Publications about RipSeq

Please find all articles, posters and more about RipSeq below.

(Click any heading below to expand and collapse)

2014 Journal of Clinical Microbiology (JCM). Published ahead of print: (JCM)
Massive parallel sequencing provides new perspectives on bacterial brain abscesses
Oyvind Kommedal (a), Marianne Thulin Wilhelmsen (a), Steinar Skrede (b,c), Roger Meisal (d), Aleksandra Jakovljev (e), Peter Gaustad (f), Nils Olav Hermansen (f), Einar Vik-Mo (g), Ole Solheim (h,i), Ole Herman Ambur (d), Oystein Saebo (j), Christina Teisner Hostmaelingen (k), Christian Helland (l,m)
a Department of Microbiology, Haukeland University Hospital, Bergen, Norway
b Department of Medicine, Haukeland University Hospital, Bergen, Norway
c Department of Clinical Science, University of Bergen, Bergen, Norway
d Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
e Department of Microbiology, St. Olav’s University Hospital, Trondheim, Norway
f Department of Microbiology, Oslo University Hospital, Oslo, Norway
g Department of Neurosurgery, Oslo University Hospital, Oslo, Norway
h Department of Neurosurgery, St. Olav’s University Hospital, Trondheim, Norway
i Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
j Isentio, Inc., Palo Alto, California, USA
k Department of Neurosurgery, University of North Norway, Tromsø, Norway
l Department of Neurosurgery, Haukeland University Hospital, Bergen, Norway
m Department of Clinical Medicine, University of Bergen, Bergen, Norway

2013 Journal of Clinical Microbiology (JCM). Vol. 51 (PDF)
Letter to editor Internet-Based Solutions for Analysis of Next-Generation Sequence Data
Mette Voldby Larsen
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark

2013 Journal of Clinical Microbiology (JCM). Vol. 51 (PDF)
Reply to 'Internet-Based Solutions for Analysis of Next-Generation Sequence Data'
Norelle L. Sherry (1,2),Timothy P. Stinear (3,4), Benjamin P. Howden (1,2,3,4)
1 Department of Microbiology, Austin Health, Melbourne, Australia
2 Austin Centre for Infection Research (ACIR), Infectious Diseases Department, Austin Health, Melbourne, Australia
3 Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australiac;
4 Department of Microbiology, Monash University, Melbourne, Australia

2013 Journal of Clinical Microbiology (JCM). Vol. 51 (PDF)
Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory
Norelle L. Sherry(1,2), Jessica L. Porter(3), Torsten Seemann (4,5), Andrew Watkins (6), Timothy P. Stinear (3,4), Benjamin P. Howden (1,2,3,4)
1 Department of Microbiology, Austin Health, Melbourne, Australia
2 Austin Centre for Infection Research (ACIR), Infectious Diseases Department, Austin Health, Melbourne, Australia
3 Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia;
4 Department of Microbiology, Monash University, Melbourne, Australia;
5 Victorian Bioinformatics Consortium, Monash University, Melbourne, Australia
6 Department of Paediatrics, Mercy Hospital for Women, Melbourne, Australia

2013 Journal of Clinical Microbiology (JCM). Vol. 51 no. 4. (PDF)
Sequencing-Based Genotyping of Mixed Human Papillomavirus Infections Using RipSeq Software.
Keith D. Tardif (1), Keith E. Simmon(2), Oyvind Kommedal (3,4), Michael T. Pyne (1) and Robert Schlaberg (1,5)
1 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
2 Isentio US, Sunnyvale, CA,
3 University of Bergen, Norway
4 Isentio AS, Bergen, Norway
5 University of Utah School of Medicine, Department of Pathology, Salt Lake City, UT

2013 Journal of Clinical Microbiology (JCM). Vol. 51 no. 4. (PDF)
Direct sequencing and RipSeq interpretation as a tool for identification of polymicrobial infections.
Wolff T Y (1), Eickhardt S (2,3), Bjornsdottir M K (2), Moser C (2), Bjarnsholt T (2,3), Hoiby N (2) and Thomsen T R (1,4)
1 The Danish Technological Institute, Life Science Division, Aarhus, Denmark
2 Department of Clinical Microbiology, Rigshospitalet, University hospital of Copenhagen, Copenhagen, Denmark
3 Department of International Health, Immunology and Microbiology, University of Copenhagen, Denmark,
4 Department of Biotechnology, Chemistry, and Environmental Engineering, Aalborg University, Aalborg, Denmark

