Described herein are systems using injectionless gel electrophoresis (GE), such as thermal GE (TGE), to selectively separate, concentrate, quantify, and/or otherwise analyze target analytes. Inline preconcentration and separation are demonstrated to resolve analytes, exemplified by resolving double-stranded miRNA-probe hybrids from excess single-stranded probes and analyzing multiple conformations of a protein. Microfluidic devices having a tapered channel are described, which improve detection sensitivity and separation resolution. The described separation strategy and microfluidic device designs establish injectionless gel electrophoresis as a simple, low-cost analysis method, for instance for analyzing clinical and pharmaceutical samples, including for miRNA, protein, and other biomolecular analyses.