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 1,201–1,300 of 1,715
Kaufman, K. M., Linghu, B., Szustakowski, J. D., Husami, A., Yang, F., Zhang, K., Filipovich, A. H., Fall, N., Harley, J. B., Nirmala, N. R., et al. (2014) · Arthritis & Rheumatology · doi:10.1002/art.38793 · Cited by 207
Macroscopic somatic clonal expansion in morphologically normal human urothelium
Li, R., Du, Y., Chen, Z., Xu, D., Lin, T., Jin, S., Wang, G., Liu, Z., Lu, M., Chen, X., et al. (2020) · Science · doi:10.1126/science.aba7300 · Cited by 206
Hayashi, M., Hinckley, C. A., Driscoll, S. P., Moore, N. J., Levine, A. J., Hilde, K. L., Sharma, K., & Pfaff, S. L. (2018) · Neuron · doi:10.1016/j.neuron.2018.01.023 · Cited by 188
Ramachandran, A., Vizán, P., Das, D., Chakravarty, P., Vogt, J., Rogers, K. W., Müller, P., Hinck, A. P., Sapkota, G. P., & Hill, C. S. (2018) · eLife · doi:10.7554/elife.31756 · Cited by 204
Genomic legacy of the African cheetah, Acinonyx jubatus
Dobrynin, P., Liu, S., Tamazian, G., Xiong, Z., Yurchenko, A. A., Krasheninnikova, K., Kliver, S., Schmidt-Küntzel, A., Koepfli, K.-P., Johnson, W., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0837-4 · Cited by 204
Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.
Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., Walker, R., Zhao, H., Chen, S., Liu, W., et al. (2017) · Science · doi:10.1126/science.aaf4791 · Cited by 202
Mutations in TAC1B : a Novel Genetic Determinant of Clinical Fluconazole Resistance in Candida auris
Rybak, J. M., Muñoz, J. F., Barker, K. S., Parker, J. E., Esquivel, B. D., Berkow, E. L., Lockhart, S. R., Gade, L., Palmer, G. E., White, T. C., et al. (2020) · mBio · doi:10.1128/mbio.00365-20 · Cited by 202
King, L. B., Walum, H., Inoue, K., Eyrich, N. W., & Young, L. J. (2016) · Biological Psychiatry · doi:10.1016/j.biopsych.2015.12.008 · Cited by 191
Noncoding RNA transcription targets AID to divergently transcribed loci in B cells
Pefanis, E., Wang, J., Rothschild, G., Lim, J., Chao, J., Rabadan, R., Economides, A. N., & Basu, U. (2014) · Nature · doi:10.1038/nature13580 · Cited by 201
The chromatin accessibility signature of human immune aging stems from CD8+ T cells
Ucar, D., Márquez, E. J., Chung, C.-H., Marches, R., Rossi, R. J., Uyar, A., Wu, T.-C., George, J., Stitzel, M. L., Palucka, A. K., et al. (2017) · Journal of Experimental Medicine · doi:10.1084/jem.20170416 · Cited by 200
De Novo Coding Variants Are Strongly Associated with Tourette Disorder
Willsey, A. J., Fernandez, T. V., Yu, D., King, R. A., Dietrich, A., Xing, J., Sanders, S. J., Mandell, J. D., Huang, A. Y., Richer, P., et al. (2017) · Neuron · doi:10.1016/j.neuron.2017.04.024 · Cited by 187
Kim, K.-T., Lee, H. W., Lee, H.-O., Song, H. J., Jeong, D. E., Shin, S., Kim, H., Shin, Y., Nam, D.-H., Jeong, B. C., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0945-9 · Cited by 198
Metabolome-microbiome signatures in the fermented beverage, Kombucha
Villarreal-Soto, S. A., Bouajila, J., Pace, M., Leech, J., Cotter, P. D., Souchard, J.-P., Taillandier, P., & Beaufort, S. (2020) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2020.108778 · Cited by 196
2000 Years of Parallel Societies in Stone Age Central Europe
Bollongino, R., Nehlich, O., Richards, M. P., Orschiedt, J., Thomas, M. G., Sell, C., Fajkošová, Z., Powell, A., & Burger, J. (2013) · Science · doi:10.1126/science.1245049 · Cited by 195
