Dirks was the first graduate student in Niles Pierce's research group at the California Institute of Technology, where his dissertation work was on algorithms and computational tools to analyze nucleic acid thermodynamics and predict their structure.

[1] His mother Suree, a Thai Chinese woman who worked in a bank at the time, his father, Michael Dirks, was a mathematics teacher at the International School Bangkok recruited from the United States.

[6] Shortly after graduation Robert and three of his classmates were one of three high school winners of the ExploraVision national scientific contest, earning them and their families a trip to Washington, D.C.

[6] He graduated summa cum laude and with Phi Beta Kappa honors,[9] from Wabash in 2000[1] with a double major in chemistry and math.

[11] Dirks wrote the initial code for the NUPACK suite of nucleic acid design and analysis tools,[12] which generates base pairing probabilities through calculation of the statistical partition function.

Dirks also developed an algorithm capable of efficiently handling certain types of pseudoknots, a class of structure that is more computationally intensive to analyze, although NUPACK only implements this ability for single RNA strands.

[13][14][15] His experimental work pioneered the hybridization chain reaction method, the first demonstration of the self-assembly of nucleic acid structures conditional on a molecular input.

[19] Dirks then worked at D. E. Shaw Research in Manhattan to develop methods for computational protein structure prediction[20] for the design of new drugs, beginning in 2006.

He rose early to commute to his job via Metro-North Railroad's Harlem Line, and returned late but devoted as much time as possible on evenings and weekends to his children.

He was riding home in the front car of his train, which his brother says he likely did to take advantage of the quieter atmosphere,[3] when it struck an SUV at a grade crossing north of Valhalla, 5 miles (8.0 km) south of the Chappaqua station.