2013 Mycoses: Diagnosis, Therapy and Prophylaxis of Fungal Diseases (M). (PDF)
Deciphering the aetiology of a mixed fungal infection by broad-range PCR with sequencing and fluorescence in situ hybridization.
V. Rickerts (1), I. McCormick Smith (1), S. Mousset (2), O. Kommedal (3) and D. N. Fredricks (4)
1 Robert Koch Institut, FG 16, Berlin, Germany
2 University Hospital, Haematology, Frankfurt, Germany
3 Isentio AS, Bergen, Norway
4 Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Devision, Seattle, USA

2012 Journal of Clinical Microbiology (JCM). (PDF)
Prosthetic Joint Infection Diagnosis using Broad-Range PCR of Biofilms Dislodged from Knee and Hip Arthroplasty Surfaces using Sonication.
Gomez E, Cazanave C, Cunningham SA, Greenwood-Quaintance KE, Steckelberg JM, Uhl JR, Hanssen AD, Karau MJ, Schmidt SM, Osmon DR, Berbari EF, Mandrekar J, Patel R.
Mayo Clinic, Rochester, USA. Division of Infectious Diseases, Department of Medicine.

2012 Journal of Clinical Microbiology (JCM) [Epub ahead of print]. (PDF)
Nocardia neocaledoniensis as a cause of human skin and soft tissue infection.
Travea McGhie (1), Robert Fader (2), John Carpenter (1), Barbara A. Brown-Elliott (3), Ravikiran Vasireddy (3), Richard J. Wallace Jr.
1 Department of Medicine, Division of Infectious Disease
2 Department of Pathology, Scott & White Healthcare; Texas A&M School of Medicine, Temple, TX 76508
3 Mycobacteria/Nocardia Laboratory, The University of Texas Health Science Center, Tyler, TX 75708

2012 Journal of Clinical Microbiology (JCM). Vol. 50, No. 4. (PDF)
Dual-priming oligonucleotides for broad-range amplification of the bacterial 16S rRNA gene directly from human clinical specimens.
Kommedal O (1), Simmons K (2), Karaca D (3), Langeland N (3), Wiker HG (1,4)
1 Section for Microbiology and Immunology, the Gade Institute, University of Bergen, Bergen, Norway
2 Isentio US LLC, Sunnyvale, California, USA
3 Institute of Medicine, University of Bergen, Bergen, Norway
4 Department of Microbiology, Haukeland University Hospital, Bergen, Norway

2012 Emerging Infectious Diseases, CDC (EID). Vol. 18, No. 4. (PDF)
Emergence of Unusual G6P[6] Rotaviruses in Children, Burkina Faso, 2009–2010.
J Nordgren (1), L W Nitiema (2), S Sharma (1), D Ouermi (2), A S Traore (2), J Simpore (2), L Svensson (1)
1 Linkoping University, Linkoping, Sweden
2 Universite de Ouagadougou, Ouagadougou, Burkina Faso

2012 Experimental Applied Acarology (EAA). [Epub ahead of print]. (PDF)
Borrelia burgdorferi sensu lato in Ixodes ricinus ticks from Norway: evaluation of a PCR test targeting the chromosomal flaB gene.
Andrew Jenkins (1), Dag Hvidsten (2), Andreas Matussek (3), Per-Eric Lindgren (4), Snorre Stuen (5), Bjorn-Erik Kristiansen (6)
1 Unilabs Telelab, Skien, Norway
2 Department of Microbiology and Infection Control, University Hospital of North Norway, Tromso, Norway
3 Clinical Microbiology Laboratory, Division of Medical Services, Department of Laboratory Medicine, Sweden
4 Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Sweden,
5 Department of Production Animal Clinical Sciences, Norwegian School of Veterinary Science, Norway,
6 Department of Microbiology and Virology, University of Tromso, Norway

2011 Journal of Medical Microbiology (JMM), Vol. 60, No. 7. (PDF)
Characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16S rRNA gene followed by DNA sequencing and RipSeq analysis.
Kommedal O (1), Lekang K (2), Langeland N (3), Wiker HG (1,4)
1 Section for Microbiology and Immunology, The Gade Institute, University of Bergen, Norway
2 Institute of Biology, University of Bergen, Norway
3 Institute of Medicine, University of Bergen, Norway
4 Department of Microbiology, Haukeland University Hospital, Norway

2011 Ornamental Plants: Types, Cultivation and Nutrition (OPTCN). (PDF)
Watery varieties: Aquarium plant diversity from aesthetic, commercial and systematic perspectives
Lehtonen S, Falck D.
University of Turku, Department. of Biology, Turku, Finland.