Delmont, T. O., Gaia, M., Hinsinger, D. D., Frémont, P., Vanni, C., Fernandez-Guerra, A., Eren, A. M., Kourlaiev, A., d'Agata, L., Clayssen, Q., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100123 · Cited by 173
Courtney, K. D., Ma, Y., Diaz de Leon, A., Christie, A., Xie, Z., Woolford, L., Singla, N., Joyce, A., Hill, H., Madhuranthakam, A. J., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-1459 · Cited by 188
Coding mutations in SORL1 and Alzheimer disease
Vardarajan, B. N., Zhang, Y., Lee, J. H., Cheng, R., Bohm, C., Ghani, M., Reitz, C., Reyes‐Dumeyer, D., Shen, Y., Rogaeva, E., et al. (2015) · Annals of Neurology · doi:10.1002/ana.24305 · Cited by 191
Autophagy Regulation of Metabolism Is Required for CD8+ T Cell Anti-tumor Immunity
DeVorkin, L., Pavey, N., Carleton, G., Comber, A., Ho, C., Lim, J., McNamara, E., Huang, H., Kim, P., Zacharias, L. G., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.037 · Cited by 185
vonHoldt, B. M., Shuldiner, E., Koch, I. J., Kartzinel, R. Y., Hogan, A., Brubaker, L., Wanser, S., Stahler, D., Wynne, C. D. L., Ostrander, E. A., et al. (2017) · Science Advances · doi:10.1126/sciadv.1700398 · Cited by 186
Tissue-resident memory CD8+ T cells shape local and systemic secondary T cell responses
Behr, F. M., Parga-Vidal, L., Kragten, N. A. M., van Dam, T. J. P., Wesselink, T. H., Sheridan, B. S., Arens, R., van Lier, R. A. W., Stark, R., & van Gisbergen, K. P. J. M. (2020) · Nature Immunology · doi:10.1038/s41590-020-0723-4 · Cited by 184
Howrigan, D. P., Rose, S. A., Samocha, K. E., Fromer, M., Cerrato, F., Chen, W. J., Churchhouse, C., Chambert, K., Chandler, S. D., Daly, M. J., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-019-0564-3 · Cited by 168
Disease tolerance mediated by microbiome E. coli involves inflammasome and IGF-1 signaling
Schieber, A. M. P., Lee, Y. M., Chang, M. W., Leblanc, M., Collins, B., Downes, M., Evans, R. M., & Ayres, J. S. (2015) · Science · doi:10.1126/science.aac6468 · Cited by 189
Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome
Nica, A. C., Ongen, H., Irminger, J.-C., Bosco, D., Berney, T., Antonarakis, S. E., Halban, P. A., & Dermitzakis, E. T. (2013) · Genome Research · doi:10.1101/gr.150706.112 · Cited by 189
Ptasinska, A., Assi, S. A., Mannari, D., James, S. R., Williamson, D., Dunne, J., Hoogenkamp, M., Wu, M., Care, M., McNeill, H., et al. (2012) · Leukemia · doi:10.1038/leu.2012.49 · Cited by 184
Drastic population fluctuations explain the rapid extinction of the passenger pigeon
Hung, C.-M., Shaner, P.-J. L., Zink, R. M., Liu, W.-C., Chu, T.-C., Huang, W.-S., & Li, S.-H. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401526111 · Cited by 186
The origin of domestication genes in goats
Zheng, Z., Wang, X., Li, M., Li, Y., Yang, Z., Wang, X., Pan, X., Gong, M., Zhang, Y., Guo, Y., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz5216 · Cited by 184
Peterson, B. A., Haak, D. C., Nishimura, M. T., Teixeira, P. J. P. L., James, S. R., Dangl, J. L., & Nimchuk, Z. L. (2016) · PLOS ONE · doi:10.1371/journal.pone.0162169 · Cited by 172
An atlas of gene regulatory elements in adult mouse cerebrum
Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Qiu, Y., Poirion, O. B., Li, B., Chiou, J., Liu, H., et al. (2021) · Nature · doi:10.1038/s41586-021-03604-1 · Cited by 185
