Optimal enzymes for amplifying sequencing libraries

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Aird, D., Ross, M. G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., & Gnirke, A. (2011) · Genome Biology · doi:10.1186/gb-2011-12-2-r18 · Cited by 1,174 · see citing works

A large genome center's improvements to the Illumina sequencing system

Quail, M. A., Kozarewa, I., Smith, F., Scally, A., Stephens, P. J., Durbin, R. M., Swerdlow, H., & Turner, D. (2008) · Nature Methods · doi:10.1038/nmeth.1270 · Cited by 732 · see citing works

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

Fisher, S., Barry, A. J., Abreu, J., Minie, B., Nolan, J., Delorey, T. M., Young, G., Fennell, T. J., Allen, A., Ambrogio, L., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-1-r1 · Cited by 683 · see citing works

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

Kozarewa, I., Ning, Z., Quail, M. A., Sanders, M. J., Berriman, M., & Turner, D. J. (2009) · Nature Methods · doi:10.1038/nmeth.1311 · Cited by 565 · see citing works

Full-length RNA-seq from single cells using Smart-seq2

Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137 · see citing works

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

Picelli, S., Björklund, Å. K., Faridani, O. R., Sagasser, S., Winberg, G., & Sandberg, R. (2013) · Nature Methods · doi:10.1038/nmeth.2639 · Cited by 2,358 · see citing works

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage

Newman, A. M., Bratman, S. V., To, J., Wynne, J. F., Eclov, N. C. W., Modlin, L. A., Liu, C. L., Neal, J. W., Wakelee, H. A., Merritt, R. E., et al. (2014) · Nature Medicine · doi:10.1038/nm.3519 · Cited by 2,220 · see citing works

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

Quail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., & Gu, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-341 · Cited by 2,031 · see citing works

Ten years of next-generation sequencing technology

van Dijk, E., Auger, H., Jaszczyszyn, Y., & Thermes, C. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.07.001 · Cited by 1,632 · see citing works

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

Smallwood, S. A., Lee, H. J., Angermueller, C., Krueger, F., Saadeh, H., Peat, J., Andrews, S. R., Stegle, O., Reik, W., & Kelsey, G. (2014) · Nature Methods · doi:10.1038/nmeth.3035 · Cited by 1,125 · see citing works

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

Koike-Yusa, H., Li, Y., Tan, E.-P., Velasco-Herrera, M. D. C., & Yusa, K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2800 · Cited by 1,064 · see citing works

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

Gohl, D. M., Vangay, P., Garbe, J., Maclean, A., Hauge, A., Becker, A., Gould, T. J., Clayton, J. B., Johnson, T. J., Hunter, R. C., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3601 · Cited by 807 · see citing works

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

Harris, S. R., Cartwright, E. J. P., Török, M. E., Holden, M. T. G., Brown, N. M., Ogilvy‐Stuart, A., Ellington, M. J., Quail, M. A., Bentley, S. D., Parkhill, J., et al. (2012) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(12)70268-2 · Cited by 568 · see citing works

Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders

Soden, S. E., Saunders, C., Willig, L. K., Farrow, E., Smith, L. D., Petrikin, J. E., LePichon, J.-B., Miller, N., Thiffault, I., Dinwiddie, D. L., et al. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3010076 · Cited by 528 · see citing works

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Xue, Y., Prado-Martinez, J., Sudmant, P. H., Narasimhan, V., Ayub, Q., Szpak, M., Frandsen, P., Chen, Y., Yngvadottir, B., Cooper, D. N., et al. (2015) · Science · doi:10.1126/science.aaa3952 · Cited by 473 · see citing works

Library preparation methods for next-generation sequencing: Tone down the bias

van Dijk, E., Jaszczyszyn, Y., & Thermes, C. (2014) · Experimental Cell Research · doi:10.1016/j.yexcr.2014.01.008 · Cited by 411 · see citing works

PCR inhibition in qPCR, dPCR and MPS—mechanisms and solutions

Sidstedt, M., Rådström, P., & Hedman, J. (2020) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-020-02490-2 · Cited by 400 · see citing works

