Did you know DNASTAR software has been cited in over 52,000 peer-reviewed publications? Every year for the past 31 years, our software has been cited in peer reviewed publications more than any competitor’s software.

Featured here are just a few recent publications citing Lasergene software for variant detection analysis, including a variety of studies using our software for whole-genome and whole-exome sequence assembly.

Determination of the Spontaneous Mutation Frequency of Ebola Virus and Exploitation of this Therapeutically
Alfson, Kendra J., Gabriella Worwa, Ricardo Carrion, and Anthony Griffiths. J. Virol. Journal of Virology 90, no. 5 (2015): 2345-355. doi:10.1128/jvi.02701-15.

Four Decades of Transmission of a Multidrug-resistant Mycobacterium tuberculosis Outbreak Strain
Eldholm, Vegard, Johana Monteserin, Adrien Rieux, Beatriz Lopez, Benjamin Sobkowiak, Viviana Ritacco, and Francois Balloux. Nature Communications Nat Comms 6 (2015): 7119. doi:10.1038/ncomms8119.

Molecular Types of Methicillin-Resistant Staphylococcus aureus and Methicillin-Sensitive S. aureus Strains Causing Skin and Soft Tissue Infections and Nasal Colonization, Identified in Community Health Centers in New York City
Gandara, Maria Pardos De La, Juan Antonio Raygoza Garay, Michael Mwangi, Jonathan N. Tobin, Amanda Tsang, Chamanara Khalida, Brianna D’orazio, Rhonda G. Kost, Andrea Leinberger-Jabari, Cameron Coffran, Teresa H. Evering, Barry S. Coller, Shirish Balachandra, Tracie Urban, Claude Parola, Scott Salvato, Nancy Jenks, Daren Wu, Rhonda Burgess, Marilyn Chung, Herminia De Lencastre, and Alexander Tomasz. J. Clin. Microbiol. Journal of Clinical Microbiology 53, no. 8 (2015): 2648-658. doi:10.1128/jcm.00591-15.

Haemophilus ducreyi Cutaneous Ulcer Strains Are Nearly Identical to Class I Genital Ulcer Strains
Gangaiah, Dharanesh, Kristen M. Webb, Tricia L. Humphreys, Kate R. Fortney, Evelyn Toh, Albert Tai, Samantha S. Katz, Allan Pillay, Cheng-Yen Chen, Sally A. Roberts, Robert S. Munson, and Stanley M. Spinola. PLoS Negl Trop Dis PLOS Neglected Tropical Diseases 9, no. 7 (2015). doi:10.1371/journal.pntd.0003918.

Genome Resequencing and Bioinformatic Analysis of SNP Containing Candidate Genes in the Autoimmune Vitiligo Smyth Line Chicken Model
Jang, Hyeon-Min, Gisela F. Erf, Kaylee C. Rowland, and Byung-Whi Kong. BMC Genomics 15, no. 1 (2014): 707. doi:10.1186/1471-2164-15-707.

Whole-exome Sequencing Identifies a Novel LRAT Mutation Underlying Retinitis Punctata albescens in a Consanguineous Pakistani Family
Jelani, Musharraf, Miyeon Jeon, Obaid Ur Rahman, Fazal Rahim, Muhammad Naeem, and Changsoo Kang. Genes Genom Genes & Genomics 37, no. 10 (2015): 845-49. doi:10.1007/s13258-015-0311-4.

A Novel Homozygous PTH1R Variant Identified through Whole-exome Sequencing Further Expands the Clinical Spectrum of Primary Failure of Tooth Eruption in a Consanguineous Saudi Family
Jelani, Musharraf, Changsoo Kang, Hussein Sheikh Ali Mohamoud, Rayan Al-Rehaili, Mona Mohammad Almramhi, Rehab Serafi, Huanming Yang, Jumana Yousuf Al-Aama, Muhammad Naeem, and Yaser Mohammad Alkhiary. Archives of Oral Biology 67 (2016): 28-33. doi:10.1016/j.archoralbio.2016.03.012.

