User:Patricia at GMMB/Joseph DeRisi Career

DeRisi has been a faculty member of the UCSF biochemistry and biophysics department since 1999. As of 2022 he is a professor of biochemistry and biophysics and is also the director of UCSF's Sandler Program for Breakthrough Biomedical Research.{{Cite web| title = Sandler Program for Breakthrough Biomedical Research: Our Leadership | work = UCSF Sandler Program for Breakthrough Biomedical Research | accessdate = 2022-10-28| url =https://pbbr.ucsf.edu/about/our-leadership}}{{Cite news| last = Hopkin| first = Karen| title = SARS, Malaria, and the Microarray| work = The Scientist Magazine| accessdate = 2022-10-17| date = 2005-11-20| url = https://www.the-scientist.com/reverse-transcript/sars-malaria-and-the-microarray-48134}}

DeRisi is known for printing the first whole-genome expression array,{{cite journal | pmid = 9381177 | volume=278 | title=Exploring the metabolic and genetic control of gene expression on a genomic scale | year=1997 | journal=Science | pages=680–6 | last1 = DeRisi | first1 = JL | last2 = Iyer | first2 = VR | last3 = Brown | first3 = PO | issue=5338 | doi = 10.1126/science.278.5338.680| bibcode=1997Sci...278..680D | citeseerx = 10.1.1.335.7937 }} performing the first broad analysis of differential gene expression in cancer cells,{{cite journal | pmid = 8944026 | doi=10.1038/ng1296-457 | volume=14 | title=Use of a cDNA microarray to analyse gene expression patterns in human cancer | year=1996 | journal=Nat Genet | pages=457–60 | last1 = DeRisi | first1 = J | last2 = Penland | first2 = L | last3 = Brown | first3 = PO | last4 = Bittner | first4 = ML | last5 = Meltzer | first5 = PS | last6 = Ray | first6 = M | last7 = Chen | first7 = Y | last8 = Su | first8 = YA | last9 = Trent | first9 = JM| issue=4 | s2cid=23091561 }} profiling gene expression throughout the lifecycle of the malaria-causing protozoan Plasmodium falciparum,{{citation

| last1 = Llinas | first1 = Manuel

| last2 = Bozdech | first2 = Zbynek

| last3 = Wong | first3 = Edith D.

| last4 = Adai | first4 = Alex T.

| last5 = Derisi | first5 = Joseph L.

| year = 2006

| title = Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains

| journal = Nucleic Acids Research

| volume = 34

| issue = 4

| pages = 1166–73

| doi = 10.1093/nar/gkj517

| pmid = 16493140

| pmc = 1380255

}} genomic characterization of the SARS-CoV-1 virus,{{citation

| last1 = Rota | first1 = Paul A.

| last2 = Oberste | first2 = M. Steven

| last3 = Monroe | first3 = Stephan S.

| last4 = Nix | first4 = W. Allan

| last5 = Campagnoli | first5 = Ray

| last6 = Icenogle | first6 = Joseph P.

| last7 = Penaranda | first7 = Silvia

| last8 = Bankamp | first8 = Bettina

| last9 = Maher | first9 = Kaija

| last10 = Bellini | first10 = William J.

| year = 2003

| title = Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome

| journal = Science

| volume = 300

| issue = 5624

| pages = 1394–9

| doi = 10.1126/science.1085952

| pmid = 12730500

| bibcode = 2003Sci...300.1394R

| doi-access = free

}} and pioneering virus discovery using gene hybridization arrays and DNA sequencing technologies.{{cite journal | pmid = 12429852 | doi=10.1073/pnas.242579699 | volume=99 | title=Microarray-based detection and genotyping of viral pathogens | pmc=137777 | year=2002 | journal=Proc Natl Acad Sci U S A | pages=15687–92 | last1 = Wang | first1 = D | last2 = Coscoy | first2 = L | last3 = Zylberberg | first3 = M | last4 = Avila | first4 = PC | last5 = Boushey | first5 = HA | last6 = Ganem | first6 = D | last7 = DeRisi | first7 = JL| issue=24 | bibcode=2002PNAS...9915687W | doi-access=free }}

In his early career, DeRisi was a pioneer of microarrays, and designed and built both hardware and software for microarrays. He was a proponent of open access to microarray technology,{{Cite news| volume = Summer 2002| last = Adams| first = Amy| title=PhD alum Joe DeRisi brings innovation to the masses | work = Stanford Medicine Magazine| accessdate = 2022-10-18| url = https://sm.stanford.edu/archive/stanmed/2002summer/md-populist.html}} and maintained a website with software and protocols for microarray operations.{{Cite news|last = Kahn| first = Jennifer| title = New Chips on the Block | work = The Economist Technology Quarterly| accessdate = 2022-10-12| date = 2006-12-02| url = https://www.economist.com/sites/default/files/special-reports-pdfs/8312145_0.pdf}} He is also a proponent of open access publishing.

