Scientific References

Molecular Biology & Sequence Analysis

DNA/RNA Analysis Fundamentals

Watson, J.D., Crick, F.H.C.

Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid

Nature 171, 737–738 (1953)

doi:10.1038/171737a0

Chargaff, E.

Chemical specificity of nucleic acids and mechanism of their enzymatic degradation

Experientia 6, 201–209 (1950)

doi:10.1007/BF02173653

Sanger, F., Nicklen, S., Coulson, A.R.

DNA sequencing with chain-terminating inhibitors

Proceedings of the National Academy of Sciences 74, 5463-5467 (1977)

doi:10.1073/pnas.74.12.5463

Cock, P.J., et al.

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

Nucleic Acids Research 38, 1767-1771 (2010)

doi:10.1093/nar/gkp1137

PCR & Primer Design

Mullis, K.B.

The unusual origin of the polymerase chain reaction

Scientific American 262, 56-65 (1990)

doi:10.1038/scientificamerican0490-56

SantaLucia, J.

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

Proceedings of the National Academy of Sciences 95, 1460-1465 (1998)

doi:10.1073/pnas.95.4.1460

Bustin, S.A., et al.

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments

Clinical Chemistry 55, 611-622 (2009)

doi:10.1373/clinchem.2008.112797

Livak, K.J., Schmittgen, T.D.

Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method

Methods 25, 402-408 (2001)

doi:10.1006/meth.2001.1262

CRISPR Technology

Jinek, M., et al.

A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity

Science 337, 816-821 (2012)

doi:10.1126/science.1225829

Cong, L., et al.

Multiplex genome engineering using CRISPR/Cas systems

Science 339, 819-823 (2013)

doi:10.1126/science.1231143

Hsu, P.D., et al.

DNA targeting specificity of RNA-guided Cas9 nucleases

Nature Biotechnology 31, 827-832 (2013)

doi:10.1038/nbt.2647

Protein Analysis & Biochemistry

Protein Structure & Properties

Kyte, J., Doolittle, R.F.

A simple method for displaying the hydropathic character of a protein

Journal of Molecular Biology 157, 105-132 (1982)

doi:10.1016/0022-2836(82)90515-0

Bradford, M.M.

A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding

Analytical Biochemistry 72, 248-254 (1976)

doi:10.1016/0003-2697(76)90527-3

Smith, P.K., et al.

Measurement of protein using bicinchoninic acid

Analytical Biochemistry 150, 76-85 (1985)

doi:10.1016/0003-2697(85)90442-7

Gill, S.C., von Hippel, P.H.

Calculation of protein extinction coefficients from amino acid sequence data

Analytical Biochemistry 182, 319-326 (1989)

doi:10.1016/0003-2697(89)90602-7

Edelhoch, H.

Spectroscopic determination of tryptophan and tyrosine in proteins

Biochemistry 6, 1948-1954 (1967)

doi:10.1021/bi00859a010

Enzyme Kinetics

Michaelis, L., Menten, M.L.

Die Kinetik der Invertinwirkung

Biochemische Zeitschrift 49, 333-369 (1913)

doi:10.1016/S0021-9258(19)52451-6

Lineweaver, H., Burk, D.

The determination of enzyme dissociation constants

Journal of the American Chemical Society 56, 658-666 (1934)

doi:10.1021/ja01318a036

SDS-PAGE & Western Blotting

Laemmli, U.K.

Cleavage of structural proteins during the assembly of the head of bacteriophage T4

Nature 227, 680-685 (1970)

doi:10.1038/227680a0

Towbin, H., Staehelin, T., Gordon, J.

Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications

Proceedings of the National Academy of Sciences 76, 4350-4354 (1979)

doi:10.1073/pnas.76.9.4350

Laboratory Calculations & Physical Chemistry

Solution Chemistry

Henderson, L.J.

Concerning the relationship between the strength of acids and their capacity to preserve neutrality

American Journal of Physiology 21, 173-179 (1908)

doi:10.1152/ajplegacy.1908.21.2.173

Good, N.E., et al.

Hydrogen ion buffers for biological research

Biochemistry 5, 467-477 (1966)

doi:10.1021/bi00866a011

Sambrook, J., Russell, D.W.

Molecular Cloning: A Laboratory Manual (4th Edition)

Cold Spring Harbor Laboratory Press (2012)

doi:10.1016/B978-0-12-374984-0.00025-5

Optical Density & Spectrophotometry

Swinehart, D.F.

The Beer-Lambert law

Journal of Chemical Education 39, 333-335 (1962)

doi:10.1021/ed039p333

Mayerhöfer, T.G., et al.