KRAS Allelic Imbalance Enhances Fitness and Modulates MAP Kinase Dependence in Cancer
Burgess, M. R., Hwang, E., Mroue, R., Bielski, C. M., Wandler, A. M., Huang, B. J., Firestone, A. J., Young, A., Lacap, J. A., Crocker, L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.01.020 · Cited by 183
Host genetic variation and its microbiome interactions within the Human Microbiome Project
Kolde, R., Franzosa, E. A., Rahnavard, G., Hall, A. B., Vlamakis, H., Stevens, C., Daly, M. J., Xavier, R. J., & Huttenhower, C. (2018) · Genome Medicine · doi:10.1186/s13073-018-0515-8 · Cited by 182
Bellenguez, C., Charbonnier, C., Grenier-Boley, B., Quenez, O., Le Guennec, K., Nicolas, G., Chauhan, G., Wallon, D., Rousseau, S., Richard, A. C., et al. (2017) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2017.07.001 · Cited by 166
Zona, L., Lupberger, J., Sidahmed-Adrar, N., Thumann, C., Harris, H. J., Barnes, A., Florentin, J., Tawar, R. G., Xiao, F., Turek, M., et al. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.02.006 · Cited by 182
Velsko, I. M., Fellows Yates, J. A., Aron, F., Hagan, R. W., Frantz, L. A. F., Loe, L., Martinez, J. B. R., Chaves, E., Gosden, C., Larson, G., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0717-3 · Cited by 170
Identification of Novel Imidazo[1,2-a]pyridine Inhibitors Targeting M. tuberculosis QcrB
Abrahams, K. A., Cox, J. A. G., Spivey, V. L., Loman, N. J., Pallen, M. J., Constantinidou, C., Fernández, R., Alemparte, C., Remuiñán, M. J., Barros, D., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052951 · Cited by 177
SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons
Zaslavsky, K., Zhang, W.-B., McCready, F. P., Rodrigues, D. C., Deneault, E., Loo, C., Zhao, M., Ross, P. J., El Hajjar, J., Romm, A., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0365-8 · Cited by 174
Resolving rates of mutation in the brain using single-neuron genomics
Evrony, G. D., Lee, E., Park, P. J., & Walsh, C. A. (2016) · eLife · doi:10.7554/elife.12966 · Cited by 163
Nilsson, M. B., Sun, H., Robichaux, J., Pfeifer, M., McDermott, U., Travers, J., Diao, L., Xi, Y., Tong, P., Shen, L., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aaz4589 · Cited by 177
The PEMDAC phase 2 study of pembrolizumab and entinostat in patients with metastatic uveal melanoma
Ny, L., Jespersen, H., Karlsson, J., Alsén, S., Filges, S., All-Eriksson, C., Andersson, B., Carneiro, A., Helgadottir, H., Levin, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25332-w · Cited by 177
Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota
Escobar-Zepeda, A., Sanchez-Flores, A., & Quirasco Baruch, M. (2016) · Food Microbiology · doi:10.1016/j.fm.2016.02.004 · Cited by 174
Vignot, S., Frampton, G. M., Soria, J.-C., Yelensky, R., Commo, F., Brambilla, C., Palmer, G., Moro-Sibilot, D., Ross, J. S., Cronin, M. T., et al. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2012.47.7737 · Cited by 175
The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy
Landau, D. A., Sun, C., Rosebrock, D., Herman, S. E. M., Fein, J., Sivina, M., Underbayev, C., Liu, D., Hoellenriegel, J., Ravichandran, S., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-02329-y · Cited by 176
Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum
Sepúlveda, V. E., Márquez, R., Turissini, D. A., Goldman, W. E., & Matute, D. R. (2017) · mBio · doi:10.1128/mbio.01339-17 · Cited by 175
Nahar, R., Zhai, W., Zhang, T., Takano, A., Khng, A. J., Lee, Y. Y., Liu, X., Lim, C. H., Koh, T. P. T., Aung, Z. W., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02584-z · Cited by 173
An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer
Xue, Y., Martelotto, L., Baslan, T., Vides, A., Solomon, M., Mai, T. T., Chaudhary, N., Riely, G. J., Li, B. T., Scott, K., et al. (2017) · Nature Medicine · doi:10.1038/nm.4369 · Cited by 174
Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis
Guo, Y., Dai, Y., Yu, H., Zhao, S., Samuels, D. C., & Shyr, Y. (2017) · Genomics · doi:10.1016/j.ygeno.2017.01.005 · Cited by 172
Genome measures used for quality control are dependent on gene function and ancestry
Wang, J., Raskin, L., Samuels, D. C., Shyr, Y., & Guo, Y. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu668 · Cited by 173
A comparative atlas of single-cell chromatin accessibility in the human brain
Li, Y. E., Preissl, S., Miller, M., Johnson, N. D., Wang, Z., Jiao, H., Zhu, C., Wang, Z., Xie, Y., Poirion, O., et al. (2023) · Science · doi:10.1126/science.adf7044 · Cited by 173
SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses
Agerer, B., Koblischke, M., Gudipati, V., Montaño-Gutierrez, L. F., Smyth, M., Popa, A., Genger, J.-W., Endler, L., Florian, D. M., Mühlgrabner, V., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abg6461 · Cited by 172
Guo, H., Wang, T., Wu, H., Long, M., Coe, B. P., Li, H., Xun, G., Ou, J., Chen, B., Duan, G., et al. (2018) · Molecular Autism · doi:10.1186/s13229-018-0247-z · Cited by 154
Self-citationRationally designed APOBEC3B cytosine base editors with improved specificity
Jin, S., Fei, H., Zhu, Z., Luo, Y., Liu, J., Gao, S., Zhang, F., Chen, Y.-H., Wang, Y., & Gao, C. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.07.005 · Cited by 159
Hibaoui, Y., Grad, I., Letourneau, A., Sailani, M. R., Dahoun, S., Santoni, F. A., Gimelli, S., Guipponi, M., Pelte, M. F., Béna, F., et al. (2014) · EMBO Molecular Medicine · doi:10.1002/emmm.201302848 · Cited by 170
Poultney, C. S., Goldberg, A. P., Drapeau, E., Kou, Y., Harony-Nicolas, H., Kajiwara, Y., De Rubeis, S., Durand, S., Stevens, C., Rehnström, K., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.09.001 · Cited by 169
Gupta, V. A., Ravenscroft, G., Shaheen, R., Todd, E. J., Swanson, L. C., Shiina, M., Ogata, K., Hsu, C., Clarke, N. F., Darras, B. T., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.020 · Cited by 168
Fleming, S. J., Chaffin, M. D., Arduini, A., Akkad, A.-D., Banks, E., Marioni, J. C., Philippakis, A. A., Ellinor, P. T., & Babadi, M. (2019) · doi:10.1101/791699 · Cited by 164
Confirmation of fifth Candida auris clade by whole genome sequencing
Spruijtenburg, B., Badali, H., Abastabar, M., Mirhendi, H., Khodavaisy, S., Sharifisooraki, J., Taghizadeh Armaki, M., de Groot, T., & Meis, J. F. (2022) · Emerging Microbes & Infections · doi:10.1080/22221751.2022.2125349 · Cited by 164
Sultana, T., van Essen, D., Siol, O., Bailly-Bechet, M., Philippe, C., Zine El Aabidine, A., Pioger, L., Nigumann, P., Saccani, S., Andrau, J.-C., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.036 · Cited by 154
Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages
Ng, C. K. Y., Dazert, E., Boldanova, T., Coto-Llerena, M., Nuciforo, S., Ercan, C., Suslov, A., Meier, M.-A., Bock, T., Schmidt, A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29960-8 · Cited by 165
Fowler, C., Rainey-Smith, S. R., Bird, S., Bomke, J., Bourgeat, P., Brown, B. M., Burnham, S. C., Bush, A. I., Chadunow, C., Collins, S., et al. (2021) · Journal of Alzheimer's Disease Reports · doi:10.3233/adr-210005 · Cited by 164
Bridge RNAs direct programmable recombination of target and donor DNA
Durrant, M. G., Perry, N. T., Pai, J. J., Jangid, A. R., Athukoralage, J. S., Hiraizumi, M., McSpedon, J. P., Pawluk, A., Nishimasu, H., Konermann, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07552-4 · Cited by 163
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D
Viñuela, A., Varshney, A., van de Bunt, M., Prasad, R. B., Asplund, O., Bennett, A., Boehnke, M., Brown, A. A., Erdos, M. R., Fadista, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18581-8 · Cited by 152
Gabriele, M., Vulto-van Silfhout, A. T., Germain, P.-L., Vitriolo, A., Kumar, R., Douglas, E., Haan, E., Kosaki, K., Takenouchi, T., Rauch, A., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.05.006 · Cited by 163
SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
Krueger, F., & Andrews, S. R. (2016) · F1000Research · doi:10.12688/f1000research.9037.2 · Cited by 163
Nanki, Y., Chiyoda, T., Hirasawa, A., Ookubo, A., Itoh, M., Ueno, M., Akahane, T., Kameyama, K., Yamagami, W., Kataoka, F., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-69488-9 · Cited by 165
Wimmers, F., Subedi, N., van Buuringen, N., Heister, D., Vivié, J., Beeren-Reinieren, I., Woestenenk, R., Dolstra, H., Piruska, A., Jacobs, J. F. M., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05784-3 · Cited by 150
A biochemical landscape of A-to-I RNA editing in the human brain transcriptome
Sakurai, M., Ueda, H., Yano, T., Okada, S., Terajima, H., Mitsuyama, T., Toyoda, A., Fujiyama, A., Kawabata, H., & Suzuki, T. (2014) · Genome Research · doi:10.1101/gr.162537.113 · Cited by 150
Subudhi, S. K., Vence, L., Zhao, H., Blando, J., Yadav, S. S., Xiong, Q., Reuben, A., Aparicio, A., Corn, P. G., Chapin, B. F., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aaz3577 · Cited by 158
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
Pulford, C. V., Perez-Sepulveda, B. M., Canals, R., Bevington, J. A., Bengtsson, R. J., Wenner, N., Rodwell, E. V., Kumwenda, B., Zhu, X., Bennett, R. J., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-00836-1 · Cited by 151
Hertel, J., Harms, A. C., Heinken, A., Baldini, F., Thinnes, C. C., Glaab, E., Vasco, D. A., Pietzner, M., Stewart, I. D., Wareham, N. J., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.035 · Cited by 162
Ooi, A., Dykema, K., Ansari, A., Petillo, D., Snider, J., Kahnoski, R., Anema, J., Craig, D., Carpten, J., Teh, B.-T., et al. (2013) · Cancer Research · doi:10.1158/0008-5472.can-12-3227 · Cited by 159
An Unexpectedly Complex Architecture for Skin Pigmentation in Africans
Martin, A. R., Lin, M., Granka, J. M., Myrick, J. W., Liu, X., Sockell, A., Atkinson, E. G., Werely, C. J., Möller, M., Sandhu, M. S., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.015 · Cited by 156
Evolutionary insight from whole‐genome sequencing of experimentally evolved microbes
