Pehr received his PhD degree in Biological Chemistry from Harvard Medical School, based on work performed at MIT in the laboratory of Peter Kim. As a graduate student, he discovered rules for predicting the structure of a universal molecular joint, the coiled‑coil motif, based on its amino‑acid sequence. These rules have impacted diverse areas of science, ranging from genome mining and protein therapeutics to nanomaterials. Additionally, he was a pioneer in the field of computational protein design --- engineering in silico the first protein‑fold family that had not previously been observed in nature, and experimentally verifying its existence.

Following postdoctoral training in combinatorial synthetic organic chemistry with Peter Schultz at Berkeley, Pehr started an independent group in the Stanford Biochemistry department. There, his lab laid a foundation for the field of directed chemical evolution. They invented a general mechanism by which DNA can program the synthesis and structure of small molecules, bringing synthetic organic chemistry under genetic control. This work enabled small-molecule discovery by "evolution in a test tube", and has been used to engineer ligands, inhibitors and substrates for a variety of protein targets. The lab's technology for creating DNA‑programmed and DNA‑tagged chemical libraries is now practiced, in various forms, by all of the large pharmaceutical companies.

Pehr's lab has also pursued the question of how protein and nucleic‑acid machines operate in complex environments. A major goal has been to measure the high‑resolution structures, dynamics and interactions of proteins directly inside cells. In related work, the lab has developed X‑ray scattering interferometry, a technique for determining the molecular elasticity and conformational ensembles of macromolecules and designed nanostructures.

Recently, Pehr's lab began studying the molecular basis for self‑organization and maintenance of animal tissues, and how these molecular processes change in the context of disease. They are developing imaging tools that read out the molecular program at play in each cell of a complex tissue. These tools are directly applicable to the clinical diagnosis of human disease and, in the context of basic research, can reveal how genomes encode multi‑cellular structures.

While at Stanford, Pehr has been a MacArthur Fellow, a Searle Scholar, a Burroughs Wellcome Fund Young Investigator and a Lucille Packard Charitable Trust Terman Fellow. He was also recognized by the MIT Technology Review Magazine as one of the top 100 innovators under the age of 35. His work has been recognized with an NIH Director's Pioneer Award and an ASMBM Young Investigator Award.