In the late 1980s and early 1990s, Baltimore played a prominent role in news stories about a case of alleged research misconduct by an MIT collaborator in another laboratory, Thereza Imanishi-Kari.
In 1975 at the age of 37, he shared the Nobel Prize for Physiology or Medicine with Howard Temin and Renato Dulbecco. The citation reads, "for their discoveries concerning the interaction between tumour viruses and the genetic material of the cell." At the time, Baltimore's greatest contribution to virology was his discovery of reverse transcriptase (RTase). Independently about the same time, Mizutani & Temin had also discovered RTase. RTase is essential for the reproduction of retroviruses such as HIV.
Also in 1975, Baltimore was an organizer of the Asilomar conference on recombinant DNA. In 1982, Baltimore was appointed the founding director of MIT's Whitehead Institute, where he remained through June 1990.
In 1981 Baltimore and Vincent Racaniello, a post-doctoral fellow in his laboratory, used recombinant DNA technology to generate a plasmid encoding the genome of poliovirus, an animal RNA virus. The plasmid DNA was introduced into cultured mammalian cells and infectious poliovirus was produced. The infectious clone, DNA encoding the genome of a virus, is a standard technique used today in the study of virology.
Baltimore then relocated to New York City and assumed the office of the president of Rockefeller University 1 July. After resigning the office 3 December 1991, Baltimore remained on the Rockefeller U. faculty and continued research until Spring 1994. He then rejoined the MIT faculty.
Baltimore has had profound influence on national policy concerning recombinant DNA research and the AIDS epidemic. He has trained many doctoral students and postdoctoral fellows, several of whom have enjoyed quite notable and distinguished research careers. Dr. Baltimore is a member of the Bulletin of the Atomic Scientists' Board of Sponsors, National Academy of Sciences USA (NAS), NAS Institute of Medicine (IOM), Amgen, Inc. Board of Directors, BB Biotech AG Board of Directors, National Institutes of Health (NIH) AIDS Vaccine Research Committee (AVRC), and numerous other organizations and their boards. He is married to Dr. Alice S. Huang.
In 1986, while a Professor of Biology at MIT and Director at Whitehead, Baltimore co-authored a scientific paper on immunology with Thereza Imanishi-Kari (an Assistant Professor of Biology who had her own laboratory at MIT) as well as four others. A postdoctoral fellow in Imanishi-Kari's laboratory, Dr. Margot O'Toole, who was not an author, reported concerns about the paper, ultimately accusing Imanishi-Kari of fabricating data in a cover-up. Baltimore, however, refused to retract the paper.
O'Toole soon dropped her challenge but the NIH, which had funded the contested paper's research, began investigating. Representative John Dingell (D-MI) also aggressively pursued it, eventually calling in U.S. Secret Service (USSS; U.S. Treasury) document examiners.
In a draft report dated March 14, 1991 and based mainly on USSS forensics findings, NIH's fraud unit, then called the Office of Scientific Integrity (OSI), accused Dr. Imanishi-Kari of falsifying and fabricating data. It also criticized Baltimore for failing to embrace O'Toole's challenge. . In less than a week, the report was leaked to the press. Baltimore and three co-authors then retracted the paper; Imanishi-Kari and Moema H. Reis did not sign the retraction.
Amid concerns raised by his prominent mentions in connection with this scandal, Dr. Baltimore resigned as President of Rockefeller University. (After leaving Rockefeller, Baltimore rejoined the MIT Biology faculty.)
In July 1992, however, the US Attorney for the District of MD, who had been investigating the case, announced he would bring neither criminal nor civil charges against Imanishi-Kari. In October 1994, however, OSI's successor, the Office of Research Integrity (ORI; HHS) found Imanishi-Kari guilty on 19 counts of research misconduct, basing its conclusions largely on Secret Service analysis of laboratory notebooks.
An HHS appeals panel began meeting in June 1995 to review all charges in detail. In June 1996 the panel ruled that the ORI had failed to prove even one of its 19 charges. Citing also repeated instances where Dr. O'Toole's allegations were "not credible", the panel dismissed all charges against Imanishi-Kari. Furthermore, as their final report stated, the HHS panel " found that much of what ORI presented was irrelevant, had limited probative value, was internally inconsistent, lacked reliability or foundation, was not credible or not corroborated, or was based on unwarranted assumptions." Neither OSI nor ORI ever accused Baltimore of research misconduct.
Yale University mathematician and AIDS denialist Serge Lang played a prominent role in public criticisms of Baltimore over this case. Lang's "Questions of Scientific Responsibility: The Baltimore Case was published in 1993, before the HHS report establishing Imanishi-Kari's innocence. Lang's study is reprinted and updated in his book, Challenges) Historian of science Daniel Kevles recounts the affair but is sympathetic to Baltimore and Imanishi-Kari in his 1998 book, The Baltimore Case Baltimore has also written his own analysis.
Baltimore has been both praised and criticized for his actions in this matter.
President Bill Clinton awarded Baltimore the National Medal of Science in 1999 for his numerous contributions to the scientific world. 8 June 2004 Rockefeller U. conferred upon Baltimore its highest honor, Doctor of Science (honoris causa).
In October 2005 Baltimore resigned the office of the president. "‘This is not a decision that I have made easily,’ Baltimore announced to the Caltech trustees, faculty, staff, and students, ‘but I am convinced that the interests of the Institute will be best served by a presidential transition at this particular time in its history...’ Former Georgia Tech Provost Dr. Jean-Lou Chameau succeeded Baltimore as President of Caltech. Dr. Baltimore remains the Millikan Professor of Biology at Caltech and is an active member of the Institute's community.
Soon after Baltimore's resignation as President, and at his request, Caltech began investigating the work Dr. Luk van Parijs had conducted while a postdoc in Baltimore's laboratory. Van Parijs first came under suspicion at MIT, for work done after he had left Baltimore's lab. After van Parijs had been fired by MIT, his doctoral supervisor also noted problems with work van Parijs did at Brigham and Women's, before leaving Harvard to go to Baltimore's lab. Concluding in March 2007, the Caltech investigation found van Parijs alone committed research misconduct and that four papers co-authored by Baltimore, van Parijs, and others require correction.