In 2002, DeRisi and his research collaborator David Wang developed the ViroChip, a DNA microarray that could be used to rapidly identify viruses in a sample of blood or tissue. He used the tool to help identify the SARS-CoV-1 virus in 2003. In 2004, DeRisi was named a MacArthur fellow (the "Genius" award) for his work with ViroChip and genomic diagnostic techniques.{{Cite news| last = Russell| first = Sabin| title = THE MACARTHUR GRANTS: BAY AREA PROFILES / His quick work on SARS gave crucial answers| work = SF Gate| accessdate = 2022-10-28| date = 2004-09-28| url = https://www.sfgate.com/bayarea/article/THE-MACARTHUR-GRANTS-BAY-AREA-PROFILES-His-2721757.php}}{{Cite web| title = Joseph DeRisi| work = Macarthur Foundation| accessdate = 2022-11-01| url = https://www.macfound.org/fellows/class-of-2004/joseph-derisi}}

DeRisi became a Howard Hughes Medical Institute (HHMI) investigator in 2005, and received financial support from HHMI for his research.{{Cite web| last = O'Brien| first = Jennifer | title = Two UCSF Scientists Named Howard Hughes Medical Institute Investigators {{!}} UC San Francisco| work = UCSF| accessdate = 2022-10-31| date = 2005-03-22| url = https://www.ucsf.edu/news/2005/03/101288/two-ucsf-scientists-named-howard-hughes-medical-institute-investigators}} He remained an investigator until 2016.{{Cite web| title = Joseph L. DeRisi| work = HHMI| format = Text | accessdate = 2022-10-31| url = https://www.hhmi.org/scientists/joseph-l-derisi}}

DeRisi and his colleagues employ metagenomic next-generation sequencing (mNGS) for applications including to identify the causal agents in cases of infectious encephalitis and meningitis and to discriminate between autoimmune and infectious causes, diagnosing cases that are difficult to decipher using traditional clinical laboratory techniques.{{Cite news| issn = 0362-4331| last = Kahn| first = Jennifer| title = The Disease Detective| work = The New York Times| accessdate = 2022-10-12| date = 2021-06-03| url = https://www.nytimes.com/2021/06/03/magazine/metagenomic-sequencing.html}}{{Cite news| last = Yong| first = Ed| title = A Simpler Way to Get to the Bottom of Mysterious Illnesses in Poor Countries| work = The Atlantic| accessdate = 2022-11-01| date = 2018-10-16| url = https://www.theatlantic.com/science/archive/2018/10/dashboard-disease-detectives/573034/}} Using metagenomic sequencing, DeRisi has identified disease-causing viruses in humans, and in animals ranging from parrots and cockatiels to honeybees and boa constrictors.{{cite journal |last1= Dubey|first1= Divyanshu |last2= Mandel-Brehm|first2= Caleigh |date= July 4, 2019|title= Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis|journal= The New England Journal of Medicine|volume= 381 |issue= 1 |pages= 47–54 |doi= 10.1056/NEJMoa1816721|pmid= 31269365 |pmc= 6800027 |doi-access= free}} He and a research partner, Don Ganem, have identified a parasite, Nosema ceranae, that appears to be responsible for colony collapse among honeybees.{{Cite web |title=UCSF Sleuths Identify Suspects in Mystery of Vanishing Honeybees |url=https://www.ucsf.edu/news/2007/04/7229/ucsf-sleuths-identify-suspects-mystery-vanishing-honeybees |access-date=October 28, 2022 |website=UCSF.com}} He has also de-bunked the relation of viruses to certain subsets of human cancer.{{cite web |last= Allday |first= Erin |date= July 15, 2019 |title= Rare disease discovery: Antibodies fighting cancer go on to attack brain | url= https://www.sfchronicle.com/bayarea/article/Rare-disease-discovery-Antibodies-fighting-14094823.php| website= sfchronicle.com | access-date= May 1, 2021}}

DeRisi and his colleague Dr. Michael Wilson used a phage display to screen antibody samples from patients with autoimmune symptoms against a library of human proteins, allowing them to identify a cancer-associated autoantigen that is the cause of the symptoms.{{Cite journal| doi = 10.1056/NEJMoa1816721| issn = 0028-4793| volume = 381| issue = 1| pages = 47–54| last1 = Mandel-Brehm| first1 = Caleigh| last2 = Dubey| first2 = Divyanshu| last3 = Kryzer| first3 = Thomas J.| last4 = O’Donovan| first4 = Brian D.| last5 = Tran| first5 = Baouyen| last6 = Vazquez| first6 = Sara E.| last7 = Sample| first7 = Hannah A.| last8 = Zorn| first8 = Kelsey C.| last9 = Khan| first9 = Lillian M.| last10 = Bledsoe| first10 = Ian O.| last11 = McKeon| first11 = Andrew| last12 = Pleasure| first12 = Samuel J.| last13 = Lennon| first13 = Vanda A.| last14 = DeRisi| first14 = Joseph L.| last15 = Wilson| first15 = Michael R.| last16 = Pittock| first16 = Sean J.| title = Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis| journal = New England Journal of Medicine| accessdate = 2022-11-01| date = 2019-07-04| url = https://doi.org/10.1056/NEJMoa1816721| pmid = 31269365}}

