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William J. Flynn grew up as the son of a train driver in Bridgeport (Connecticut). He received his Bachelor of Arts in 1975 from the University of Rhode Island with summa cum laude. He then studied Latin American studies at the University of Arizona , from which he graduated in 1976 with a Master of Arts .

In 1977 he started working for the container company Sea-Land . First he worked in Caracas, later he was responsible for the Central America area from 1983 to 1987 from Guatemala. With the takeover of Sea-Land in 1986 by CSX Corporation, he came to this group. From the beginning of the 1990s he was responsible for the Asian market with the container ports in Hong Kong and China. From 2000 he worked in advertising for CSX Transportation and strategic planning for CSX Corporation.

In 2002 he left CSX and took over the logistics company GeoLogistics as President and Chief Executive Officer. He managed to drive the company back into profitability and to initiate the sale to an investor in 2005.

He then was CEO and President of the cargo airline Atlas Air Worldwide Holdings until January 1, 2020 . During that time, he increased revenue from $ 1.1 billion to $ 3 billion between 2009 and 2019. He has been Chairman of the Board of the airline since August 2019.

On April 15, 2020, he took over the position of President of the rail passenger transport company Amtrak, succeeding Richard Anderson .

Bill retired from Amtrak in February of 2022. In addition to NanoVapor , he is a board member and advisor to several logistics and airspace companies.