“Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip” –Arjang Hassibi, Arun Manickam, Rituraj Singh, Sara Bolouki, Ruma Sinha, Kshama B Jirage, Mark W McDermott, Babak Hassibi, Haris Vikalo, Gelareh Mazarei, Lei Pei, Luc Bousse, Mark Miller, Mehrdad Heshami, Michael P Savage, Michael T Taylor, Nader Gamini, Nicholas Wood, Pallavi Mantina, Patrick Grogan, Peter Kuimelis, Piyush Savalia, Scott Conradson, Yuan Li, Rich B Meyer, Edmond Ku, Jessica Ebert, Benjamin A Pinsky, Gregory Dolganov, Tran Van, Kirsten A Johnson, Pejman Naraghi-Arani, Robert G Kuimelis & Gary Schoolnik,
Nature Biotechnology: doi:10.1030/nbt4139
“An array-based melt curve analysis method for the identification and classification of closely related pathogen strains” –Arjang Hassibi Jessica Ebert Sara Bolouki Alexander Anemogiannis Gelareh Mazarei Yuan Li Kirsten A Johnson Tran Van Pallavi Mantina Taraneh Gharooni Kshama Jirage Lei Pei Ruma Sinha Arun Manickam Amin Zia Pejman Naraghi-Arani Gary Schoolnik Robert G Kuimelis
Biology Methods and Protocols, Volume 3, Issue 1, 1 January 2018, bpy005,
Centers for Disease Control (CDC): “Visual OMP (version 4.2) software (DNA Software, Inc., Ann Arbor, MI) was used to design and simulate the performance of the O-group PCR primers and capture probes.” — Fitzgerald,C., Collins,M., van Duyne,S., Mikoleit,M., Brown,T., Fields,P. (2007) “Multiplex, Bead-Based Suspension Array for Molecular Determination of Common Salmonella Serogroups”, Journal of Clinical Microbiology, 45, 3323-3334.
U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) / Boston University: “The microarray DNA probe design from candidate sequences was carried out using the commercial software oligonucleotide modeling platform (OMP) (available at ), which implements a state-of-the-art hybridization model (SantaLucia and Hicks, 2004).” — Tembe, W., Zavaljevski, N., Bode, E., Chase, C., Geyer, J., Wasieloski, L., Benson, G., Reifman, J. (2007) “Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays”, Bioinformatics, 23, 5-13.
U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID): “The specific primer and TaqMan minor groove binding (MGB) probe sequences were designed using Visual OMP version 184.108.40.206 for Windows (DNA Software).” — Ulrich,M.P., Norwood,D.A., Christensen,D.R., Ulrich,R.L. (2006). “Using real time PCR to specifically detect Burkholderia mallei”, Journal of Medical Microbiology, 55, 551-559.
Harvard University: “We are grateful to […] DNA Software for assistance with codon screening.” — Gartner Z.J., Tse B.N., Grubina R., Doyon J.B., Snyder T.M., Liu D.R. (2004). “DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles”, Science, 305, 1601-1605.
Harvard University: “We thank DNA Software for assistance with screening coding and annealing sequences.” — Kanan M.W., Rozenman M.M., Sakurai K., Snyder T.M., Liu D.R. (2004). “Reaction discovery enabled by DNA-templated synthesis and in vitro selection”, Nature, 431, 545-549.
Merck & Co. Inc./ Universitat de Barcelona / Los Alamos National Laboratory / Howard Hughes Medical Institute / University of California, Berkley: “… we obtain for the free energy of unfolding… excellent agreement with the result obtained using the Visual OMP from DNA software…” — Collin,D., Ritort,F., Jarzynski,C., Smith,S.B., Tinoco,I.,Jr., Bustamante,C. (2005). “Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies”,Nature, 437, 231-234.
EraGen Biosciences Inc. / U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID): “Because the approach of mixing primer sets from separate assays was unsuccessful, we decided to construct new assays using new multiplex primer design software called Visual OMP… The new designs obtained… demonstrated similar limits of detection yet a noticeable improvement in sensitivity and specificity over the previously developed triplex assays… The current availability of RTx reagents and Visual OMP design software should allow others to compare multiplexed probe-based systems with the RTx probe-free system.” — Moser,M.J., Christensen,D.R., Norwood,D., Prudent,J.R. (2006). “Multiplexed Detection of Antrax-Related Toxin Genes”, Journal of Molecular Diagnostics, 8, 89-96.
EraGen Biosciences Inc. / Emory University: “The same effects of mismatch types were predicted by simulations using the software Oligonucleotide Modeling Platform (OMP, DNA Software, Inc., Ann Arbor, MI) by Lee and co-workers…” — Moser,M.J., Ruckstuhl,M., Larsen,C.A., Amanda, J.S., Kozlowski,M., Bassit,L., Sharma,P.L., Schinazi,R.F., Prudent,J.R. (2005). “Quantifying Mixed Populations of Drug-Resistant Human Immunodeficiency Virus Type 1”,Antimicrobial Agents and Chemotherapy, 49, 3334-3340.