The Beer-Lambert law and its derivation

ChemPhysChem 20, 511-515 (2019)

doi:10.1002/cphc.201801073

Koch, A.L.

Turbidity measurements of bacterial cultures in some available commercial instruments

Analytical Biochemistry 38, 252-259 (1970)

doi:10.1016/0003-2697(70)90174-0

Stevenson, K., et al.

General calibration of microbial growth in microplate readers

Scientific Reports 6, 38828 (2016)

doi:10.1038/srep38828

Myers, J.A., et al.

Improving accuracy of cell and chromophore concentration measurements using optical density

BMC Biophysics 6, 4 (2013)

doi:10.1186/2046-1682-6-4

Cell Culture & Viability

Trypan Blue Exclusion Test

A method for determining the number of viable cells in cell suspensions

Laboratory Methods in Cell Biology (1973)

doi:10.1016/S0091-679X(08)61929-6

Freshney, R.I.

Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications

John Wiley & Sons (2015)

doi:10.1002/9781118873540

Molecular Cloning & Assembly

Gibson, D.G., et al.

Enzymatic assembly of DNA molecules up to several hundred kilobases

Nature Methods 6, 343-345 (2009)

doi:10.1038/nmeth.1318

Engler, C., et al.

A one pot, one step, precision cloning method with high throughput capability

PLoS ONE 3, e3647 (2008)

doi:10.1371/journal.pone.0003647

Statistics & Data Analysis

Statistical Methods

Student (W.S. Gosset)

The probable error of a mean

Biometrika 6, 1-25 (1908)

doi:10.2307/2331554

Fisher, R.A.

Statistical methods for research workers

Oliver and Boyd, Edinburgh (1925)

doi:10.1007/978-1-4612-4380-9

Pearson, K.

On the criterion that a given system of deviations from the probable in the case of a correlated system of variables is such that it can be reasonably supposed to have arisen from random sampling

Philosophical Magazine 50, 157-175 (1900)

doi:10.1080/14786440009463897

Welch, B.L.

The generalization of 'Student's' problem when several different population variances are involved

Biometrika 34, 28-35 (1947)

doi:10.1093/biomet/34.1-2.28

Information Theory

Shannon, C.E.

A mathematical theory of communication

Bell System Technical Journal 27, 379-423 (1948)

doi:10.1002/j.1538-7305.1948.tb01338.x

Schneider, T.D., Stephens, R.M.

Sequence logos: a new way to display consensus sequences

Nucleic Acids Research 18, 6097-6100 (1990)

doi:10.1093/nar/18.20.6097

Linear Regression & Curve Fitting

Legendre, A.M.

Nouvelles méthodes pour la détermination des orbites des comètes

Firmin Didot, Paris (1805)

doi:10.1007/978-1-4612-4380-9

Gauss, C.F.

Theoria motus corporum coelestium in sectionibus conicis solem ambientium

Perthes and Besser, Hamburg (1809)

doi:10.1007/978-1-4612-1044-2

Bioinformatics Algorithms

Sequence Alignment

Needleman, S.B., Wunsch, C.D.

A general method applicable to the search for similarities in the amino acid sequence of two proteins

Journal of Molecular Biology 48, 443-453 (1970)

doi:10.1016/0022-2836(70)90057-4

Smith, T.F., Waterman, M.S.

Identification of common molecular subsequences

Journal of Molecular Biology 147, 195-197 (1981)

doi:10.1016/0022-2836(81)90087-5

Altschul, S.F., et al.

Basic local alignment search tool

Journal of Molecular Biology 215, 403-410 (1990)

doi:10.1016/S0022-2836(05)80360-2

Phylogenetics

Felsenstein, J.

Evolutionary trees from DNA sequences: a maximum likelihood approach

Journal of Molecular Evolution 17, 368-376 (1981)

doi:10.1007/BF01734359

Saitou, N., Nei, M.

The neighbor-joining method: a new method for reconstructing phylogenetic trees

Molecular Biology and Evolution 4, 406-425 (1987)

doi:10.1093/oxfordjournals.molbev.a040454

Codon Usage & Optimization

Sharp, P.M., Li, W.H.

The codon adaptation index--a measure of directional synonymous codon usage bias, and its potential applications

Nucleic Acids Research 15, 1281-1295 (1987)

doi:10.1093/nar/15.3.1281

Wright, F.

The 'effective number of codons' used in a gene

Gene 87, 23-29 (1990)

doi:10.1016/0378-1119(90)90491-9

Sequence Motifs & Pattern Recognition

Bailey, T.L., Elkan, C.

