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Citations and Reviews

Author and Details
Down-Regulatory Effects of miR-211 on Long Non-Coding RNA SOX2OT and SOX2 Genes in Esophageal Squamous Cell Carcinoma

Shafiee, Mohammad, Seyed Ahmad Aleyasin, Mohammad Vasei, Shahriar Semnani, Seyed Javad Mowla
Cell Journal 17, no. 4 (2016): 593.

Common AZFc structure may possess the optimal spermatogenesis efficiency relative to the rearranged structures mediated by non-allele homologous recombination

Yang, Bo, Yong-yi Ma, Yun-qiang Liu, Lei Li, Dong Yang, Wen-ling Tu, Ying Shen, Qiang Dong, and Yuan Yang
Scientific reports 5 (2015), Article number: 10551.

Association between the Advanced Glycosylation End Product-Specific Receptor Gene and Cardiovascular Death in Older Men Biros, Erik, Corey S. Moran, Paul E. Norman, Graeme J. Hankey, Bu B. Yeap, Osvaldo P. Almeida, Leon Flicker, Richard White, Rhondda Jones, and Jonathan Golledge
PloS one 10, no. 7 (2015).
Canonical single nucleotide polymorphisms (SNPs) for high-resolution subtyping of Shiga-toxin producing Escherichia coli (STEC) O157: H7 Griffing, Sean M., Duncan R. MacCannell, Amber J. Schmidtke, Molly M. Freeman, Eija Hyytiä-Trees, Peter Gerner-Smidt, Efrain M. Ribot, and James L. Bono
PloS one 10, no. 7 (2015): e0131967.
Identification of reference genes for quantitative expression analysis of MicroRNAs and mRNAs in barley under various stress conditions Ferdous, Jannatul, Yuan Li, Nicolas Reid, Peter Langridge, Bu-Jun Shi, and Penny J. Tricker
PloS one 10, no. 3 (2015): e0118503.
High-resolution microscopy of active ribosomal genes and key members of the rRNA processing machinery inside nucleolus-like bodies of fully-grown mouse oocytes Shishova, Kseniya V., Yuriy M. Khodarovich, Elena A. Lavrentyeva, and Olga V. Zatsepina
Experimental cell research 337, no. 2 (2015): 208-218.
The Generation of Insulin Producing Cells from Human Mesenchymal Stem Cells by MiR-375 and Anti-MiR-9 Jafarian, Arefeh, Mohammad Taghikani, Saeid Abroun, Amir Allahverdi, Maryam Lamei, Niknam Lakpour, and Masoud Soleimani
PloS one 10, no. 6 (2015): e0128650.

Eight New Genomes and Synthetic Controls Increase the Accessibility of Rapid Melt-MAMA SNP Typing of Coxiella burnetii

Edvin Karlsson, Anna Macellaro, Mona Byström, Mats Forsman, Dimitrios Frangoulidis, Ingmar Janse, Pär Larsson, Petter Lindgren, Caroline Öhrman, Bart van Rotterdam, Andreas Sjödin and Kerstin Myrtennäs, PLoS One. 2014; 9(1): e85417.


Rapid Molecular Characterization of Acinetobacter baumannii Clones with rep-PCR and Evaluation of Carbapenemase Genes by New Multiplex PCR in Hospital District of Helsinki and Uusimaa

Tanja Pasanen, Suvi Koskela, Sointu Mero, Eveliina Tarkka, Päivi Tissari, Martti Vaara, and Juha Kirveskari PLoS One. 2014; 9(1): e85854.


Development of a Cost-Effective Method for Capripoxvirus Genotyping Using Snapback Primer and dsDNA Intercalating Dye

Esayas Gelaye, Charles Euloge Lamien, Roland Silber, Eeva S. M. Tuppurainen,Reingard Grabherr and Adama Diallo
PLoS One. 2013; 8(10): e75971.


Comparison between Chondrogenic Markers of Differentiated Chondrocytes from Adipose Derived Stem Cells and Articular Chondrocytes In Vitro

Mohmmad Mardani,Batool Hashemibeni, Malek Masoud Ansar, Sayeed Hamid Zarkesh Esfahani, Mohmmad Kazemi, Vahid Goharian, Nafiseh Esmaeili and Ebrahim Esfandiary,
Iran J Basic Med Sci. 2013 June; 16(6): 763–773.


Simultaneous Quantification of Multiple Bacteria by the BactoChip Microarray Designed to Target Species-Specific Marker Genes

Annalisa Ballarini,Nicola Segata,Curtis Huttenhower and Olivier Jousson
PLoS One. 2013; 8(2): e55764.


Transcriptome analysis of embryo maturation in maize

Keat Thomas Teoh, Deborah Vicuna Requesens, Shivakumar P Devaiah, Daniel Johnson, Xiuzhen Huang, John A Howard and Elizabeth E Hood
BMC Plant Biol. 2013; 13: 19.


The influence of cerebrospinal fluid on epidermal neural crest stem cells may pave the path for cell-based therapy

Sareh Pandamooz, Mohammad Naji, Farid Alinezhad, Amin Zarghami,and Mohsen Pourghasem
Stem Cell Res Ther. 2013; 4(4): 84.


Detection of the intercellular adhesion gene cluster (ica) in clinical Staphylococcus aureus isolates

Amirmorteza Ebrahimzadeh Namvar, Babak Asghari, Fatemeh Ezzatifar, Gholamreza Azizi, and Abdolaziz Rastegar Lari
GMS Hyg Infect Control. 2013; 8(1): Doc03.


Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

Andrew R. Mahon, Christopher L. Jerde, Matthew Galaska, Jennifer L. Bergner, W. Lindsay Chadderton, David M. Lodge, Margaret E. Hunter, and Leo G. Nico
PLoS One. 2013; 8(3): e58316


Expert Guide-Definitive qPCR Assay Design

Stephen Bustin,


Selection of reference genes for qPCR in hairy root cultures of peanut

Jose Condori, Cesar Nopo-Olazabal, Giuliana Medrano and Fabricio Medina-Bolivar
BMC Research Notes 2011, 4:392; Published: 10 October 2011


ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design

Marco Severgnini, Paola Cremonesi, Clarissa Consolandi, Giada Caredda, Gianluca De Bellis, Bianca Castiglioni. ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design. Nucleic acids research. 2009 Sep;37(16): e109


A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling.

Birgitte Tauris, Søren Borg, Per L Gregersen, Preben B Holm. A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling. Journal of experimental botany. 2009;60(4): 1333-47


Direct Sequence Detection of Structured H5 Influenza Viral RNA

Matthew B. Kerby, Sarah Freeman, Kristina Prachanronarong, Andrew W.
Artenstein, Steven M. Opal and Anubhav Tripathi
Journal of Molecular Diagnostics 2008, Vol. 10, No. 3


Occurrence and Genetic Diversity of Bacillus anthracis Strains Isolated in an Active Wool-Cleaning Factory

Pierre Wattiau, Silke R. Klee, David Fretin, Mieke Van Hessche, Marie Ménart,
Tatjana Franz, Camille Chasseur, Patrick Butaye, Hein Imberechts
Applied and Environmental Microbiology, July 2008, p. 4005-4011, Vol. 74, No. 13


Design of Microarray Probes for Detection of Mutations

Almeida, P. Carreto, L. Oliveira, J.L.
Parque Tecnol. de Cantanhede, Cantanhede;
Biocomputation, Bioinformatics and Biomedical Technologies, 2008. Page(s): 137-142
BIOTECHNO '08. International Conference on
Publication Date: June 29 2008-July 5 2008. Page(s): 137-142


Validation of reference genes for qPCR studies on Caco-2 cell differentiation

Claudia Pianaa, Michael Wirtha, Stefan Gerbesb, Helmut Viernsteina,
Franz Gabora and Stefan Toegela
European Journal of Pharmaceutics and Biopharmaceutics, 2008 - Elsevier


Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing

Sadia Bekal, J. P. Craig, M. E. Hudson, T. L. Niblack, L. L. Domier and K. N. Lambert
Journal Molecular Genetics and Genomics;Issue Volume 279, Number 5 / May, 2008 Pages 535-543


Detection and characterisation of human metapneumovirus from children with acute respiratory symptoms in north-west England, UK

M. Hopkins, C. Redmond, J. Shaw, I. Hart, C. Hart, R. Smyth, M. Semple ELSEVIER
Journal of Clinical Virology, July 2008, Volume 42, Issue 3, Pages 273-279


Comparison between chondroprotective effects of glucosamine, curcumin and diacerein in IL-1ß-stimulated C-28/I2 chondrocytes

S. Toegel, S. Wu, C. Piana, F. Unger, M. Wirth, M. Goldring, F. Gabor, H. Viernstein
Osteoarthritis and Cartilage, October 2008, Volume 16, Issue 10, Pages 1205-1212


AlleleID: A Pathogen Detection and Identification System

Arun Apte and Siddharth Singh
Methods Mol Biol. 2007;402:329-46
PMID: 17951804 [PubMed - indexed for MEDLINE]


Characterizing the Meiotic Failure and Transcriptional Aberrations Caused by Mutation of A-Myb in Mice

Barash, Alexander
2007 - dspace.library.cornell.edu


Salmonid host response to infectious hematopoietic necrosis (IHN) virus: Cellular receptors, viral control and novel pathways of defence

Kristina Miller, Garth Traxlera, Karia Kaukinena, Shaorong Lia, Jon Richarda and Norma Ginther
Aquaculture; Volume 272, Supplement 1, 2007, Pages S217-S237


Selection of reliable reference genes for qPCR studies on chondroprotective action

Toegel S, Huang W, Piana C, Unger FM, Wirth M, Goldring MB, Gabor F, Viernstein H.
BMC Mol Biol. 2007; 8: 13.
PMCID: 1820791


Species Identification Assays/Cross Species Assays/Allele Identification Assays

AlleleID® aligns sequences using ClustalW and analyzes conserved and species specific regions. You can then use the program for real time PCR primer design (SYBR® Green primer design included) and dual labeled probe design (TaqMan® probes, TaqMan® MGB probes and molecular beacons). These assays are designed to detect only the strain (strain detection) or species of interest from the mix.

Sophisticated Algorithms for Assay Success

Highly specific oligos are designed by avoiding regions of significant homologies found by automatically interpreting BLAST search results. Real time PCR primer & probe efficiency is enhanced by avoiding template secondary structures. "Minimal Set", one of the most innovative features in the program, helps design the fewest number of allele specific oligonucleotide primers and dual labeled probes that uniquely identify each of the desired species/strain/taxa from the mix, lowering assay costs. For taxa or cross species assays, this feature is especially useful when the group or taxa is highly dissimilar. For a partial set of pre-designed, proven set of primers, AlleleID® can design compatible primers and probes for the rest of sequences for species identification or taxa specific assays.


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