurology · doi:10.1212/wnl.0000000000002627 · Cited by 69
A demonstration of conservation genomics for threatened species management
Wright, B. R., Farquharson, K. A., McLennan, E. A., Belov, K., Hogg, C. J., & Grueber, C. E. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13211 · Cited by 69
Alidousty, C., Baar, T., Martelotto, L. G., Heydt, C., Wagener, S., Fassunke, J., Duerbaum, N., Scheel, A. H., Frank, S., Holz, B., et al. (2018) · The Journal of Pathology · doi:10.1002/path.5110 · Cited by 69
Mechanistic Basis for Maintenance of CHG DNA Methylation in Plants
Fang, J., Jiang, J., Leichter, S. M., Liu, J., Biswal, M., Khudaverdyan, N., Zhong, X., & Song, J. (2022) · Nature Communications · doi:10.1038/s41467-022-31627-3 · Cited by 69
HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy
Jiang, Q., Braun, D. A., Clauser, K. R., Ramesh, V., Shirole, N. H., Duke-Cohan, J. E., Nabilsi, N., Kramer, N. J., Forman, C., Lippincott, I. E., et al. (2025) · Cell · doi:10.1016/j.cell.2025.01.046 · Cited by 68
Xiong, Q., Feng, J., Li, S.-T., Zhang, G.-Y., Qiao, Z.-X., Chen, Z., Wu, Y., Lin, Y., Li, T., Ge, F., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.046003 · Cited by 64
Wahane, S., Zhou, X., Zhou, X., Guo, L., Friedl, M.-S., Kluge, M., Ramakrishnan, A., Shen, L., Friedel, C. C., Zhang, B., et al. (2021) · Science Advances · doi:10.1126/sciadv.abd8811 · Cited by 67
The genomic landscape of 8-oxodG reveals enrichment at specific inherently fragile promoters
Gorini, F., Scala, G., Di Palo, G., Dellino, G. I., Cocozza, S., Pelicci, P. G., Lania, L., Majello, B., & Amente, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa175 · Cited by 67
Metadata
- Authors
- Li, H., & Durbin, R.
- Affiliations
- Wellcome Sanger Institute (GB)
- Corresponding author
- Durbin, Richard
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-05-18
- Volume
- 25
- Issue
- 14
- Pages
- 1754-1760
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2705234
- OpenAlex
- W2103441770
- Cited by
- 58,607
- References
- 32
- Citations by year
- 2026: 3541 · 2025: 4985 · 2024: 5800 · 2023: 5335 · 2022: 5575 · 2021: 5916 · 2020: 5161 · 2019: 4192 · 2018: 3819 · 2017: 3299 · 2016: 2900 · 2015: 2520 · 2014: 2193 · 2013: 1586 · 2012: 1007
- FWCI
- 233.42
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (077192/Z/05/Z)
- Broad Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- short-read alignment, Burrows-Wheeler transform, BWA, gapped alignment, indels, backward search, variant calling, resequencing, human genome, DNA sequencing
- MeSH terms
- Algorithms, Software, Sequence Alignment, Sequence Analysis, DNA, Genomics
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