2010 Journal of Medical Microbiology (JMM). Vol. 59, No. 4. (PDF)
Direct 16S rRNA gene sequencing of polymicrobial culture-negative samples with analysis of mixed chromatograms.
Hartmeyer G N, Justesen
U S Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark

2010 Journal of Clinical Microbiology (JCM). Vol. 48, No. 9. (PDF)
Simultaneous Sequencing Analysis of The 16S rRNA and rpoB Genes Using RipSeq Software to Identify Mycobacterium Species.
Keith E. Simmon (1), Oyvind Kommedal (2,3), Oystein Saebo (3), Bjarte Karlsen (3) and Cathy A. Petti (1,4)
1 Associated Regional and University Pathologists (ARUP), Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
2 University of Bergen, The Gade Institute, Section for Microbiology and Immunology, Bergen, Norway
3 iSentio AS, Bergen, Norway
4 University of Utah School of Medicine, Departments of Medicine and Pathology, Salt Lake City, Utah

2010 Journal of Infection (JOI), Vol 60, Issue 6. (PDF)
Shuttleworthia satelles Endocarditis: Evidence of Non-Dental Human Disease.
Neel B. Shahe (1), Rakesh M. Suri (2), Rowlens M. Melduni (2), Robin Patel (3), Oyvind Kommedal (4), Oystein Saebo (4), Daniel R. Gustafson (5), Walter R. Wilson (3), Larry M. Baddour (3)
1 Mayo Clinic College of Medicine, Department of Internal Medicine, Mayo Clinic School of Graduate Medical Education, Rochester, USA
2 Mayo Clinic College of Medicine, Department of Cardiovascular Surgery, Mayo Clinic School of Graduate Medical Education, Rochester, USA
3 Mayo Clinic College of Medicine, Division of Infectious Diseases, Mayo Clinic School of Graduate Medical Education, Rochester, USA
4 iSentio AS, Bergen, Norway
5 Mayo Clinic College of Medicine, Division of Clinical Microbiology, Mayo Clinic School of Graduate Medical Education, Rochester, USA

2009 Journal of Clinical Microbiology (JCM). Vol 47, No. 11. (PDF)
Direct 16S rRNA Gene Sequencing from Clinical Specimens, with Special Focus on Polybacterial Samples and Interpretation of Mixed DNA Chromatograms
Kommedal O (1,2), Kvello K (2), Skjaastad R (1), Langeland N (3,4), Wiker H G (1,2)
1 Department of Microbiology and Immunology, Haukeland University Hospital, Bergen, Norway
2 Section for Microbiology and Immunology, the Gade Institute, University of Bergen, Bergen, Norway
3 Institute of Medicine, University of Bergen, Bergen, Norway
4 Department of Medicine, Haukeland University Hospital, Bergen, Norway

2008 Journal of Clinical Microbiology (JCM), Vol. 46, No. 11. (PDF)
Analysis of Mixed Sequencing Chromatograms and Its Application in Direct 16S rRNA Gene Sequencing of Polymicrobial Samples.
Kommedal O, Karlsen B, Saebo O
iSentio AS, Bergen, Norway.

2012 ECCMID (PDF)
Direct sequencing and RipSeq analysis as a tool for identification of polymicrobial bactaeremia
Wolff T Y, Eickhardt S, Moser C, Bjarnsholt T, Nielsen P H, Hoiby N, Lorenzen J, Thomsen T R. Aarhus, Copenhagen, Aalborg, Denmark

2012 ECCMID (PDF)
How Liquid Based Microbiology can change the workflow in the Microbiology laboratories
Fontana C, Favaro M, Favalli C
1 Universita Tor Vergata, Biochimiche, , Roma, Italy
2 Universita Tor Vergata, Lab Microbiologia, Policlinico, Roma, Italy

2012 ECCMID (PDF)
RipSeq Single, advancing the quality of a bacterial reference database through social curation
Cathy A. Petti (1), Keith E. Simmon (2), Bjarte Karlsen (2), Oystein Saebo (2), Oyvind Kommedal (2)
1 TriCore Reference Laboratories, Albuquerque, NM, USA
2 Isentio AS, Bergen, Norway

