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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html> <head> <title>Welcome to the DeRisi Lab</title> <link href="derisilab.css" rel="stylesheet" type="text/css"> </head> <body> <table border="0" cellspacing="0" cellpadding="0" align="center" bgcolor="#FFFFFF"> <tr><td width="800"> <table border="0" cellspacing="0" cellpadding="0" align="center" > <tr> <td id="menu_bar_top" colspan="2" class="menubar" align="middle" bgcolor="#000000"> <center> <a href='http://www.ncbi.nlm.nih.gov/BLAST/'>BLAST</a> :: <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed'>PubMed</a> :: <a href='http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi'>Entrez</a> :: <a href='http://www.plasmodb.org'>PlasmoDB</a> :: <a href='http://www.yeastgenome.org/'>SGD</a> :: <a href='http://czbiohub.org'>CZ Biohub</a> :: <a href='http://www.plos.org'>PLoS</a> :: <a href='http://directory.ucsf.edu/people_search.jsp'>Directory</a> :: <a href='http://www.ucsf.edu'>UCSF</a> </center> </td> </tr> <tr> <td colspan="2" bgcolor="#000000"> <img src='images/pentamers.jpg' width='800' height='160'> </td> </tr> <tr> <td id="menu_bar_main" class="menubar" align='middle' colspan='2' bgcolor="#000000"> <center> <a href='index.php'>News</a> :: <a href='index.php?page=research'>Research</a> :: <a href='index.php?page=publications'>Publications</a> :: <a href='index.php?page=data'>Data</a> :: <a href='index.php?page=software'>Software</a> :: <a href='index.php?page=3D'>3D Printables</a> :: <a href='index.php?page=people'>People</a> :: <a href='index.php?page=contact'>Contact</a> </center> </td> </tr> <tr> <td width='242' height='100%' valign='top' class='hlink' id='left_cell' > <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2024-05-05 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/Autoreactome-2024.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=387' ><img src='webicons/JCI-Icon-2024.jpg' class='iconbox' border='0'></a> Unveiling the proteome-wide autoreactome enables enhanced evaluation of emerging CAR T cell therapies in autoimmunity<br><i>J Clin Invest 2024</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2924-08-07 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/anderson2024.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=389' ><img src='webicons/misc2024.jpg' class='iconbox' border='0'></a> Molecular mimicry in multisystem inflammatory syndrome in children<br><i>Nature Portfolio, 2024</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2024-07-01 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/Phage_Immuno.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=388' ><img src='webicons/saravaz.jpg' class='iconbox' border='0'></a> Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease<br><i>American College of Rheumatology, 2024</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2024-07-01 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/Pluvinage-VitaminB12.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=385' ><img src='webicons/Pluvinage-icon.jpg' class='iconbox' border='0'></a> Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency<br><i>Sci Tran Med 2024</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2024-05-02 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/Colin-MSPredict-2024.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=386' ><img src='webicons/Colin-Predict-Icon.jpg' class='iconbox' border='0'></a> An autoantibody signature predictive for multiple sclerosis<br><i>Nat Med 2024</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2023-03-24 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/schrom.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=363' ><img src='webicons/schromj.jpg' class='iconbox' border='0'></a> Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges<br><i>PLOS One, 2023</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2023-02-15 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/greenhouse.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=365' ><img src='webicons/greenhouse1.jpg' class='iconbox' border='0'></a> Antibodies to repeat-containing antigens in Plasmodium falciparum are exposure-dependent and short-lived in children in natural malaria infections<br><i>eLife, 2023</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2023-01-23 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/pittock1.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=366' ><img src='webicons/pittock2.jpg' class='iconbox' border='0'></a> Dual ankyrinG and subpial autoantibodies in a man with well-controlled HIV infection with steroid-responsive meningoencephalitis: A case report<br><i>Frontiers, 2023</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2023-01-29 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/cchiu.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=367' ><img src='webicons/cchiupic.jpg' class='iconbox' border='0'></a> Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline<br><i>Emerging Infectious Diseases, 2023</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2023-01-04 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/maderaarticle.