Genotype-by-sequencing of the Plant-pathogenic Fungi Pyrenophora teres and Sphaerulina musiva Utilizing Ion Torrent Sequence Technology
Leboldus, Jared M., Kasia Kinzer, Jonathan Richards, Zhu Ya, Changhui Yan, Timothy L. Friesen, and Robert Brueggeman. Molecular Plant Pathology 16, no. 6 (2014): 623-32. doi:10.1111/mpp.12214.

Genomic Deletions and Mutations Resulting in the Loss of Eight Genes Reduce the in Vivo Replication Capacity of Meleagrid herpesvirus 1
Mahony, Timothy J., Robyn N. Hall, Stephen Walkden-Brown, Joanne Meers, Jennifer L. Gravel, Lani West, Vanessa Hardy, A.f.m. Fakhrul Islam, Elizabeth V. Fowler, and Neena Mitter. Virus Genes 51, no. 1 (2015): 85-95. doi:10.1007/s11262-015-1216-7.

Comparative Genomic Analysis of Rapid Evolution of an Extreme-Drug-Resistant Acinetobacter baumannii Clone
Tan, Sean Yang-Yi, Sing Lin Chua, Yang Liu, Neils Hoiby, Leif Percival Andersen, Michael Givskov, Zhijun Song, and Liang Yang. Genome Biology and Evolution 5, no. 5 (2013): 807-18. doi:10.1093/gbe/evt047.

Share your publication with us, and we will post it here! Contact Katie Maxfield at maxfieldk@dnastar.com or cite DNASTAR in your publications.

Did you know DNASTAR software has been cited in over 52,000 peer-reviewed publications? Every year for the past 31 years, our software has been cited in peer-reviewed journals more than any competitor’s software.

Featured here are just a few publications citing our Lasergene Molecular Biology Suite. Check them out to see how researchers around the world are using our software in their studies — from cloning and primer design, to sequence assembly and analysis.

Bacterial Community Structure Influenced by Coscinodiscus Sp. in the Vistula River Plume
Ameryk, Anetta, Richard L. Hahnke, Sławomira Gromisz, Janina Kownacka, Mariusz Zalewski, Lena Szymanek, Joanna Całkiewicz, Julita Dunalska, and Jens Harder. Oceanologia 56, no. 4 (2014): 825-56. doi:10.5697/oc.56-4.825.

Metabolism of Sialic Acid by Bifidobacterium Breve UCC2003
Egan, M., M. O’connell Motherway, M. Ventura, and D. Van Sinderen. Applied and Environmental Microbiology 80, no. 14 (2014): 4414-426. doi:10.1128/aem.01114-14.

Neuropeptide Receptor Transcript Expression Levels and Magnitude of Ionic Current Responses Show Cell Type-Specific Differences in a Small Motor Circuit

Garcia, V. J., N. Daur, S. Temporal, D. J. Schulz, and D. Bucher. Journal of Neuroscience 35, no. 17 (2015): 6786-800. doi:10.1523/jneurosci.0171-15.2015.

Identification, Sequencing and Comparative Analysis of PBp15.S Plasmid from the Newly Described Entomopathogen Bacillus Pumilus 15.1

Garcia-Ramon, Diana C., Maria Jose Luque-Navas, C. Alfonso Molina, Coral Del Val, Antonio Osuna, and Susana Vilchez. Plasmid 82 (2015): 17-27. doi:10.1016/j.plasmid.2015.09.001.

Characterisation and Genetic Diversity of Pepper Leafroll Virus, a New Bipartite Begomovirus Infecting Pepper, Bean and Tomato in Peru

Martínez-Ayala, A., S. Sánchez-Campos, F. Cáceres, L. Aragón-Caballero, J. Navas-Castillo, and E. Moriones. Ann Appl Biol Annals of Applied Biology 164, no. 1 (2013): 62-72. doi:10.1111/aab.12074.

