He began his current tenure at Columbia as the founding director of the Jerome L. and Dawn Greene Infectious Disease Laboratory from 2002 to 2007, which transitioned to the John Snow Professorship he holds at present.

These molecular biological methods, including MassTag-PCR, the GreeneChip diagnostic, and High Throughput Sequencing, are a major step towards identifying and studying new viral pathogens that emerge locally throughout the globe.

A major node in a global network of investigators working to address the challenges of pathogen surveillance and discovery, Dr. Lipkin has trained over 30 internationally based scientists in these state-of-the art diagnostic techniques.

Lipkin also directs the World Health Organization Collaborating Centre for Diagnostics in Zoonotic and Emerging Infectious Diseases, the only academic center, and one of two in the US (the other is CDC), that participates in outbreak investigation for the WHO.

He is Honorary Director of the Beijing Infectious Disease Center, Chair of the Scientific Advisory Board of the Institut Pasteur de Shanghai and serves on boards of the Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, the Guangzhou Institute for Biomedicine and Health, the EcoHealth Alliance,[10] Tetragenetics, and 454 Life Sciences Corporation.

He identified AIDS-associated immunological abnormalities and inflammatory neuropathy, which he showed could be treated with plasmapheresis and demonstrated early life exposure to viral infections affects neurotransmitter function.

[19] Once it was apparent the viral infections could selectively alter behavior and steady state brain levels of neurotransmitter mRNAs, the next step was to look for infectious agents which could be used as probes to map anatomic and functional domains in the central nervous system (CNS).

[20] By the mid-1990s, it was asserted that "Borna disease is a neurotropic negative-strand RNA virus that infects a wide range of vertebrate hosts," causing "an immune-mediated syndrome resulting in disturbances in movement and behavior.

[23] After nearly two decades of inquiry, the first blinded case-controlled study of the link between BDV and psychiatric illness[24] was completed by the researchers at Columbia University's Center for Infection and Immunity in a joint effort that concluded there is no association between the two.

Lipkin noted that "it was concern over the potential role of BDV in mental illness and the inability to identify it using classical techniques that led us to develop molecular methods for pathogen discovery.

[14] It was determined potential routes for the spread of West Nile virus throughout New York (and the Eastern United States) originated from predominantly mosquitoes, but also possible from infected birds or human beings.

Advanced hospital facilities were at the greatest risk as they were most susceptible to virus transmission, so it was the "classical gumshoe epidemiology" of "contact tracing and isolation" that brought swift action against the epidemic.

"[30] This brought the development of real-time polymerase chain reaction technology, which essentially allowed for the detection of infection at earlier time points as the process, in this instance, targets the N gene sequence and amplify the analysis in a closed system.

[31] Test kits were developed with this PCR-based assay analysis[32] and 10,000 were hand-delivered to Beijing during the height of the outbreak by Lipkin, whereupon he trained local clinical microbiologists on the proper usage.

[38] Middle East respiratory syndrome (MERS) was first reported in Saudi Arabia during June 2012 when a local man was initially diagnosed with acute pneumonia and later died of kidney failure.

[39] With the rare opportunity, Lipkin's team created a mobile lab able to fit in six pieces of personal luggage and was transported from New York to Saudi Arabia via commercial flight to complete the analysis of samples.

In September 2017, the NIH awarded a $9.6 million grant to Columbia University for the "CfS for ME/CFS" intended for the pursuit of basic research and the development of tools to help both physicians and patients effectively monitor the course of the illness.

[49] Acute flaccid myelitis (AFM) is a serious condition of the spinal cord with symptoms including rapid onset of arm or leg weakness, decreased reflexes, difficulty moving the eyes, speaking, or swallowing may also occur.

In August 2019, Lipkin and Dr. Nischay Mishra published a collaborative study with the CDC in analyzing serological data for serum and cerebrospinal fluid (CSF) samples of AFM patients.

[51][52] In October, the University of California, San Francisco published a separate collaborative study with the CDC that confirmed the presence of antibodies to enterovirus in AFM patient CSF samples using phage display (VirScan).

He said that a series of government missteps helped spread the virus around the world very rapidly, and criticized the US and UK's responses, calling them slow, and blamed insufficient and inadequate testing and tracing for rising fatality numbers.

In the US, he singled out as an issue what he saw as an inconsistency in advice, including by president Trump, and highlighted the need for national leadership, while acknowledging states had the ability to make decisions in certain areas.

[57] After his trip to China, Lipkin maintained links with Lu Jiahai, his research partner at Sun Yat-sen University in Guangzhou, and Zhong Nanshan, to try to establish the origins of the virus.

[61] Their efforts, aimed at finding out whether the virus emerged in other parts of China and circulated before it was first discovered in Wuhan in December, include antibody tests of nationwide blood bank samples from pneumonia patients which predate the pandemic, which led to a collaboration with the Chinese Centers for Disease Control and Prevention.

The international research team also began studying blood samples from different wild animals which it deemed potential origins of the virus, in order to understand animal-to-human transmission.

In the example of Ebola, which is incapable of airborne transfer, Lipkin believes that "researchers could make a case for the need to determine how the virus could evolve in nature by engineering a more dangerous version in the lab."