2011 ECCMID (PDF)
Molecular pathogen detection (16S rDNA-PCR/sequencing) in culture-negative infections
Nolte O, Labor Dr. Brunner
Konstanz, Germany

2010 ECCMID (PDF)
Dissection of polybacterial clinical samples using group specific broad-range primers and DNA sequencing followed by RipSeq analysis
Kommedal O.
University of Bergen, The Gade Institute Section for Microbiology and Immunology, Norway and Isentio AS, Bergen, Norway

2010 ASM (PDF)
Application of RipSeq Mixed Software in Identification of Bacteria by 16S ribosomal RNA Gene Sequencing
Hall L, Connelly B J (1), Kommdal O (2), Saebo O F (2), Patel F (1), Ihde S M (1), Gustafson D R (1), Rosenblatt J E (1), Wengenack N L (1)
1 Mayo Clinic, Rochester, USA
2 Isentio, Bergen, Norway

2010 ASMCM (PDF)
Evaluation of the GenBank BLAST and RipSeq by Isentio for sequence comparisons of DNA obtained from Corneal scrapings in patients with suspected ophthalmic infections
Grankvist A, Kjellin E, Welinder-Olsson
Sahlgrenska University Hospital, Clinical Bacteriology Laboratory, Gothenburg, Sweden

2009 ICCAC (PDF)
Identification of Polymicrobial Bacteremia by 16S rRNA Sequencing with RipSeq(TM) Software
Tesic V (1,2), Simmon K E (3), Petti A (1,2)
1 ARUP Laboratories, Salt Lake City, USA
2 University of Utah, USA
3 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, USA

2009 ASM (PDF)
Identification of Mixed Infections of Mycobacterium species from Culture with 16S rRNA Gene Sequencing and RipSeq Software
Smith G L (1), Tesic V (1,2), Simmon K E (3), Petti A (1,2)
1 ARUP Laboratories, Salt Lake city, USA
2 Univ of Utah, Salt Lake City, ARUP, USA
3 ARUP Inst for Clinical and Experimental Pathology, Salt Lake City, USA

2008 ICCAC (PDF)
Simultaneous Sequence Analysis of Two Loci to Identify Mycobacterium spp.
Simmon K E (1), Kommedal O (2), Karlsen B (2), Saebo O (2), Petti A (1,3)
1 ARUP, Institute for Clinical and Experimental Pathology, Salt Lake City, USA
2 Isentio, Bergen, Norway
3 University of Utah School of Medicine, Department of Medicin and Pathology, Salt Lake City, USA

RipSeq Mixed

RipSeq Mixed is an online software tool for rapid bacterial identification, with focus on analyzing mixed clinical samples. Through the use of advanced algorithms, we remove the need for manual isolation and re-cultivation of colonies from poly-microbial samples prior to 16S rDNA sequencing. This makes direct sequencing relevant for a broader range of clinical samples, including abscesses and pleural fluids.
Pathogenomix RipSeq Mixed (PDF)
RipSeq Single

DNA target sequencing is the prevailing method for accurate identification of human pathogens. With the introduction of RipSeq Single and the already established RipSeq Mixed, Isentio now makes RipSeq software the complete package for DNA target sequence based identification.
Pathogenomix RipSeq Single (PDF)
RipSeq NGS

Using our novel algorithms RipSeq will process your targeted NGS sequence file locally, and reduce the information needed to upload by a factor of 1000:1, while still retaining resolution and specificity. This means no lengthy file upload, and no costly big data file storage. After upload, the cloud based RipSeq will analyze the uploaded reads against any of our curated Ripseq DB databases - no matter the target. All this in less than 5 minutes! Including reporting!
Pathogenomix RipSeq Single (PDF)
RipSeq Mixed Examples

RipSeq Mixed is a computer program able to read and interpret mixed chromatograms containing up to three individual sequences (ref. JCM, Nov. 2009). Through the use of advanced algorithms we remove the need for culture and manual separation of the present bacteria prior to sequencing.
Pathogenomix RipSeq Mixed Examples (PDF)
RipSeq Mixed handles InDels

RipSeq Mixed is an online application able to read and interpret mixed sequencing chromatograms through the use of advanced algorithms. The RipSeq Mixed module can automatically handle and identify indel copy variants in DNA sequences obtained from pure bacterial isolates.
Pathogenomix RipSeq Mixed InDels (PDF)

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