Identification and Characterization of an Oleate Hydratase-encoding Gene from Bifidobacterium Breve

O’connell, Kerry Joan, Mary O’connell Motherway, Alan A. Hennessey, Florian Brodhun, R. Paul Ross, Ivo Feussner, Catherine Stanton, Gerald F. Fitzgerald, and Douwe Van Sinderen. Bioengineered 4, no. 5 (2013): 313-21. doi:10.4161/bioe.24159.

Functional Characterization of the Bacterial Iac Genes for Degradation of the Plant Hormone Indole-3-Acetic Acid

Scott, Jeness C., Isaac V. Greenhut, and Johan H. J. Leveau. J Chem Ecol Journal of Chemical Ecology 39, no. 7 (2013): 942-51. doi:10.1007/s10886-013-0324-x.

An Endogenous Ribonuclease Inhibitor Regulates the Antimicrobial Activity of Ribonuclease 7 in the Human Urinary Tract

Spencer, John D., Andrew L. Schwaderer, Tad Eichler, Huanyu Wang, Jennifer Kline, Sheryl S. Justice, Daniel M. Cohen, and David S. Hains. Kidney International 85, no. 5 (2014): 1179-191. doi:10.1038/ki.2013.395.

Identification and Functional Analysis of Mitogen-activated Protein Kinase Kinase Kinase (MAPKKK) Genes in Canola (Brassica Napus L.)

Sun, Y., C. Wang, B. Yang, F. Wu, X. Hao, W. Liang, F. Niu, J. Yan, H. Zhang, B. Wang, M. K. Deyholos, and Y.-Q. Jiang. Journal of Experimental Botany 65, no. 8 (2014): 2171-188. doi:10.1093/jxb/eru092.

Identification of Tobacco Streak Virus in Cranberry and the Association of TSV with Berry Scarring

Wells-Hansen, L. D., J. J. Polashock, N. Vorsa, B. E. L. Lockhart, and P. S. Mcmanus. Plant Disease 100, no. 4 (2016): 696-703. doi:10.1094/pdis-06-15-0710-re.

An Improved Detection and Quantification Method for the Coral Pathogen Vibrio Coralliilyticus

Wilson, Bryan, Andrew Muirhead, Monika Bazanella, Carla Huete-Stauffer, Luigi Vezzulli, and David G. Bourne. PLoS ONE 8, no. 12 (2013). doi:10.1371/journal.pone.0081800.

Share your publication with us, and we will post it here! Contact Katie Maxfield at maxfieldk@dnastar.com and cite DNASTAR in your publications!

Did you know DNASTAR software has been cited in over 52,000 peer-reviewed publications? Every year for the past 31 years, our software has been cited in peer reviewed publications more than any competitor’s software.

Featured here are some recent publications citing Lasergene for bacterial genome assembly.
Share your publication with us, and we will post it here! Contact us a dnastar-info@dnastar.com and cite DNASTAR in your publications.

Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens

Adnan A. K. Al-Rubaye, M. Brian Couger , Sohita Ojha, Jeff F. Pummill, Joseph A. Koon II, Robert F. Wideman Jr., and Douglas D. Rhoads

PLoS ONE (November 2015) vol. 10 no.11 doi:10.1371/journal.pone.0143336

Genome Mining and Transcriptional Analysis of Bacteriocin Genes in Enterococcus faecium CRL1879

N. Suarez, K. Bonacina, EM Hebert, and L Saavedra

Data Mining Genomics Proteomics (October 2015) vol. 6 no. 180 doi:10.4172/2153-0602.1000180

MreC and MreD Proteins Are Not Required for Growth of Staphylococcus aureus

Andreia C. Tavares, Pedro B. Fernandes, Rut Carballido-López, Mariana G. Pinho

PLoS ONE (October 2015) vol. 10 no.10 doi:10.1371/journal.pone.0140523

Auxenochlorella protothecoides and Prototheca wickerhamii Plastid Genome Sequences Give Insight Into the Origins of Non-photosynthetic Algae