Single‐tube library preparation for degraded DNA

Carøe, C., Gopalakrishnan, S., Vinner, L., Mak, S. S. T., Sinding, M. S., Castruita, J. A. S., Wales, N., Sicheritz‐Pontén, T., & Gilbert, M. T. P. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12871 · Cited by 331 · see citing works

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Olova, N. N., Krueger, F., Andrews, S., Oxley, D., Berrens, R. V., Branco, M. R., & Reik, W. (2018) · Genome biology · doi:10.1186/s13059-018-1408-2 · Cited by 312 · see citing works

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

Tan, B., Ng, C., Nshimyimana, J. P., Loh, L. L., Gin, K. Y., & Thompson, J. R. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01027 · Cited by 298 · see citing works

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

Faircloth, B. C., & Glenn, T. C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042543 · Cited by 291 · see citing works

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

Warinner, C., Speller, C., & Collins, M. J. (2014) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0376 · Cited by 256 · see citing works

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

Bagnoli, J., Ziegenhain, C., Janjic, A., Wange, L. E., Vieth, B., Parekh, S., Geuder, J., Hellmann, I., & Enard, W. (2018) · Nature Communications · doi:10.1038/s41467-018-05347-6 · Cited by 242 · see citing works

High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq

Behrens, A., Rodschinka, G., & Nedialkova, D. D. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.01.028 · Cited by 248 · see citing works

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

Page, A. J., Silva, N. H. D., Hunt, M., Quail, M. A., Parkhill, J., Harris, S. R., Otto, T. D., & Keane, J. A. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000083 · Cited by 240 · see citing works

Single-cell RNA-sequencing: The future of genome biology is now

Picelli, S. (2016) · RNA Biology · doi:10.1080/15476286.2016.1201618 · Cited by 237 · see citing works

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

Barquist, L., Mayho, M., Cummins, C. A., Cain, A. K., Boinett, C. J., Page, A. J., Langridge, G. C., Quail, M. A., Keane, J. A., & Parkhill, J. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw022 · Cited by 230 · see citing works

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

Bryant, J. M., Harris, S. R., Parkhill, J., Dawson, R., Diacon, A. H., van Helden, P. D., Pym, A. S., Mahayiddin, A. A., Chuchottaworn, C., Sanne, I., et al. (2013) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(13)70231-5 · Cited by 205 · see citing works

Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria

Otto, T. D., Gilabert, A., Crellen, T., Böhme, U., Arnathau, C., Sanders, M. J., Oyola, S. O., Okouga, A. P., Boundenga, L., Willaume, E., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0162-2 · Cited by 185 · see citing works

Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA

Broadbent, K. M., Broadbent, J. C., Ribacke, U., Wirth, D. F., Rinn, J. L., & Sabeti, P. C. (2015) · BMC Genomics · doi:10.1186/s12864-015-1603-4 · Cited by 180 · see citing works

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

Weinert, L. A., Chaudhuri, R. R., Wang, J., Peters, S. E., Corander, J., Jombart, T., Baig, A., Howell, K. J., Vehkala, M., Välimäki, N., et al. (2015) · Nature Communications · doi:10.1038/ncomms7740 · Cited by 171 · see citing works

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

Hykin, S. M., Bi, K., & McGuire, J. A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0141579 · Cited by 163 · see citing works

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity

Wymant, C., Hall, M. D., Ratmann, O., Bonsall, D., Golubchik, T., de Cesare, M., Gall, A., Cornelissen, M. T. E., & Fraser, C. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx304 · Cited by 160 · see citing works

Improved Protocols for the Illumina Genome Analyzer Sequencing System

Quail, M. A., Swerdlow, H., & Turner, D. (2009) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1802s62 · Cited by 156 · see citing works

Improved workflows for high throughput library preparation using the transposome-based nextera system

Lamble, S., Batty, E. M., Attar, M., Buck, D., Bowden, R. J., Lunter, G. A., Crook, D. W., El‐Fahmawi, B., & Piazza, P. (2013) · BMC Biotechnology · doi:10.1186/1472-6750-13-104 · Cited by 149 · see citing works

