About Us

We are a small bioinformatics consulting company founded by Alfred Simkin and Charlie Simkin that specializes in teaching, training, and novel pipeline development. We strive to be thoughtful, patient, and careful listeners, and to let our clients guide us with the skills, questions, or tools they are most interested in exploring. In our training, rather than adopting a one-size-fits-all approach, our goal is to listen carefully to the learning needs of our clients, and then help them take ownership of their data by empowering learners to write their own customized tools, spreading their knowledge to additional learners. In our pipeline development, rather than offering pre-built solutions, we strive to write code that is customized to our users’ needs and simple to follow. We have strong core competencies with most bioinformatics tools, but we’re also willing to explore new topics and enjoy writing algorithms that solve new types of problems. We try to approach each problem with the recognition that every person has different skills and needs, and that everyone has something of value to contribute.

Alfred is an Assistant Professor at Brown University, and is physically located in Raleigh, North Carolina, where he collaborates with the IDEEL research consortium at UNC Chapel Hill to develop software for large scale amplicon sequencing of drug resistance mutations in malaria, mainly through the Seekdeep and MIPTools software packages.

We’ve also included a link to Alfred’s Resume.

Alfred’s specialties are teaching, Python, and automated pipeline development with Snakemake. Alfred also has experience with RNA sequence expression analysis, algorithm development, software containerization, and simulation, among other skills. You can visit our past projects page for examples of problems we have solved in the past.

Alfred completed a PhD in molecular evolution at Umass Chan Medical School in 2014, working under Jeff Jensen, Fen-Biao Gao, and William Theurkauf, studying the evolution of noncoding RNA molecules from the piRNA and miRNA pathways. This was followed by a postdoctoral fellowship with Andrew Grimson at Cornell University where he developed a method for simulating neutrally evolving 3′ UTR sequences to model the expected turnover rates of miRNA binding sites. Alfred taught Genetics lecture and lab for 4 and a half years at Elon University as a tenure track assistant professor before working to establish a bioinformatics core as a research professor at Umass Chan Medical school. Alfred spent a brief time working as a staff scientist in the genomics group at IDEXX laboratories before joining Brown University in November of 2022.