Dong Yan, Yun Wang, Tatsuya Murakami, Yue Shen, Jianhui Gong, Huifeng Jiang, David R. Smith, Jean-Francois Pombert, Junbiao Dai, and Qingyu Wu

Scientific Reports (September 2015) vol. 5: 14465 doi: 10.1038/srep14465

Molecular Types of Methicillin-Resistant Staphylococcus aureus and Methicillin-Sensitive S. aureus Strains Causing Skin and Soft Tissue Infections and Nasal Colonization, Identified in Community Health Centers in New York City

Maria Pardos de la Gandara, Juan Antonio Raygoza Garay, Michael Mwangi, Jonathan N. Tobin, Amanda Tsang, Chamanara Khalida, Brianna D’Orazio, Rhonda G. Kost, Andrea Leinberger-Jabari, Cameron Coffran, Teresa H. Evering, Barry S. Coller, Shirish Balachandra, Tracie Urban, Claude Parole, Scott Salvato, Nancy Jenks, Daren Wu, Rhonda Burgess, Marilyn Chung, Herminia de Lencastre, and Alexander Tomasz

Journal of Clinical Microbiology (August 2015) vol. 53 no. 8  doi:10.1128/JCM.00591-15

Evaluation of Lactococcus lactis Isolates from Nondairy Sources with Potential Dairy Applications Reveals Extensive Phenotype-Genotype Disparity and Implications for a Revised Species

Daniel Cavanagh, Aidan Casey, Eric Altermann, Paul D. Cotter, Gerald F. Fitzgerald, Olivia McAuliffe

Applied Environmental Microbiology (April 2015) vol. 81:3961–3972. doi:10.1128/AEM.04092-14

Genomes of Sequence Type 121 Listeria monocytogenes Strains Harbor Highly Conserved Plasmids and Prophages

Stephan Schmitz-Esser, Anneliese Müller, Beatrix Stessl, and Martin Wagner

Frontiers in Microbiology (April 2015) vol. 6 no. 380 doi: 10.3389/fmicb.2015.00380

Complete Genome of Pseudomonas chlororaphis Strain UFB2, a Soil Bacterium with Antibacterial Activity Against Bacterial Canker Pathogen of Tomato

Peng Deng, Xiaoqiang Wang, Sonya M. Baird and Shi-En Lu

Standards in Genomic Sciences (2015) vol. 10 no. 117 doi: 10.1186/s40793-015-0106-x

Draft Genome Sequence of Raoultella planticola, Isolated from River Water

Narayanan Jothikumar, Amy Kahler, Nancy Strockbine, Lori Gladney, and Vincent R. Hill

Genome Announcements (October 2014)vol. 2 no.5 doi: 10.1128/genomeA.01061-14

Draft Genome Sequence of the Aromatic Hydrocarbon-Degrading Bacterium Sphingobium sp. Strain Ant17, Isolated from Antarctic Soil

Evelien M. Adriaenssens, Leandro D. Guerrero, Thulani P. Makhalanyane, Jackie M. Aislabie, and Don A. Cowan

Genome Announcements (April 2014) vol. 2 no. 2 doi: 10.1128/genomeA.00212-14

Identification and Characterization of Spontaneous Deletions within the Sp11-Sp12 Prophage Region of Escherichia coli O157:H7 Sakai

Chun Chen, Carrie R. Lewis, Kakolie Goswami, Elisabeth L. Roberts, Chitrita DebRoy, and Edward G. Dudley

Applied Environmental Microbiology (March 2013) vol. 79 no.6 doi: 10.1128/AEM.03682-12

Genomic Analysis and Secondary Metabolite Production in Bacillus amyloliquefaciens AS 43.3: A Biocontrol Antagonist of Fusarium Head Blight

Christopher A. Dunlap, Michael J. Bowman, and David A. Schisler

Biological Control (February 2013) vol. 64 no. 2 doi:10.1016/j.biocontrol.2012.11.002