High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population

Cubillos, F. A., Parts, L., Salinas, F., Bergström, A., Scovacricchi, E., Zia, A., Illingworth, C. J. R., Mustonen, V., Ibstedt, S., Warringer, J., et al. (2013) · Genetics · doi:10.1534/genetics.113.155515 · Cited by 137 · see citing works

Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview

Deshmukh, R. A., Joshi, K., Bhand, S., & Roy, U. (2016) · MicrobiologyOpen · doi:10.1002/mbo3.383 · Cited by 137 · see citing works

Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections

Lerch, A., Koepfli, C., Hofmann, N., Messerli, C., Wilcox, S., Kattenberg, J. H., Betuela, I., O’Connor, L., Müeller, I., & Felger, I. (2017) · BMC Genomics · doi:10.1186/s12864-017-4260-y · Cited by 120 · see citing works

Systematic comparison of small RNA library preparation protocols for next-generation sequencing

Dard-Dascot, C., Naquin, D., d’Aubenton-Carafa, Y., Alix, K., Thermes, C., & van Dijk, E. (2018) · BMC Genomics · doi:10.1186/s12864-018-4491-6 · Cited by 123 · see citing works

Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

Weinert, L. A., Chaudhuri, R. R., Wang, J., Peters, S. E., Corander, J., Jombart, T., Baig, A., Howell, K. J., Vehkala, M., Välimäki, N., et al. (2015) · Nature Communications · doi:10.1038/ncomms8272 · Cited by 122 · see citing works

Analytical characterization of biosimilar antibodies and Fc-fusion proteins

Beck, A., Diemer, H., Ayoub, D., Debaene, F., Wagner‐Rousset, E., Carapito, C., DORSSELAER, A. V., & Cianférani, S. (2013) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2013.02.014 · Cited by 119 · see citing works

Bias in RNA‐seq Library Preparation: Current Challenges and Solutions

Shi, H., Zhou, Y., Jia, E., Pan, M., Bai, Y., & Ge, Q. (2021) · BioMed Research International · doi:10.1155/2021/6647597 · Cited by 113 · see citing works

Quantifying Molecular Bias in DNA Data Storage

Chen, Y.-J., Takahashi, C. N., Organick, L., Stewart, K., Ang, S. D., Weiss, P., Peck, B., Seelig, G., Ceze, L., & Strauss, K. (2019) · doi:10.1101/566554 · Cited by 109 · see citing works

Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum

Siegel, T. N., Hon, C.-C., Zhang, Q., Lopez-Rubio, J.-J., Scheidig‐Benatar, C., Martins, R. M., Sismeiro, O., Coppée, J., & Scherf, A. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-150 · Cited by 109 · see citing works

Exploring the accuracy of amplicon‐based internal transcribed spacer markers for a fungal community

Li, S., Deng, Y., Wang, Z., Zhang, Z., Kong, X., Zhou, W., Yi, Y., & Qu, Y. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13097 · Cited by 105 · see citing works

Improved Protocols for Illumina Sequencing

Bronner, I. F., Quail, M. A., Turner, D., & Swerdlow, H. (2014) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1802s80 · Cited by 105 · see citing works

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

Gao, Y., Yurkovich, J. T., Seo, S. W., Kabimoldayev, I., Dräger, A., Chen, K., Sastry, A. V., Fang, X. D., Mih, N., Yang, L., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky752 · Cited by 102 · see citing works

Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting

Cotten, M. L., Petrova, V. N., Phan, M. V. T., Rabaa, M. A., Watson, S. J., Ong, S. H., Kellam, P., & Baker, S. G. (2014) · Journal of Virology · doi:10.1128/jvi.01333-14 · Cited by 101 · see citing works

Direct Induction of Trophoblast Stem Cells from Murine Fibroblasts

Kubaczka, C., Senner, C. E., Cierlitza, M., Araúzo-Bravo, M. J., Kuckenberg, P., Peitz, M., Hemberger, M., & Schorle, H. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.08.005 · Cited by 97 · see citing works

Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq

Chappell, L., Ross, P., Orchard, L., Russell, T. J., Otto, T. D., Berriman, M., Rayner, J. C., & Llinás, M. (2020) · BMC Genomics · doi:10.1186/s12864-020-06787-5 · Cited by 92 · see citing works