DETTMAN, J. R., RODRIGUE, N., MELNYK, A. H., WONG, A., BAILEY, S. F., & KASSEN, R. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05484.x · Cited by 160
Yucel, N., Wang, Y. X., Mai, T., Porpiglia, E., Lund, P. J., Markov, G., Garcia, B. A., Bendall, S. C., Angelo, M., & Blau, H. M. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.05.092 · Cited by 159
Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract
Burnham, P., Dadhania, D., Heyang, M., Chen, F., Westblade, L. F., Suthanthiran, M., Lee, J. R., & De Vlaminck, I. (2018) · Nature Communications · doi:10.1038/s41467-018-04745-0 · Cited by 160
Wang, X., Wang, H., Sun, V., Tuan, H.-F., Keser, V., Wang, K., Ren, H., Lopez, I., Zaneveld, J. E., Siddiqui, S., et al. (2013) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2013-101558 · Cited by 159
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning
Ing-Simmons, E., Vaid, R., Bing, X. Y., Levine, M., Mannervik, M., & Vaquerizas, J. M. (2021) · Nature Genetics · doi:10.1038/s41588-021-00799-x · Cited by 159
Girdhar, K., Hoffman, G. E., Jiang, Y., Brown, L., Kundakovic, M., Hauberg, M. E., Francoeur, N. J., Wang, Y.-C., Shah, H., Kavanagh, D. H., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0187-0 · Cited by 139
A gut microbial signature for combination immune checkpoint blockade across cancer types
Gunjur, A., Shao, Y., Rozday, T., Klein, O., Mu, A., Haak, B. W., Markman, B., Kee, D., Carlino, M. S., Underhill, C., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-02823-z · Cited by 165
Alzheimer's Disease Genetics Consortium, Wetzel-Smith, M. K., Hunkapiller, J., Bhangale, T. R., Srinivasan, K., Maloney, J. A., Atwal, J. K., Sa, S. M., B Yaylaoglu, M., Foreman, O., et al. (2014) · Nature Medicine · doi:10.1038/nm.3736 · Cited by 153
Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain
Okhovat, M., Berrio, A., Wallace, G., Ophir, A. G., & Phelps, S. M. (2015) · Science · doi:10.1126/science.aac5791 · Cited by 155
Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription
Cong, R., Das, S., Ugrinova, I., Kumar, S., Mongelard, F., Wong, J., & Bouvet, P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks720 · Cited by 155
Stewart, E., McEvoy, J., Wang, H., Chen, X., Honnell, V., Ocarz, M., Gordon, B., Dapper, J., Blankenship, K., Yang, Y., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.07.012 · Cited by 153
A comparison of brain gene expression levels in domesticated and wild animals
Albert, F. W., Somel, M., Carneiro, M., Aximu-Petri, A., Halbwax, M., Thalmann, O., Blanco-Aguiar, J. A., Plyusnina, I. Z., Trut, L., Villafuerte, R., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002962 · Cited by 154
Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency
Wenger, J. W., Piotrowski, J., Nagarajan, S., Chiotti, K., Sherlock, G., & Rosenzweig, F. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002202 · Cited by 154
Mondal, M., Casals, F., Xu, T., Dall'Olio, G. M., Pybus, M., Netea, M. G., Comas, D., Laayouni, H., Li, Q., Majumder, P. P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3621 · Cited by 149
Pouyet, F., Aeschbacher, S., Thiéry, A., & Excoffier, L. (2018) · eLife · doi:10.7554/elife.36317 · Cited by 153
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation
Baek, S., & Lee, I. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.06.012 · Cited by 151
Kim, S.-Y., Kim, S.-M., Lim, S., Lee, J. Y., Choi, S.-J., Yang, S.-D., Yun, M. R., Kim, C. G., Gu, S. R., Park, C., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-5026 · Cited by 151
A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers
Ferrari, A., Vincent-Salomon, A., Pivot, X., Sertier, A.-S., Thomas, E., Tonon, L., Boyault, S., Mulugeta, E., Treilleux, I., MacGrogan, G., et al. (2016) · Nature Communications · doi:10.1038/ncomms12222 · Cited by 150
Ortinski, P. I., O’Donovan, B., Dong, X., & Kantor, B. (2017) · Molecular Therapy - Methods & Clinical Development · doi:10.1016/j.omtm.2017.04.002 · Cited by 146
Shulman, D. S., Klega, K., Imamovic-Tuco, A., Clapp, A., Nag, A., Thorner, A. R., Van Allen, E., Ha, G., Lessnick, S. L., Gorlick, R., et al. (2018) · British Journal of Cancer · doi:10.1038/s41416-018-0212-9 · Cited by 149
Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
Yaeger, R., Mezzadra, R., Sinopoli, J., Bian, Y., Marasco, M., Kaplun, E., Gao, Y., Zhao, H., Paula, A. D. C., Zhu, Y., et al. (2023) · Cancer Discovery · doi:10.1158/2159-8290.cd-22-0405 · Cited by 144
Giraldo, M., Lopera, F., Siniard, A. L., Corneveaux, J. J., Schrauwen, I., Carvajal, J., Muñoz, C., Ramirez-Restrepo, M., Gaiteri, C., Myers, A. J., et al. (2013) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2013.02.016 · Cited by 147
Genomic copy number predicts esophageal cancer years before transformation
Killcoyne, S., Gregson, E., Wedge, D. C., Woodcock, D. J., Eldridge, M. D., de la Rue, R., Miremadi, A., Abbas, S., Blasko, A., Kosmidou, C., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-1033-y · Cited by 149
Miller, A., Asmann, Y., Cattaneo, L., Braggio, E., Keats, J., Auclair, D., Lonial, S., The MMRF CoMMpass Network, Russell, S. J., & Stewart, A. K. (2017) · Blood Cancer Journal · doi:10.1038/bcj.2017.94 · Cited by 145
Vardarajan, B. N., Ghani, M., Kahn, A., Sheikh, S., Sato, C., Barral, S., Lee, J. H., Cheng, R., Reitz, C., Lantigua, R., et al. (2015) · Annals of Neurology · doi:10.1002/ana.24466 · Cited by 148
Feichtinger, J., Hernández, I., Fischer, C., Hanscho, M., Auer, N., Hackl, M., Jadhav, V., Baumann, M., Krempl, P. M., Schmidl, C., et al. (2016) · Biotechnology and Bioengineering · doi:10.1002/bit.25990 · Cited by 148
Łabaj, P. P., Leparc, G. G., Linggi, B. E., Markillie, L. M., Wiley, H. S., & Kreil, D. P. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr247 · Cited by 141
Three-dimensional bio-printing of primary human hepatocellular carcinoma for personalized medicine
Xie, F., Sun, L., Pang, Y., Xu, G., Jin, B., Xu, H., Lu, X., Xu, Y., Du, S., Wang, Y., et al. (2021) · Biomaterials · doi:10.1016/j.biomaterials.2020.120416 · Cited by 147
Click chemistry enables preclinical evaluation of targeted epigenetic therapies
Tyler, D. S., Vappiani, J., Cañeque, T., Lam, E. Y. N., Ward, A., Gilan, O., Chan, Y.-C., Hienzsch, A., Rutkowska, A., Werner, T., et al. (2017) · Science · doi:10.1126/science.aal2066 · Cited by 146
Genome-wide Association of Yorkie with Chromatin and Chromatin-Remodeling Complexes
Oh, H., Slattery, M., Ma, L., Crofts, A., White, K. P., Mann, R. S., & Irvine, K. D. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.01.008 · Cited by 145
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