Large Plasmids of Escherichia coli and Salmonella Encode Highly Diverse Arrays of Accessory Genes on Common Replicon Families

Laura E. Williams, Joy Wireman, Valda C. Hilliard, Anne O. Summers

Plasmid (January 2013) vol. 69 no.1:36-48. doi: 10.1016

Lasergene Genomics Suite makes it easy to integrate gene ontology data into your RNA-Seq, ChIP-Seq, microarray and variant analysis projects. See for yourself in our 60-second video, and check out the rest of our Quick Tips to see more Lasergene workflows in under a minute!

Webinar: Highly Accurate Protein Structure Prediction in NovaFold

When: Wednesday, May 18th at 12:00 PM EDT

Would you like to hear from our experts about what’s new in NovaFold version 13? Want to get a first look at our upcoming protein docking functionality? Join us for a webinar next week, where DNASTAR Senior Scientist Dr. Steve Darnell and Vice President Dr. Tom Lynch will discuss how NovaFold utilizes the award-winning I-TASSER algorithm, combined with proprietary technologies, to produce the most accurate model structures in an easy-to-use interface.

Learn more about our offering for protein structure prediction on our website and watch the two-minute video below to see how easy it is to predict a protein structure with NovaFold:

From molecular biology to genomics to structural biology, Lasergene 13 has something for everyone. This release is filled with new features and enhancements for easier research, and more accurate and comprehensive results. So what’s new in Lasergene 13? Visit our website to find out, then download a fully functional free trial version to experience it for yourself.

What’s new in Lasergene 13?

Did you know Lasergene is cited in peer reviewed publications more often than any other sequence analysis software? Check out our latest blog post to see highlights of 12 recent publications in which scientists use the Lasergene Molecular Biology Suite to perform DNA, RNA and protein sequence alignment.

Did you know DNASTAR software has been cited in over 52,000 peer-reviewed publications? Every year for the past 31 years, our software has been cited in peer reviewed publications more than any competitor’s software.

Featured here are some recent publications citing Lasergene for multiple sequence alignments.
Share your publication with us, and we will post it here! Contact Ellie Thomas for details at thomase@dnastar.com or cite DNASTAR in your publications.

Identification of Four Squid Species by Quantitative Real-Time Polymerase Chain Reaction

Ye Jian, Feng Junli, Liu Shasha, Zhang Yanping, Jiang Xiaona, Dai Zhiyuan

Molecular and Cellular Probes (2016 Feb) 30(1):22-9. doi: 10.1016/j.mcp.2016.01.001

Capsicum annuum Transcription Factor WRKYa Positively Regulates Defense Response Upon TMV Infection and is a Substrate of CaMK1 and CaMK2

Sung Un Huh, Gil-Je Lee, Ji Hoon Jung, Yunsik Kim, Young Jin Kim & Kyung-Hee Paek

Scientific Reports (2015) 5: 7981 doi:10.1038/srep07981

Molecular Cloning and Characterization of amh and dax1 Genes and Their Expression During Sex Inversion in Rice-Field Eel Monopterus albus

Qing Hu, Wei Guo, Yu Gao, Rong Tang, and Dapeng Lia

Scientific Reports (2015) 5, 16667; doi: 10.1038/srep16667

Targeting Synthetic Human Papillomavirus (HPV) L2 Disulfide-Induced N-Terminus Conformational Epitopes for Pan-HPV Vaccine Development

Sujita Khanal, Eric Daniel Ferraris, Maryam Zahin, Joongho Joh, Shin-je Ghim, Alfred Bennett Jenson

Experimental and Molecular Pathology (2015 Oct) 99(2):330–334 doi:10.1016/j.yexmp.2015.06.021

Mitochondrial Single Nucleotide Polymorphisms in Ceratitis capitata (Diptera: Tephritidae) Can Distinguish Sterile, Released Flies from Wild Flies in Various Regions of the World