Sequence-Defined Transposon Mutant Library of Burkholderia thailandensis

Gallagher, L. A., Ramage, E. R., Patrapuvich, R., Weiss, E. J., Brittnacher, M. J., & Manoil, C. (2013) · mBio · doi:10.1128/mbio.00604-13 · Cited by 94 · see citing works

Single-cell genomics for dissection of complex malaria infectionsPreprint

Nair, S., Nkhoma, S. C., Serre, D., Zimmerman, P. A., Gorena, K. M., Daniel, B. J., Nosten, F. H., Anderson, T. J. C., & Cheeseman, I. H. (2014) · Genome Research · doi:10.1101/gr.168286.113 · Cited by 91 · see citing works

The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo

Henikoff, S., Ramachandran, S., Krassovsky, K., Bryson, T. D., Codomo, C. A., Brogaard, K., Widom, J., Wang, J.-P., & Henikoff, J. G. (2014) · eLife · doi:10.7554/elife.01861 · Cited by 88 · see citing works

Novel Determinants of Antibiotic Resistance: Identification of Mutated Loci in Highly Methicillin-Resistant Subpopulations of Methicillin-Resistant Staphylococcus aureus

Dordel, J., Kim, C. K., Chung, M., de la Gándara, M. P., Holden, M. T. G., Parkhill, J., de LENCASTRE, H., Bentley, S. D., & Tomasz, A. (2014) · mBio · doi:10.1128/mbio.01000-13 · Cited by 88 · see citing works

A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq

Logan, G., Freimanis, G., King, D. J., Valdazo‐González, B., Bachanek‐Bankowska, K., Sanderson, N. D., Knowles, N. J., King, D. P., & Cottam, E. M. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-828 · Cited by 87 · see citing works

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

Jurasz, H., Pawłowski, T., & Perlejewski, K. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.745076 · Cited by 83 · see citing works

Rolling circle amplification shows a sinusoidal template length-dependent amplification bias

Joffroy, B., Uca, Y. O., Prešern, D., Doye, J. P. K., & Schmidt, T. L. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1238 · Cited by 84 · see citing works

Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency

Rulands, S., Lee, H. J., Clark, S. J., Angermueller, C., Smallwood, S. A., Krueger, F., Mohammed, H., Dean, W., Nichols, J., Rugg‐Gunn, P. J., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2018.06.012 · Cited by 83 · see citing works

Genomic Analysis of Isolates From the United Kingdom 2012 Pertussis Outbreak Reveals That Vaccine Antigen Genes Are Unusually Fast Evolving

Sealey, K. L., Harris, S. R., Fry, N. K., Hurst, L. D., GORRINGE, A. R., Parkhill, J., & Preston, A. (2014) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiu665 · Cited by 80 · see citing works

Assessment of the latest NGS enrichment capture methods in clinical context

García‐García, G., Baux, D., Faugère, V., Moclyn, M., Koenig, M., Claustres, M., & Roux, A. (2016) · Scientific Reports · doi:10.1038/srep20948 · Cited by 80 · see citing works

One Pot Use of Combilipases for Full Modification of Oils and Fats: Multifunctional and Heterogeneous Substrates

Arana‐Peña, S., Carballares, D., Berenguer‐Murcia, Á., Alcántara, A. R., Rodrigues, R. C., & Fernández‐Lafuente, R. (2020) · Catalysts · doi:10.3390/catal10060605 · Cited by 80 · see citing works

Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome

Dinwiddie, D. L., Smith, L. D., Miller, N., Atherton, A. M., Farrow, E., Strenk, M. E., Soden, S. E., Saunders, C., & Kingsmore, S. F. (2013) · Genomics · doi:10.1016/j.ygeno.2013.04.013 · Cited by 80 · see citing works

Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya

Henson, S., Boinett, C. J., Ellington, M. J., Kagia, N., Mwarumba, S., Nyongesa, S., Mturi, N., Kariuki, S., Scott, J. A. G., Thomson, N. R., et al. (2017) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2017.07.006 · Cited by 81 · see citing works

