They were suspended for more than an hour between Manhattan and Queens, officials said.
Riders were stranded for more than 2 hours after a 7 train got stuck near Queensboro Plaza.
Service on the 3, 4, 5, 6, A, D, E, F, G, N and R trains will be affected this weekend, the MTA said.
Officers were investigating a large duffel bag that was left unattended in front of the Myrtle Ave stop.
Work will affect the 2, 3, 4, 5, 6, 7, A, E, F, G, J, M, Q and two shuttle lines, the MTA said.
Problems at Union Square sparked widespread service disruptions on the 4, 5 and 6 trains Monday.
The B57 and B61 buses will be rerouted through Mill Street beginning Jan. 26, officials said.
The 1, 2, 3, 4, 5, 6, 7, A, C, E, F, G, J, M, N, Q, R and S lines will be affected, the MTA said.
The victim was taken to Elmhurst hospital in serious condition, FDNY says.
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