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=372' ><img src='webicons/maderapic1.jpg' class='iconbox' border='0'></a> Prolonged silent carriage, genomic virulence potential and transmission between staff and patients characterize a neonatal intensive care unit (NICU) outbreak of methicillin-resistant Staphylococcus aureus (MRSA)<br><i>Cambridge University Press, 2023</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2023-03-02 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/Rosenberg1.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=364' ><img src='webicons/rosen1.jpg' class='iconbox' border='0'></a> Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps<br><i>Science Direct, 2023</i> <br class='clearfix' /> </div></td></tr></table><br> <table border='0' cellspacing='0' cellpadding='0'> <tr> <td width='6' height='20' id='left_rbar'></td> <td width='100' height='20' valign='middle' id='middle_rbar' class='menubar'>2024-05-23 </td> <td width='128' height='20' valign='middle' align='right' id='middle_rbar' class='menubar'> <a href='pdfs/breathe24.pdf' target='_blank'>[ PDF ]</a></td> <td width='6' height='20' id='right_rbar'></td> </tr></table> <table border='0' cellspacing='0' cellpadding='0'> <tr><td><div class='leftbox'><a href='index.php?pdf=381' ><img src='webicons/breathe.jpg' class='iconbox' border='0'></a> Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation<br><i>Nature Portfolio, 2024</i> <br class='clearfix' /> </div></td></tr></table><br></td><td width='558' valign='top' id='right_cell'><a name='anchor-284'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_gbar'></td> <td width='380' height='20' valign='middle' id='middle_gbar' class='menubar'>2024-07-07 :: Evidence for Molecular Mimicry in MIS-C</td> <td width='150' height='20' valign='middle' align='right' id='middle_gbar' class='menubar'> <a href='index.php?news=284'> More... </a> </td><td width='6' height='20' id='right_gbar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><center><img src = 'module_pictures/MISC-Art-525p.jpg'></center><br>While children were largely spared during the SARS-CoV-2 pandemic, <a href=' https://www.childrenshospital.org/conditions/mis-c' class='menubar3'>Multisystem inflammatory syndrome in children (MIS-C)</a> is one of the enduring mysteries of the early years of COVID. MIS-C manifests as a severe post-COVID inflammatory syndrome affecting multiple organ systems and often requires extreme measures of life support. Despite numerous investigations, the underlying drivers of MIS-C for the majority of cases remained unclear. <p> In close collaboration with numerous laboratories and clinicians across the country, including the <a href='https://czbiohub.org' class='menubar3'> Chan Zuckerberg Biohub SF </a>, Baylor, Univ. of Mississippi, Emory, Univ of Alabama at Birmingham, Univ. of Pennsylvania, Nicklaus Children鈥檚 Hospital, Univ. of North Carolina Chapel Hill, Univ. of Utah, Arkansas Children鈥檚 Hospital, Cincinnati Children鈥檚 Hospital, Indiana University, Children鈥檚 Mercy Kansas City, Vanderbilt, Cooperman Barnabas Medical Center, Univ. of South Carolina Charleston, Univ. of Colorado, the CDC, St. Jude Children鈥檚 Hospital, and UCSF, we report a significant breakthrough that sheds light on the origins of this severe disease. <br></p> <br><a href='https://www.nature.com/articles/s41586-024-07722-4'>Read the paper here.</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-244'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_gbar'></td> <td width='380' height='20' valign='middle' id='middle_gbar' class='menubar'>2021-05-02 :: For Readers of The Premonition by Michael Lewis</td> <td width='150' height='20' valign='middle' align='right' id='middle_gbar' class='menubar'> <a href='index.php?news=244'> More... </a> </td><td width='6' height='20' id='right_gbar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><img src='module_icons/BookCover.jpg' class='iconbox'><b><i>The Premonition: A Pandemic Story</i></b>, by Michael Lewis, is a new book that describes the efforts of scientists and public health officials before and during the 2020 coronavirus pandemic. Readers may be interested in reading the original papers from the DeRisi Lab that are described in the book. PDFs of the original papers, ordered by mention in the book, are detailed below. This includes supporting information and links to online lectures by Dr. DeRisi.<br>Additional resources are at the <a href='https://czbiohub.org' class='menubar3'> Chan Zuckerberg Biohub.