EraGen Biosciences Inc. / Department of Pediatrics and Medicine / Wisconsin State Laboratory of Hygiene / University of Wisconsin: “…candidate primer sets were selected within these conserved sequences with computer software (Visual Oligonucleotide Modeling Platform; DNA Software, Inc.), according to the following criteria: appropriate melting temperature, minimal secondary-structure formation, minimal interactions with the other primers in multiplex settings, and no interaction with human sequences.” — Wai-Ming Lee, Kris Grindle, Tressa Pappas, David J. Marshall, Michael J. Moser, Edward L. Beaty, Peter A. Shult, James R. Prudent, and James E. Gern. (2007). “High-Throughput, Sensitive, and Accurate Multiplex PCR-Microsphere Flow Cytometry System for Large-Scale Comprehensive Detection of Respiratory Viruses”, Journal of Clinical Microbiology, p. 2626–2634
University of Michigan /Kyushu University: “Melting temperature as a measure of hybridization stability is calculated using the nearest neighbor thermodynamics model (28) with licensed software Oligonucleotide Modeling Platform (OMP; ). Observing that OMP calculations correlated with experimental Tm better than our in-house program containing publicly available parameters…” — Lee,I., Ajay,S.S., Chen,H., Maruyama,A., Wang,N., McInnis,M.G., Athey,B.D. (2008). “Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)”, Nucleic Acids Research, 36, e27.
University of Michigan / Wayne State University: “Most hybridization Tm calculations were done using OMP software (DNA Software, Inc., Ann Arbor, MI;http://www.dna-software.com). The software simulates and predicts nucleic acid hybridization in solution and produces structural and thermodynamic parameters. OMP predicts nucleotide acid structures utilizing dynamic programming methods (30) and calculates their reactions in equilibrium based on nearest neighbor calculations, which determine `thermal’ Tm using equation 2. OMP calculates `actual’ Tm considering competing secondary structures of oligonucleotides… Nearest neighbor Tm calculations, especially using OMP, showed an excellent linear correlation with experimental Td for single-mismatched pairs….” — Lee,I., Dombkowski,A.A., Athey,B.D. (2004). “Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray”, Nucleic Acids Research, 32, 681-690.
Michigan State University / University of Michigan: “The same effects of mismatch types were predicted by simulations using the software Oligonucleotide Modeling Platform (OMP, DNA Software, Inc., Ann Arbor, MI) by Lee and co-workers (43).” — Wick,L.M., Rouillard,J.M., Whittam,T.S., Gulari,E., Tiedje,J.M., Hashsham,S.A. (2006). “On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes”, Nucleic Acids Research, 34, e26.
Medigenes Co. / KAIST (Korea Advanced Institute of Science and Technology) / Yonsei University College of Medicine / Harvard School of Dental Medicine / Yale University School of Medicine / CambridgeMED Co.: “Visual OMP [/Products/VisualOMP/index.htm] is a software for probe design, which was optimized to maximize the specificity of the probes. This program has been integrated in an engine for visualizing target and oligo structures, thermodynamics modeling, and built-in BLAST and ClustalW.” — Yoo,S.M., Keum,K.C., Yoo,S.Y., Choi,J.Y., Chang,K.H., Yoo,N.C., Yoo,W.M., Kim,J.M., Lee,D., Lee,S.Y. (2004). “Development of DNA Microarray for Pathogen Detection”, Biotechnology and Bioprocess Engineering, 9, 93-99.
Providence Portland Medical Center: “… and Visual OMP software were used to design and simulate the performance of the primers and the probe.” — Kohlhepp S.J., Hardick J., Gaydos C. (2005). “Chlamydia pneumoniae in Peripheral Blood Mononuclear Cells Isolated from Individuals Younger than 20 Years or Older than 60 Years”, Journal of Clinical Microbiology, 43, 3030.
Chung-Ho Memorial Hospital / Kaohsiung Medical University / Sung Hua Biotech Co., Ltd.: “Using a version of OMP (Oligonucleotide Modeling Platform, DNA Software, Ann Arbor, MI), DNA software tailored to the specifics of membrane-array assay, probe sequences for each target are designed and a single best candidate is selected.” — Wang,J.Y., Yeh,C.S., Chen,Y.F., Wu,C.H., Hsieh,J.S., Huang,T.J., Huang, S.Y., Lin,S.R. (2006). “Development and evaluation of a colorimetric membrane-array method for the detection of circulating tumor cells in the peripheral blood of Taimanese patients with colorectal cancer”,International Journal of Molecular Medicine, 17, 737-747.
Kaohsiung Medical University Hospital / Kaohsiung Medical University / Tri-Service General Hospital, Taipei /Kaohsiung Municipal Hsiao-Kang Hospital: “Using a version of OMP (Oligonucleotide Modeling Platform, DNA Software, Ann Arbor, MI, USA), DNA software tailored to probe sequences for each target are designed and a single best candidate is selected…” — Wang,J.Y., Wang,Y.H., Jao,S.W., Lu,C.Y., Kuo,C.H., Hu,H.M., Hsieh,J.S., Chong,I.W., Cheng,T.L., Lin,S.R. (2006). “Molecular mechanisms underlying the tumorigenesis of colorectal adenomas: Correlation to activated K-ras oncogene”, Oncology Reports, 16, 1245-1252.