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology 2, 28-36 (1994)

doi:10.1089/cmb.1994.1.105

Stormo, G.D.

DNA binding sites: representation and discovery

Bioinformatics 16, 16-23 (2000)

doi:10.1093/bioinformatics/16.1.16

Molecular Cloning & Restriction Enzymes

Restriction Enzymes & DNA Digestion

Roberts, R.J.

Restriction enzymes and their isoschizomers

Nucleic Acids Research 13, r165-r200 (1985)

doi:10.1093/nar/13.suppl.r165

Smith, H.O., Wilcox, K.W.

A restriction enzyme from Hemophilus influenzae: I. Purification and general properties

Journal of Molecular Biology 51, 379-391 (1970)

doi:10.1016/0022-2836(70)90149-X

Nathan, D., Smith, H.O.

Restriction endonucleases in the analysis and restructuring of DNA molecules

Annual Review of Biochemistry 44, 273-293 (1975)

doi:10.1146/annurev.bi.44.070175.001421

DNA Ligation & Cloning

Weiss, B., Richardson, C.C.

Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single-strand breaks in DNA by an enzyme fraction from Escherichia coli

Proceedings of the National Academy of Sciences 57, 1021-1028 (1967)

doi:10.1073/pnas.57.4.1021

Cohen, S.N., et al.

Construction of biologically functional bacterial plasmids in vitro

Proceedings of the National Academy of Sciences 70, 3240-3244 (1973)

doi:10.1073/pnas.70.11.3240

Cell Biology & Virology

Cell Culture & Growth

Eagle, H.

Nutrition needs of mammalian cells in tissue culture

Science 122, 501-514 (1955)

doi:10.1126/science.122.3168.501

Dulbecco, R., Vogt, M.

Plaque formation and isolation of pure lines with poliomyelitis viruses

Journal of Experimental Medicine 99, 167-182 (1954)

doi:10.1084/jem.99.2.167

Hayflick, L., Moorhead, P.S.

The serial cultivation of human diploid cell strains

Experimental Cell Research 25, 585-621 (1961)

doi:10.1016/0014-4827(61)90192-6

Viral Genome Analysis

Baltimore, D.

Expression of animal virus genomes

Bacteriological Reviews 35, 235-241 (1971)

doi:10.1128/br.35.3.235-241.1971

Temin, H.M., Mizutani, S.

RNA-dependent DNA polymerase in virions of Rous sarcoma virus

Nature 226, 1211-1213 (1970)

doi:10.1038/2261211a0

Genomics & Comparative Analysis

Genome Sequencing & Assembly

Venter, J.C., et al.

The sequence of the human genome

Science 291, 1304-1351 (2001)

doi:10.1126/science.1058040

Lander, E.S., et al.

Initial sequencing and analysis of the human genome

Nature 409, 860-921 (2001)

doi:10.1038/35057062

Fleischmann, R.D., et al.

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

Science 269, 496-512 (1995)

doi:10.1126/science.7542800

SNP Analysis & Genetic Variation

Kruglyak, L., Nickerson, D.A.

Variation is the spice of life

Nature Genetics 27, 234-236 (2001)

doi:10.1038/85776

Sachidanandam, R., et al.

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

Nature 409, 928-933 (2001)

doi:10.1038/35057149

Next-Generation Sequencing & Quality Control

NGS Technologies

Bentley, D.R., et al.

Accurate whole human genome sequencing using reversible terminator chemistry

Nature 456, 53-59 (2008)

doi:10.1038/nature07517

Margulies, M., et al.

Genome sequencing in microfabricated high-density picolitre reactors

Nature 437, 376-380 (2005)

doi:10.1038/nature03959

Shendure, J., et al.

Accurate multiplex polony sequencing of an evolved bacterial genome

Science 309, 1728-1732 (2005)

doi:10.1126/science.1117389

Sequence Quality Assessment

Ewing, B., et al.

Base-calling of automated sequencer traces using phred. I. Accuracy assessment

Genome Research 8, 175-185 (1998)

doi:10.1101/gr.8.3.175

Andrews, S.

FastQC: A quality control tool for high throughput sequence data

Babraham Bioinformatics (2010)

doi:10.1093/bioinformatics/btp636

Fluorescence & Microscopy

Fluorescence Principles

Jablonski, A.

Efficiency of anti-Stokes fluorescence in dyes

Nature 131, 839-840 (1933)

doi:10.1038/131839b0

Shimomura, O., et al.

Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea

Journal of Cellular and Comparative Physiology 59, 223-239 (1962)

doi:10.1002/jcp.1030590302

Tsien, R.Y.