</a> <br><br><br><br> <b><i>Chapter 6: The Original Papers and Supporting Information</i></b><br> <br> <i>Papers from the first SARS, 2003</i><br> <ul> <li> <a href='http://derisilab.ucsf.edu/pdfs/Ksiazek_NEJM03.pdf' class='menubar3'>2003 - Identification of SARS coronavirus</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/Wangetal_PLos_2005.pdf' class='menubar3'>2003 - Using the ViroChip and Sequencing to recover SARS-1 genome sequence</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/Rota_Science03.pdf' class='menubar3'>2003 - Genome characterization of SARS coronavirus</a><br> </li> <li> <a href='https://www.youtube.com/watch?v=08Xz4UYyI8E' class='menubar3'>Lecture: HHMI 2010, SARS and other Viral Mysteries</a><br> </li> <li> <a href='https://www.youtube.com/watch?v=bKBTi88p2cs' class='menubar3'>Lecture: HHMI 2010, Viral Hunter's Toolkit</a><br> </li> </ul> <i>Snake Arenavirus - Discovery and Characterization</i><br> <ul> <li> <a href='http://derisilab.ucsf.edu/pdfs/mBio-2012-Stenglein-sm.pdf' class='menubar3'>2012 - Identification of reptile arenavirus in boas and pythons</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/Stenglein_PLoS_2015.pdf' class='menubar3'>2015 - An engine of viral diversity in snake arenaviruses</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/Stenglein2017.pdf' class='menubar3'>2017 - Proving Koch's Postulates and snake arenavirus</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/Koelhoffer_JMolBiol_2013.pdf' class='menubar3'>2013 - Snake arenavirus and Ebola - GP Protein Structure</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/vey034.pdf' class='menubar3'>2018 - Ebola Virus replicates in Boa cells just fine.</a><br> </li> <li> <a href='https://www.ibiology.org/microbiology/genome-sequencing/' class='menubar3'>Lecture: - Metagenomics for Virus Discovery: Snakes!</a><br> </li> <li> <a href='https://www.ibiology.org/microbiology/genome-sequencing/' class='menubar3'>Podcast: - Discussing Snake Viruses with Adam Savage!</a><br> </li> <li> <a href='https://www.microbe.tv/twiv/twiv-196-an-arena-for-snakes/' class='menubar3'>Podcast: - TWiV, An arena for snakes.</a><br> </li> </ul> <i>The Red Phone: Metagenomics for Infectious Disease Discovery in Humans</i><br> <ul> <li> <a href='http://derisilab.ucsf.edu/pdfs/jamaneurology.Wilson.pdf' class='menubar3'>2018 - The Red Phone. Case series of patients</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/Wilson_AnnalNeuro_20152.pdf' class='menubar3'>2015 - Diagnosis of Balamuthia in a fatal case of encephalitis</a><br> </li> <li> <ahref='https://www.ucsf.edu/news/2015/09/131516/next-gen-genomic-tests-identify-brain-eating-amoeba' class='menubar3'>2015 - UCSF News: Next-Gen Genomic Tests, Brain Eating Amoeba</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/MBio.pdf' class='menubar3'>2018 - Searching for drugs to fight Balamuthia infection</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/AnnNeuro_Wilson_2017.pdf' class='menubar3'>2017 - Discovery of Cache Valley Virus in a fatal case of encephalitis</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/Neurology.pdf' class='menubar3'>2018 - The good news, and the bad news. Worms in the brain.</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/GenomeMedicine-Doan-2016.pdf' class='menubar3'>2016 - Metagenomics for infections in the eye.</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/nejmoa1401268.pdf' class='menubar3'>2014 - Diagnosis of Leptosporosis in a young child.</a><br> </li> </ul> <br> <i>A platform for global monitoring of infectious disease: <b>IDseq</b></i><br> <ul> <li> <a href='https://idseq.net' class='menubar3'>2020 - The IDseq Platform</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/GigaScience-2020.pdf' class='menubar3'>2020 - The IDseq Platform technical paper</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/mBio.02877-19.pdf' class='menubar3'>2020 - IDseq in action: Dhaka, Bangladesh</a><br> </li> <li> <a href='https://www.youtube.com/watch?v=CWizlAFKKL4' class='menubar3'>2019 - Mini-documentary: Infectious Disease Detectives in Bangladesh</a><br> </li> <li> <a href='https://www.oculus.com/experiences/media/138425597437093/2292875140835046/' class='menubar3'>2019 - VR Version Mini-documentary: Infectious Disease Detectives in Bangladesh</a><br> </li> <li> <a href='https://public.idseq.net/covid-19?utm_source=idseq&utm_medium=banner&utm_campaign=covid-19' class='menubar3'>2020 - IDseq in action: Cambodia</a><br> </li> </ul> <b><i>Chapter 10: The COVID-19 Pandemic</i></b><br> <ul> <li> <a href='http://derisilab.ucsf.edu/pdfs/CLIAHUB-PLoSPathogen-2020.pdf' class='menubar3'>2020 - The CLIAHUB: Volunteer driven clinical testing</a><br> </li> <li> <a href='https://www.youtube.com/watch?v=LgRQge1y0U8' class='menubar3'>Video Clip - The CLIAHUB at the Chan Zuckerberg Biohub</a><br> </li> <li> <a href='https://www.nbcbayarea.com/news/local/digital-originals/mission-critical-priscilla-chan-and-the-fight-against-covid-19-in-san-franciscos-latino-community/2517904/' class='menubar3'>News Clip - Priscilla Chan and the fight against COVID-19</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/ciaa1234.pdf' class='menubar3'>2020 - The disproportionate burden of COVID-19 in San Francisco</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/ciaa1234.pdf' class='menubar3'>2020 - The disproportionate burden of COVID-19 in San Francisco</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/CID-L452R-DeRisi-2021.pdf' class='menubar3'>2020 - Genomic Epidemiology in Action in San Francisco</a><br> </li> <li> <a href='http://derisilab.ucsf.edu/pdfs/JID-2021-DeRisi.pdf' class='menubar3'>2020 - Deployment of Rapid Antigen Tests in SF: Field Performance</a><br> </li> </ul> <br class='clearfix' /></div></td></tr></table><br></td> </tr> </table> </body> </html>