The 1, 2, 3, 5, 6, 7, A, C, D, E, F and 42nd Street Shuttle will all be affected.
A 33-year-old woman was robbed by two men who took her purse on Greene Street, police said.
Work is scheduled along the 1, 2, 4, 5, 6, A, C, E, F, G, N, R and S lines.
The A, C and F trains will be shut down between Manhattan and Brooklyn in the future, the MTA said.
At 5 a.m. Thursday, 1 train service to South Ferry resumed following Hurricane Sandy.
The 1, 2, and 3 trains will shut down from 10 p.m. to 5 a.m. for four nights beginning Monday, June 25.
The closures are part of the FASTTRACK program, which shuts downs stations to repair and clean them.
A water main break suspended service on the 1-2-3 subway lines Downtown, MTA officials said.
DOT said the new select bus service has increased rider traffic along the M15 line by 30 percent.
The public will get the chance to weigh in on the new First and Second Avenue express buses Wednesday.
There will be no 7 train service from Times Square to Queensboro Plaza and disruptions on the 1 train uptown and downtown.
The city has reportedly handed out more than 15,200 tickets to drivers who trespass in the Select Bus Service lanes.
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