DeRisi’s lab at UCSF also conducts research to understand the genetics of the malaria-causing pathogen Plasmodium falciparum, the causative agent of the most deadly form of human malaria.{{Cite news| issn = 0362-4331| last = Wade| first = Nicholas| title = New Chink in the Armor Of the Malaria Parasite | work = The New York Times| accessdate = 2022-11-01| date = 2003-08-12| url = https://www.nytimes.com/2003/08/12/science/new-chink-in-the-armor-of-the-malaria-parasite.html}} DeRisi's group has developed candidate drugs to cure malaria.{{cite journal |last1= Jiménez-Díaz |first1= María |last2= Ebert|first2= Daniel |date= December 1, 2014|title= (+)-SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium|journal= Proceedings of the National Academy of Sciences of the United States of America|volume= 111 |issue= 50 |pages= E5455-62 |doi= 10.1073/pnas.1414221111|pmid= 25453091 |pmc= 4273362 |bibcode= 2014PNAS..111E5455J |doi-access= free}} In 2011, the group determined the function of the apicoplast, a unique organelle in apicomplexans, identifying the target of an anti-malarial drug that was a preclinical candidate.{{Cite news| last = Palca| first = Joe| title = A Remnant From Algae In Malaria Parasite May Prove Its Weakness| work = NPR| accessdate = 2022-11-01| date = 2011-08-30| url = https://www.npr.org/sections/health-shots/2011/08/31/140069350/a-remnant-from-algae-in-malaria-parasite-may-prove-its-weakness}}{{Cite journal| doi = 10.1371/journal.pbio.1001138| issn = 1545-7885| volume = 9| issue = 8| pages = –1001138| last1 = Yeh| first1 = Ellen| last2 = DeRisi| first2 = Joseph L.| title = Chemical Rescue of Malaria Parasites Lacking an Apicoplast Defines Organelle Function in Blood-Stage Plasmodium falciparum| journal = PLOS Biology| accessdate = 2022-11-01| date = 2011-08-30| url = https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001138}}

In 2016, DeRisi became the co-president of the newly established CZ Biohub, alongside Stephen Quake.{{Cite journal| doi = 10.1038/s41587-020-0685-y| issn = 1546-1696| volume = 38| issue = 10| pages = 1116ñ1120| last = DeFrancesco| first = Laura| title = The making of the Biohub| journal = Nature Biotechnology| accessdate = 2022-05-13| date = 2020-09-11| url = https://www.nature.com/articles/s41587-020-0685-y}} After joining CZ Biohub, DeRisi established a team of developers to create a cloud-based metagenomic diagnostic platform based on code from his lab at UCSF. The platform, then named IDSeq, was initially launched for testing by a small group in 2018.{{Cite news| issn = 1059-1028| last = Molteni| first = Megan| title = A Disease Tracker Backed by Gates and Zuckerberg Tackles Covid-19| work = Wired |date = 2020-03-10| accessdate = 2022-11-01| url = https://www.wired.com/story/a-disease-tracker-backed-by-gates-and-zuckerberg-tackles-covid-19/}} The development and computing costs were backed by the Chan Zuckerberg Initiative and CZ Biohub. The platform is used to rapidly identify pathogens from metagenomic sequencing data,{{Cite journal|last1=Kalantar|first1=Katrina L|last2=Carvalho|first2=Tiago|last3=de Bourcy|first3=Charles F A|last4=Dimitrov|first4=Boris|last5=Dingle|first5=Greg|last6=Egger|first6=Rebecca|last7=Han|first7=Julie|last8=Holmes|first8=Olivia B|last9=Juan|first9=Yun-Fang|last10=King|first10=Ryan|last11=Kislyuk|first11=Andrey|date=October 2020|title=IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring|journal=GigaScience|volume=9|issue=10|doi=10.1093/gigascience/giaa111|pmid=33057676|pmc=7566497|issn=2047-217X|doi-access=free}} and as of 2022 is known as CZ-ID.{{Cite journal| doi = 10.1038/s41467-022-31600-0| issn = 2041-1723| volume = 13| issue = 1| pages = 3937| last1 = Mick| first1 = Eran| last2 = Tsitsiklis| first2 = Alexandra| last3 = Spottiswoode| first3 = Natasha| last4 = Caldera| first4 = Saharai| last5 = Serpa| first5 = Paula Hayakawa| last6 = Detweiler| first6 = Angela M.| last7 = Neff| first7 = Norma| last8 = Pisco| first8 = Angela Oliveira| last9 = Li| first9 = Lucy M.| last10 = Retallack| first10 = Hanna| last11 = Ratnasiri| first11 = Kalani| last12 = Williamson| first12 = Kayla M.| last13 = Soesanto| first13 = Victoria| last14 = Simões| first14 = Eric A. F.| last15 = Smith| first15 = Christiana| last16 = Abuogi| first16 = Lisa| last17 = Kistler| first17 = Amy| last18 = Wagner| first18 = Brandie D.| last19 = DeRisi| first19 = Joseph L.| last20 = Ambroggio| first20 = Lilliam| last21 = Mourani| first21 = Peter M.| last22 = Langelier| first22 = Charles R.| title = Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children| journal = Nature Communications| accessdate = 2022-11-30| date = 2022-07-08| url = https://www.nature.com/articles/s41467-022-31600-0}}

