Directed-assembly of nanowire-based devices will enable the development of integrated circuits with new functions that extend well beyond mainstream digital logic. For example, nanoelectromechanical resonators are very attractive for chip-based sensor arrays because of their potential for ultrasensitive mass detection. In this letter, we introduce a new bottom-up assembly method to fabricate large-area nanoelectromechanical arrays each having over 2,000 single-nanowire resonators. The nanowires are synthesized and chemically functionalized before they are integrated onto a silicon chip at predetermined locations. Peptide nucleic acid probe molecules attached to the nanowires before assembly maintain their binding selectivity and recognize complementary oligonucleotide targets once the resonator array is assembled. The two types of cantilevered resonators we integrated here using silicon and rhodium nanowires had Q-factors of approximately 4,500 and approximately 1,150, respectively, in vacuum. Taken together, these results show that bottom-up nanowire assembly can offer a practical alternative to top-down fabrication for sensitive chip-based detection.