Plasmodium falciparum genetic crosses in a humanized mouse model

Vaughan, A. M., Pinapati, R. S., Cheeseman, I. H., Camargo, N. M., Fishbaugher, M. E., Checkley, L. A., Nair, S., Hutyra, C. A., Nosten, F. H., Anderson, T. J. C., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3432 · Cited by 79 · see citing works

Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing

Oyola, S. O., Gu, Y., Manske, M., Otto, T. D., O’Brien, J., Alcock, D., MacInnis, B. L., Berriman, M., Newbold, C., Kwiatkowski, D. P., et al. (2012) · Journal of Clinical Microbiology · doi:10.1128/jcm.02507-12 · Cited by 77 · see citing works

Genome specialization and decay of the strangles pathogen, Streptococcus equi , is driven by persistent infectionPreprint

Harris, S. R., Robinson, C., Steward, K. F., Webb, K., Paillot, R., Parkhill, J., Holden, M. T. G., & Waller, A. S. (2015) · Genome Research · doi:10.1101/gr.189803.115 · Cited by 75 · see citing works

Genome‐wide profiling of chromosome interactions in P lasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation

Lemieux, J. E., Kyes, S., Otto, T. D., Feller, A., Eastman, R. T., Pinches, R. A., Berriman, M., Su, X., & Newbold, C. (2013) · Molecular Microbiology · doi:10.1111/mmi.12381 · Cited by 74 · see citing works

High Throughput Sequencing for the Detection and Characterization of RNA Viruses

Fitzpatrick, A., Rupnik, A., O’Shea, H., Crispie, F., Keaveney, S., & Cotter, P. D. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.621719 · Cited by 68 · see citing works

Signal amplification by enzymatic tools for nucleic acids

Miao, P., Tang, Y., Wang, B., Yin, J. B., & Ning, L. (2015) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2014.12.006 · Cited by 68 · see citing works

Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing

Aigrain, L., Gu, Y., & Quail, M. A. (2016) · BMC Genomics · doi:10.1186/s12864-016-2757-4 · Cited by 68 · see citing works

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

David, S., Mentasti, M., Tewolde, R., Aslett, M. A., Harris, S. R., Afshar, B., Underwood, A. P., Fry, N. K., Parkhill, J., & Harrison, T. G. (2016) · Journal of Clinical Microbiology · doi:10.1128/jcm.00432-16 · Cited by 67 · see citing works

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

Croucher, N. J., Finkelstein, J. A., Pelton, S. I., Parkhill, J., Bentley, S. D., Lipsitch, M., & Hanage, W. P. (2015) · Scientific Data · doi:10.1038/sdata.2015.58 · Cited by 66 · see citing works

Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing

Vembar, S. S., Seetin, M. G., Lambert, C. C., Nattestad, M., Schatz, M. C., Baybayan, P. A., Scherf, A., & Smith, M. L. (2016) · DNA Research · doi:10.1093/dnares/dsw022 · Cited by 65 · see citing works

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii

Boinett, C. J., Cain, A. K., Hawkey, J., Nhu, T. D. H., Nhu, N. T. K., Thanh, D. P., Dordel, J., Campbell, J. I., Lan, N. P. H., Mayho, M., et al. (2019) · Microbial Genomics · doi:10.1099/mgen.0.000246 · Cited by 65 · see citing works

Off‐target assessment of CRISPR ‐ C as9 guiding RNA s in human i PS and mouse ES cells

Tan, E., Li, Y., Velasco‐Herrera, M. D. C., Yusa, K., & Bradley, A. (2014) · genesis · doi:10.1002/dvg.22835 · Cited by 63 · see citing works

DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides

Laos, R., Thomson, J. M., & Benner, S. A. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00565 · Cited by 62 · see citing works

Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

Fookes, M. C., Hadfield, J., Harris, S. R., Parmar, S., Unemo, M., Jensen, J. S., & Thomson, N. R. (2017) · BMC Genomics · doi:10.1186/s12864-017-4399-6 · Cited by 61 · see citing works

Plastid Genome Assembly Using Long‐read data

Zhou, W., Armijos, C. E., Lee, C., Lu, R., Wang, J., Ruhlman, T. A., Jansen, R. K., Jones, A. M., & Jones, C. D. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13787 · Cited by 63 · see citing works