In 2020, early in the COVID-19 pandemic, DeRisi led a team that turned an empty lab space adjacent to the CZ Biohub into a CLIA-certified COVID-19 testing facility in eight days.{{cite web | date= October 21, 2020 |title= A Model for the Nation: Building a COVID-19 Testing Lab in Only Eight Days | url= https://chanzuckerberg.com/blog/a-model-for-the-nation-building-a-covid-19-testing-lab-in-only-eight-days/ | website= chanzuckerberg.com | access-date= May 1, 2021}}{{cite news |last= Lewis |first= Michael |date= April 16, 2020 |title= The Covid Test Lab That Could Save America | url= https://www.bloomberg.com/opinion/articles/2020-04-17/chan-zuckerberg-biohub-is-ready-for-coronavirus-tests-to-come | website= bloomberg.com | access-date= May 1, 2021}} CLIAhub became one of the nation's leading COVID-19 testing centers, processing thousands of tests per day and becoming a model for the nation.{{cite news |last= Lewis |first= Michael |date= May 8, 2020 |title= Armed With Swabs, Covid Hunters Stalk Their Prey | url= https://www.bloomberg.com/opinion/articles/2020-05-08/covid-19-hunters-of-chan-zuckerberg-biohub-stalk-mission-district | website= bloomberg.com | access-date= May 1, 2021}}{{cite news |last= Lewis |first= Michael |date= June 21, 2020 |title= The New Weapon in the Covid-19 War| url= https://www.bloomberg.com/graphics/2020-opinion-chan-zuckerberg-biohub-covid-tracing/| website= bloomberg.com | access-date= May 1, 2021}}{{cite news |last= Lewis |first= Michael |date= April 7, 2020 |title= In Berkeley, Hunting Toilet Paper and Dodging Hikers| url= https://www.bloomberg.com/opinion/articles/2020-04-08/virus-robs-america-of-toilet-paper-nasal-swabs-and-tom-dempsey| website= bloomberg.com | access-date= May 1, 2021}} DeRisi’s early warning of the pandemic and development of rapid testing technology was documented by Michael Lewis in his book The Premonition: A Pandemic Story.{{Cite news| issn = 0362-4331| last = Confessore| first = Nicholas| title = Michael Lewis Chronicles the Story of Covid’s Cassandras| work = The New York Times| accessdate = 2022-11-01| date = 2021-05-06| url = https://www.nytimes.com/2021/05/06/books/review/the-premonition-michael-lewis.html}}{{Cite news| issn = 0261-3077| last = O’Connell| first = Mark| title = The Premonition by Michael Lewis review – a pandemic story| work = The Guardian| accessdate = 2022-11-01| date = 2021-05-05| url = https://www.theguardian.com/books/2021/may/05/the-premonition-by-michael-lewis-review-a-pandemic-story}} At the same time, DeRisi became an active proponent of developing a national COVID-19 surveillance system to identify and monitor mutations in the COVID-19 virus.{{cite web |last= Dunn |first= Lauren |date= January 8, 2021 |title= As U.K. variant spreads in U.S., scientists warn that country isn't doing enough to track Covid strains| url= https://www.nbcnews.com/health/health-news/u-k-variant-spreads-u-s-scientists-warn-country-isn-n1253467| website= NBCNews.com| access-date= May 1, 2021}}{{cite web |last= Allday |first= Erin |date= January 23, 2021 |title= The inside story of how the Bay Area coronavirus variant was discovered| url= https://www.sfchronicle.com/bayarea/article/Bay-Area-scientists-hunting-for-coronavirus-15891829.php| website= sfchronicle.com | access-date= May 1, 2021}}

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