José Manuel da Costa Alves Marques graduated in Computer Science Engineering from Universidade Nova de Lisboa in 1977, after taking the first 3 years in Electrical Engineering at IST. This Bologna-style course was the first in Computer Science and Engineering in the country. With a scholarship from the French government, he obtained his PhD in Computer Architecture from Institut National Polytechnique de Grenoble in 1980. He achieved Aggregation at Instituto Superior Técnico in 1988.

Following his PhD, he was associated with VLSI connected companies in France. However, a contact with Prof. Tribolet, who was establishing the structure of INESC, led him to return to Portugal where he became the first employee at INESC.

In 1981, he started his activity at Instituto Superior Técnico. Leveraging his teaching experience at UNL and his PhD, he proposed the Computers specialization for the Master's in Electrical and Computer Engineering (MEEC) in 1982. This profile introduced a set of foundational computer science and engineering disciplines at Técnico.

In 1989, he proposed the Bachelor's in Computer Science and Engineering (LEIC) with contributions from various departments, particularly DEM and DM,  although its core discipline set came from the computers profile of MEEC.

He established the scientific area of Architecture and Operating Systems, which has remained one of the cornerstones of computer science engineering education. Among numerous courses he created and taught, special mention goes to the Operating Systems and Distributed Systems courses, for both of which he co-authored textbooks with several professors in the field. More recently, a MOOC for operating systems was developed, covering the entire course, serving as an experimental tool for Técnico's courses using digital technologies.

At INESC, he was the National Director from 1990 to 2000, responsible for the Computers and Information Systems area. Starting in 1991, he conceived and coordinated a wide range of technological transfer infrastructures in computer technology, financed by the PEDIP program.

He has been an administrator at AITEC - Tecnologias de Informação, SA, from March 1990 to the present day. AITEC was responsible for creating over 60 Technology-Based Companies in the areas of Information Technologies and Electronics, standing out as a unique case in seed capital in Portugal.

He was a founding member and proponent for the establishment of the Department of Computer Science and Engineering (DEI) in 1997. He led the preparatory work in 1997 and the first semester of 1998, including negotiations and adjustments,  that were concluded in June 1998 with the approval from the Coordinating Scientific Council. The new Department's activity began in the academic year 98/99.

He has been the President of the Board of Directors at Link Consulting since its establishment in 1999 until today. This company, which is among the leading national consultancy firms with significant technological involvement in the field of information technologies, has a history of innovation closely linked to the market it serves.

On October 29, 2024, he was honoured with the title of Emeritus Professor of Universidade de Lisboa.