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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-152'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2014-02-16 :: VFam</td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=152'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><center><img src = 'module_pictures/vFam-logo-525.jpg'></center><br>vFam is a HMMER3 database of profile hidden Markov models (HMMs) built from all the viral proteins present in RefSeq. Use of the vFam database may provide greater sensitivity for the detection of highly divergent viral proteins than the use of traditional alignment tools, such as BLAST. <br><a href='software/vFam/'>Click here to go to the vFam download page.</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-124'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2012-07-07 :: AZ50XT Feature Height Calculator </td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=124'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><center><img src = 'module_pictures/az50xt-banner.jpg'></center><br>This is an online tool for helping users identify the pre-bake dimensions required to produce features with desired dimensions after baking. The tool will calculate pre-bake dimensions, closing pressures, and look up all empirical measurements of valves within stated tolerances of the specified dimensions. <br> Fordyce, P.M.*, Diaz-Botia, C.A.*, DeRisi, J.L., & R. Gomez-Sjoberg<br><b><i>Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via photoresist flow</b></i><br> Submitted to Lab on a Chip (2012)<br><a href='http://derisilab.ucsf.edu/software/AZ50XT/AZ50XTToolInput.html'>Click here to use the tool.</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-138'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2011-04-01 :: PRICE</td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=138'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><center><img src = 'module_pictures/PRICE.jpg'></center><br>We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of pre-assembled contigs. It was designed to address the challenge of assembling viral genomes that constituted a small minority of the reads within ultra-deep, short-read, metagenomic, shotgun datasets. PRICE has already enabled the discovery of several novel virus genomes from such complex datasets.<br> <b>The early online edition of the PRICE paper, published in G3, is</b> <a href='http://www.g3journal.org/content/early/2013/03/22/g3.113.005967.abstract'>here.</a><br><a href='http://derisilab.ucsf.edu/software/price/index.html'>Download PRICE</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-105'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2010-06-12 :: HMMSplicer</td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=105'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><center><img src = 'module_pictures/HMMSplicer_Logo_525_rna.jpg'></center><br>HMMSplicer discovers splice sites in high throughput sequencing datasets without using gene models. HMMSplicer can also be used to find non-canonical junctions as well. HMMSplicer was benchmarked on publickly available <i>A. thaliana</i>, <i>H. sapiens</i>, and <i>P. falciparum</i> datasets and performs well on all genomes. Information about the datasets tested, including the exact command parameters and the final results, is provided. HMMSplicer is implemented in Python and is freely available for all. <br><a href='/software/HMMSplicer/hmmSplicer-0.9.5.tar.gz'>Download HMMSplicer! (Updated Nov 25th 2010 - Version: 0.9.5)</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-96'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2010-01-01 :: VersaCount</td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=96'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><img src='module_icons/versa_count_logo.jpg' class='iconbox'>VersaCount is a simple application to assist with the counting of cells by microscopy. When used with a numeric keypad, it can significantly increase counting efficiency when compared with a traditional clicker. Although it was designed for malaria work, it can be customized for a wide variety of cell counting applications. VersaCount was written by Charlie Kim.<br><a href='software/versacount/VersaCount_v1.0.zip'>Download VersaCount v1.0</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-50'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2006-12-01 :: ExpressionNet</td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=50'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><img src='module_icons/BN.jpg' class='iconbox'>ExpressionNet is a program written by Jingchun Zhu that uses Bayesian network learning algorithms to explore relationships among random variables to generate network models. The software has been used to study the transcriptional response to environmental perturbations in budding yeast. Details of the program and the study of yeast transcription using Bayesian Networks was published in PLoS ONE.<br> <a href='http://expressionnet.sourceforge.net/'>Click here for further information, demo data, etc.</a><br> <a href='software/expressionnet/ExpressionNet.pdf'>Download basic documentation here.</a><br><br><a href='software/expressionnet/ExpressionNet.zip'>Download ExpressionNet v1.0</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-41'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2005-08-30 :: E-Predict</td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=41'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><img src='module_icons/epredict.jpg' class='iconbox'>DNA microarrays may be used to identify microbial species present in environmental and clinical samples. However, automated tools for reliable species identification based on observed microarray hybridization patterns are lacking. We present an algorithm, E-Predict, for microarray-based species identification.<br><a href='http://derisilab.ucsf.edu/software/epredict/index.html'>E-Predict Software Download Page</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-46'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2005-03-01 :: ArrayOligoSelector</td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=46'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><center><img src = 'module_pictures/AOS_Logo.jpg'></center><br>ArrayOligoSelector (AOS) is an open source program developed by Jingchun Zhu for the purpose of systematically designing gene-specific long oligonucleotide probes for entire genomes. For each open reading frame, the program optimizes oligo selection based upon several parameters, including uniqueness, complexity, secondary structure, GC content, and 3' end proximity.<br> <a href='http://arrayoligosel.sourceforge.net/'>AOS also is hosted at SourceForge.</a> This site contains documentation and a user-friendly how-to.<br> For more information, download an excerpt from Jing's thesis describing the AOS algorithm and implementation <a href='software/aos/chapter2.pdf'>here.</a><br><br><a href='software/aos/ArrayOligoSelector3.8.4.tar'>Download AOS v3.8.4</a><br class='clearfix' /></div></td></tr></table><br><a name='anchor-43'></a> <table border='0' cellspacing='0' cellpadding='0'> <tr><td width='6' height='20' id='left_greybar'></td> <td width='380' height='20' valign='middle' id='middle_greybar' class='menubar'>2007-01-01 :: ArrayMaker v2</td> <td width='150' height='20' valign='middle' align='right' id='middle_greybar' class='menubar'> <a href='index.php?software=43'> More... </a> </td><td width='6' height='20' id='right_greybar'></td> </tr></table><table border='0' cellspacing='0' cellpadding='0'><tr><td><div class='rightbox'><center><img src = 'module_pictures/screen_welcome.jpg'></center><br>ArrayMaker 2 provides high performance robotic control of microarrayer robots with an incredibly intuitive, easy to use interface. ArrayMaker 2 is optimized for use with the new generation of ultra fast linear servo driven arrayers, yet it is backwards compatible with the original MGuide style of ball-screw driven arrayers. <br><a href='http://derisilab.ucsf.edu/software/arraymaker/ArrayMaker_v260.zip'>Download ArrayMaker v2.60</a><br class='clearfix' /></div></td></tr></table><br></td> </tr> </table> </body> </html>