An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments

Heyer, E. E., Özadam, H., Ricci, E. P., Cenik, C., & Moore, M. J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1235 · Cited by 58 · see citing works

Noncoding RNAs as emerging regulators of Plasmodium falciparum virulence gene expression

Vembar, S. S., Scherf, A., & Siegel, T. N. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.06.013 · Cited by 56 · see citing works

Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium

Kristoffersen, S. M., Haase, C. P., Weil, M. R., Passalacqua, K. D., Niazi, F., Hutchison, S. K., Desany, B. A., Kolstø, A., Tourasse, N. J., Read, T. D., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-4-r30 · Cited by 55 · see citing works

Comparative genome analysis of Wolbachia strain wAu

Sutton, E. R., Harris, S. R., Parkhill, J., & Sinkins, S. P. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-928 · Cited by 53 · see citing works

Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

Gao, Y., Lim, H. G., Verkler, H., Szubin, R., Quach, D., Rodionova, I. A., Chen, K., Yurkovich, J. T., Cho, B., & Palsson, B. Ø. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab735 · Cited by 53 · see citing works

Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing

Ji, X., Zhou, L., Li, C., Shi, Y., Wu, M., Zhang, Y., Fei, X., & Zhao, G. (2020) · Journal of Molecular Neuroscience · doi:10.1007/s12031-019-01472-z · Cited by 52 · see citing works

Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila

David, S., Sánchez-Busó, L., Harris, S. R., Marttinen, P., Rusniok, C., Buchrieser, C., Harrison, T. G., & Parkhill, J. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006855 · Cited by 51 · see citing works

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA

Boltz, V. F., Rausch, J. W., Shao, W., Hattori, J., Luke, B. T., Maldarelli, F. M., Mellors, J. W., Kearney, M. F., & Coffin, J. M. (2016) · Retrovirology · doi:10.1186/s12977-016-0321-6 · Cited by 50 · see citing works

Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice

Friedrich, M. J., Rad, L., Bronner, I., Strong, A. J., Wang, W., Weber, J., Mayho, M., Ponstingl, H., Engleitner, T., Grove, C., et al. (2017) · Nature Protocols · doi:10.1038/nprot.2016.164 · Cited by 47 · see citing works

SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing

Quail, M. A., Smith, M., Jackson, D. K., Leonard, S. R., Skelly, T., Swerdlow, H., Gu, Y., & Ellis, P. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-110 · Cited by 49 · see citing works

Facilitating Structure-Function Studies of CFTR Modulator Sites with Efficiencies in Mutagenesis and Functional Screening

Molinski, S. V., Ahmadi, S., Hung, M., & Bear, C. E. (2015) · SLAS DISCOVERY · doi:10.1177/1087057115605834 · Cited by 48 · see citing works

Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses

Baker, K. S., Campos, J., Pichel, M. G., Gaspera, A. D., Duarte-Martínez, F., Chacón, E. C., Bolaños-Acuña, H. M., Guzmán‐Verri, C., Mather, A. E., Velasco, S. D., et al. (2017) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2017.03.021 · Cited by 48 · see citing works

A ‘culture’ shift: Application of molecular techniques for diagnosing polymicrobial infections

Zhang, Y., Hu, A., Andini, N., & Yang, S. S. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.02.013 · Cited by 44 · see citing works

Evidence for improved DNA repair in the long-lived bowhead whale

Firsanov, D., Zacher, M., Tian, X., Sformo, T. L., Zhao, Y., Tombline, G., Lu, J. Y., Zheng, Z., Perelli, L., Gurreri, E., et al. (2025) · Nature · doi:10.1038/s41586-025-09694-5 · Cited by 44 · see citing works

Genomic Advances in Avian Malaria Research

Videvall, E. (2019) · Trends in Parasitology · doi:10.1016/j.pt.2018.12.005 · Cited by 44 · see citing works

Transcriptional profiling to address molecular determinants of endometrial receptivity – Lessons from studies in livestock species

Ulbrich, S. E., Groebner, A. E., & Bauersachs, S. (2012) · Methods · doi:10.1016/j.ymeth.2012.10.013 · Cited by 43 · see citing works

Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires’ Disease

David, S., Afshar, B., Mentasti, M., Ginévra, C., Podglajen, I., Harris, S. R., Chalker, V. J., Jarraud, S., Harrison, T. G., & Parkhill, J. (2017) · Clinical Infectious Diseases · doi:10.1093/cid/cix153 · Cited by 43 · see citing works

Forensic Microbiology: When, Where and How

Nodari, R., Arghittu, M., Bailo, P., Cattaneo, C., Creti, R., D’Aleo, F., Saegeman, V., Franceschetti, L., Novati, S., Fernández-Rodríguez, A., et al. (2024) · Microorganisms · doi:10.3390/microorganisms12050988 · Cited by 44 · see citing works

A performance evaluation of Nextera XT and KAPA HyperPlus for rapid Illumina library preparation of long-range mitogenome amplicons

Ring, J. D., Sturk‐Andreaggi, K., Peck, M. A., & Marshall, C. K. (2017) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2017.04.003 · Cited by 41 · see citing works

Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses

Mitchell, C., Steward, K. F., Charbonneau, A. R. L., Walsh, S., Wilson, H. J., Timoney, J. F., Wernery, U., Joseph, M., Craig, D., van Maanen, K., et al. (2021) · Microbial Genomics · doi:10.1099/mgen.0.000528 · Cited by 41 · see citing works

Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean Distribution

Suárez‐Esquivel, M., Baker, K. S., Ruiz‐Villalobos, N., Hernández-Mora, G., Calvo, E. B., González-Barrientos, R., Castillo-Zeledón, A., Jiménez-Rojas, C., Chacón‐Díaz, C., Cloeckaert, A., et al. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx137 · Cited by 40 · see citing works

Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA

Tilak, M., Botero-Castro, F., Galtier, N., & Nabholz, B. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy022 · Cited by 40 · see citing works

Synthetic Oligonucleotide Libraries Reveal Novel Regulatory Elements in Chlamydomonas Chloroplast mRNAs

Specht, E. A., & Mayfield, S. P. (2012) · ACS Synthetic Biology · doi:10.1021/sb300069k · Cited by 40 · see citing works

Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems

Pereira, R. P. A., Peplies, J., Brettar, I., & Höfle, M. G. (2017) · BMC Microbiology · doi:10.1186/s12866-017-0987-5 · Cited by 38 · see citing works

Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia

Gislason, A. S., Turner, K. H., Domaratzki, M., & Cardona, S. T. (2017) · Microbial Genomics · doi:10.1099/mgen.0.000140 · Cited by 36 · see citing works

Improved Protocols for Illumina Sequencing

Bronner, I. F., Quail, M. A., Turner, D., & Swerdlow, H. (2013) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1802s79 · Cited by 38 · see citing works

Length and GC-Biases During Sequencing Library Amplification: A Comparison of Various Polymerase-Buffer Systems with Ancient and Modern DNA Sequencing Libraries

Dabney, J., & Meyer, M. (2012) · BioTechniques · doi:10.2144/000113809 · Cited by 316 · see citing works

Evaluation of Whole Transcriptome Amplification Methods by RNA-Seq

Vallandingham, J., Fleharty, B., Peak, A., Staehling‐Hampton, K., Perera, A. G., Li, H., & Zueckert‐Gaudenz, K. (2013) · Europe PMC (PubMed Central) · Cited by 2 · see citing works

Systems Biology Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single

Link, C., Barcodes, M., Shiroguchi, K., Jia, T. Z., Sims, P. A., Xie, X. S., & Xie, X. S. (2016)

Tools for Enhancing Sequence Diversity and Reducing Bias in DNA-seq Library Preparation

Ramani, S., Obermoeller, D., & Toloue, M. (2011) · doi:10.1038/an8082

FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nature methods 7: 130–132. Available: http://www.pubmedcentral.nih.gov/ articlerender.fcgi?artid = 2861772&tool = pmcentrez&rendertype = abstract. Accessed: 13

Mamanova, L., Andrews, R. M., James, K., Sheridan, E. M., Peter, D., Langford, C. F., Ost, T. W. B., Collins, J. E., & Turner, D. (2010)