Arlene Parubrub, Ruel Reyes, Catherine J. Smallridge, Bill Woods, David S Haymer

Journal of Economic Entomology (Impact Factor: 1.51) (2015 Feb) 108(1). DOI: 10.1093/jee/tou027

Complete Genome Sequence of Hypervirulent and Outbreak-Associated Acinetobacter baumannii Strain LAC-4: Epidemiology, Resistance Genetic Determinants and Potential Virulence Factors

Hong-Yu Ou, Shan N. Kuang, Xinyi He, Brenda M. Molgora, Peter J. Ewing, Zixin Deng, Melanie Osby, Wangxue Chen & H. Howard Xu

Scientific Reports (2015) 5: 8643 doi:10.1038/srep08643

Generation of a Recombinant Gag Virus-Like-Particle Panel for the Evaluation of p24 Antigen Detection by Diagnostic HIV Tests

Beatrice N. Vetter , Vanessa Orlowski, Katrien Fransen, Christoph Niederhauser, Vincent Aubert, Marcel Brandenberger, Diana Ciardo, Günter Dollenmaier, Thomas Klimkait, Stephan Regenass, Patrick Schmid, Volkmar Schottstedt, Franziska Suter-Riniker, Sabine Yerly, Cyril Shah, Jürg Böni, Jörg Schüpbach

PLoS ONE (2014 Oct) 9(10): e111552. doi:10.1371/journal.pone.0111552

Phylogenetic Diversity of Classical Swine Fever Virus (CSFV) Field Isolates from Outbreaks in China Between 2008 and 2011

Tao Lin, Xiangrui Li, Huochun Yao, Zuzhang Wei, Runxia Liu, Yu Deng, Shaolun Zhai, Wenliang Li, Lichang Sun, Jinxue Long, Hongbiao Zhang, Jiaqi Lu and Shishan Yuan

Asian Journal of Animal and Veterinary Advances (2013) 8:449-460. DOI: 10.3923/ajava.2013.449.460

Foot-and-Mouth Disease Virus Carrier Status in Bos grunniens Yaks

Huiyun Chang, Yanbin Ma, Tong Lin, Guozheng Cong, Junzheng Du and Jinling Ma

Virology Journal (2013) 10:81 DOI: 10.1186/1743-422X-10-81

A Magneto-DNA Nanoparticle System for Target Specific Bacterial Identification

Hyun Jung Chung, Cesar M. Castro, Hyungsoon Im, Hakho Lee, and Ralph Weissleder

Nature Nanotechnology (2013 May) 8(5): 369–375.

Large Plasmids of Escherichia coli and Salmonella Encode Highly Diverse Arrays of Accessory Genes on Common Replicon Families

Williams LE, Wireman J, Hilliard VC, Summers AO

Plasmid. (2013 Jan) 69(1):36-48. doi: 10.1016/j.plasmid.2012.08.002

Duplication and Diversification of the Spermidine/Spermine N1-acetyltransferase 1 Genes in Zebrafish

Yi-Chin Lien, Ting-Yu Ou, Yu-Tzu Lin, Po-Chih Kuo, Han-Jia Lin

PLoS ONE (2013 Jan) 8(1): e54017. doi:10.1371/journal.pone.0054017

Webinar: RNA-Seq for Non-Model Organisms

When: Wednesday, April 27th at 12:00 PM EDT

Would you like to see how you can perform gene expression analysis for any organism, even without a reference genome? Join us for a webinar next week, where we will demonstrate our new workflow for RNA-Seq in non-model organisms.

Check out the video below, which shows how to assemble a plant transcriptome using our new de novo assembly and annotation workflow, then tune in to next week’s webinar to see how to use annotated transcripts for downstream gene expression analysis.

The Lasergene Structural Biology Suite allows you to run a protein structure prediction in just three steps. In 60 seconds, you can see how it’s done with this week’s Quick Tip video. Check out the rest of our Quick Tips to see more Lasergene workflows in under a minute!