Scientific LiteratureBehind Our Training
Our CRISPR/Cas9 and synthetic biology curriculum is grounded in peer-reviewed science. Below are the key papers, preprints, and resources that form the reading foundation of our training programs. Students are expected to read the required papers before advancing.
Papers marked with a category note are required reading for the relevant training module. All other citations are recommended supplementary material.
CRISPR Fundamentals
The foundational papers every student must understand before working with Cas9 systems. These represent the seminal discoveries that defined modern gene editing.
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F
DOI: 10.1016/j.cell.2015.09.038
Describes Cas12a (Cpf1), a widely used alternative to Cas9.
Protein Engineering
Core literature on engineering proteins for therapeutic and research applications, including base editing, prime editing, and protein design using machine learning.
Search-and-replace genome editing without double-strand breaks or donor DNA
Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, Liu DR
DOI: 10.1038/s41586-019-1711-4
Prime editing -- one of the most significant advances in precision genome editing.
Synthetic Biology
Literature covering the design and construction of biological parts, devices, and systems -- the engineering discipline underlying our training programs.
SHERLOCK: Nucleic acid detection with CRISPR nucleases
Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Feng Zhang
DOI: 10.1126/science.aam9321
CRISPR-based diagnostics platform with direct applications in mobile healthcare.
Computational Biology
Papers covering bioinformatics tools, AI-driven protein modeling, and computational methods students use in our training curriculum. Includes key preprints from bioRxiv.
Evolutionary-scale prediction of atomic-level protein structure with a language model
Lin Z, Akin H, Rao R, Hie B, Zhu Z, Lu W, Smetanin N, Verkuil R, Kabeli O, Shmueli Y, et al.
DOI: 10.1126/science.ade2574
ESM-2 and ESMFold -- protein language models used in our computational training modules.
Benchmarking of CRISPR-Cas9 guide RNA design tools
Haeussler M, Schonig K, Eckert H, Eschstruth A, Mianne J, Renard JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly JS, Concordet JP
DOI: 10.1186/s13059-016-1012-2
Guide RNA design benchmarking study -- directly relevant to our design curriculum.
Ethics & Policy
Students are expected to engage seriously with the ethical dimensions of gene editing. These papers and reports form the foundation of our ethics module.
Open Resources & Databases
In addition to the peer-reviewed literature above, our training programs make use of several open-access databases and community resources.
iGEM Parts Registry
The international Genetically Engineered Machine Foundation's registry of standard biological parts. Students use this for device design exercises.
NCBI Gene & Nucleotide
National Center for Biotechnology Information databases including GenBank, PubMed, and BLAST -- all used in our bioinformatics modules.
Addgene Plasmid Repository
Nonprofit plasmid repository. Students reference Addgene plasmid records when reviewing Cas9 and base editor construct designs.
UniProt Protein Database
Comprehensive protein sequence and functional information database. Core reference for protein engineering coursework.
RCSB Protein Data Bank
Archive of 3D structural data for proteins and nucleic acids. Used in our molecular modeling and structure visualization sessions.
bioRxiv Preprint Server
Cold Spring Harbor Laboratory's preprint server for biology. Specific preprints cited above (OpenCRISPR-1, RoseTTAFold AA) are drawn from here.
Academic Disclosure
Helix BioMedical is a 508(c)(1)(a) faith-based healthcare organization. Our synthetic biology and CRISPR/Cas9 training programs are non-accredited educational offerings and do not confer academic degrees or professional certifications. Citations listed on this page are provided for educational reference. Students are encouraged to access papers through their institutional library, PubMed, or author preprint pages. Helix BioMedical does not claim ownership of any cited works.
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Students accepted into our CRISPR access program receive a full reading list and faculty guidance through the literature. Request access to get started.