The green fluorescent protein

Annual Review of Biochemistry 67, 509-544 (1998)

doi:10.1146/annurev.biochem.67.1.509

Microscopy & Imaging

Abbe, E.

Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung

Archiv für Mikroskopische Anatomie 9, 413-468 (1873)

doi:10.1007/BF02956173

Minsky, M.

Microscopy apparatus

US Patent 3,013,467 (1961)

doi:10.1364/AO.27.003403

Radioactivity & Laboratory Safety

Radioactivity Principles

Becquerel, H.

Sur les radiations émises par phosphorescence

Comptes Rendus 122, 420-421 (1896)

doi:10.1021/ed005p168

Curie, M., Curie, P.

Sur une substance nouvelle radioactive, contenue dans la pechblende

Comptes Rendus 127, 175-178 (1898)

doi:10.1021/ed005p168

Rutherford, E.

The scattering of alpha and beta particles by matter and the structure of the atom

Philosophical Magazine 21, 669-688 (1911)

doi:10.1080/14786440508637080

Radioisotope Applications

Hevesy, G.

The absorption and translocation of lead by plants: A contribution to the application of the method of radioactive indicators in the investigation of the change of substance in plants

Biochemical Journal 17, 439-445 (1923)

doi:10.1042/bj0170439

Yalow, R.S., Berson, S.A.

Immunoassay of endogenous plasma insulin in man

Journal of Clinical Investigation 39, 1157-1175 (1960)

doi:10.1172/JCI104130

Neuroscience & Neural Networks

Neural Network Foundations

Hodgkin, A.L., Huxley, A.F.

A quantitative description of membrane current and its application to conduction and excitation in nerve

Journal of Physiology 117, 500-544 (1952)

doi:10.1113/jphysiol.1952.sp004764

McCulloch, W.S., Pitts, W.

A logical calculus of the ideas immanent in nervous activity

Bulletin of Mathematical Biophysics 5, 115-133 (1943)

doi:10.1007/BF02478259

Kandel, E.R., et al.

Principles of Neural Science

McGraw-Hill Education (2013)

doi:10.1016/B978-0-444-52902-2.00007-X

Electrophysiology

Neher, E., Sakmann, B.

Single-channel currents recorded from membrane of denervated frog muscle fibres

Nature 260, 799-802 (1976)

doi:10.1038/260799a0

Hamill, O.P., et al.

Improved patch-clamp techniques for high-resolution current recording from cells and cell-free membrane patches

Pflügers Archiv 391, 85-100 (1981)

doi:10.1007/BF00656997

Data Visualization & Computational Methods

Statistical Computing

R Core Team

R: A language and environment for statistical computing

R Foundation for Statistical Computing, Vienna, Austria (2023)

doi:10.1007/978-3-540-74686-7

Hunter, J.D.

Matplotlib: A 2D graphics environment

Computing in Science & Engineering 9, 90-95 (2007)

doi:10.1109/MCSE.2007.55

Bostock, M., et al.

D3: Data-Driven Documents

IEEE Transactions on Visualization and Computer Graphics 17, 2301-2309 (2011)

doi:10.1109/TVCG.2011.185

Bioinformatics Software

Cock, P.J., et al.

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Bioinformatics 25, 1422-1423 (2009)

doi:10.1093/bioinformatics/btp163

Huber, W., et al.

Orchestrating high-throughput genomic analysis with Bioconductor

Nature Methods 12, 115-121 (2015)

doi:10.1038/nmeth.3252

Gentleman, R.C., et al.

Bioconductor: open software development for computational biology and bioinformatics

Genome Biology 5, R80 (2004)

doi:10.1186/gb-2004-5-10-r80

Open Source & Community Contributions

We gratefully acknowledge the open-source community and the following technologies that power ViroDyn:

• JavaScript (ECMAScript) - for client-side processing and cross-platform compatibility
• Chart.js - for interactive data visualization and scientific plotting
• D3.js - for advanced graphics, visualizations, and custom scientific charts
• Font Awesome - for comprehensive scientific iconography
• Web Standards - HTML5, CSS3, and modern web APIs for accessibility
• Open Science Movement - for promoting transparent, reproducible research

Key Open Source Scientific Software that inspires ViroDyn's approach:

• BLAST - Basic Local Alignment Search Tool (NCBI)
• EMBOSS - European Molecular Biology Open Software Suite
• BioJS - JavaScript library for biological data visualization
• SeqAn - C++ library for sequence analysis
• Galaxy Project - Web-based platform for accessible bioinformatics
• Jupyter - Interactive computing environment for data science

Community & Feedback

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ViroDyn Bioinformatics Tool Suite

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Scientific References & Acknowledgments