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Find the double jquery.js include and remove it.";errorMessage="<span style='font-size:16px;color:#BC0C06;'>"+errorMessage+"</span>" jQuery(sliderID).show().html(errorMessage);} var tpj=jQuery;tpj.noConflict();var revapi22;tpj(document).ready(function(){if(tpj("#rev_slider_22_1").revolution==undefined){revslider_showDoubleJqueryError("#rev_slider_22_1");}else{revapi22=tpj("#rev_slider_22_1").show().revolution({sliderType:"standard",jsFileLocation:"https://www.sabetilab.org/wp-website/wp-content/plugins/revslider/public/assets/js/",sliderLayout:"fullwidth",dottedOverlay:"none",delay:9000,navigation:{keyboardNavigation:"off",keyboard_direction:"horizontal",mouseScrollNavigation:"off",onHoverStop:"on",touch:{touchenabled:"on",swipe_threshold:75,swipe_min_touches:1,swipe_direction:"horizontal",drag_block_vertical:false}},gridwidth:960,gridheight:350,lazyType:"none",shadow:0,spinner:"spinner0",stopLoop:"on",stopAfterLoops:0,stopAtSlide:1,shuffle:"off",autoHeight:"off",hideThumbsOnMobile:"off",hideSliderAtLimit:0,hideCaptionAtLimit:0,hideAllCaptionAtLilmit:0,debugMode:false,fallbacks:{simplifyAll:"off",nextSlideOnWindowFocus:"off",disableFocusListener:false,}});}});/*]]>*/</script> </div></div> <style type="text/css">#pre-footer-area:after{border-top-color:#fff}</style><div id="main-content" style="background-color: #ffffff;"><div class="container"><div class="row fullwidth main-row"><div id="page-4236" class="post-4236 page type-page status-publish hentry"><div class="col-12 hb-main-content"><div class="vc_row element-row row"><div class="vc_col-sm-12 wpb_column vc_column_container"><div class="wpb_wrapper"><div class="wpb_raw_code wpb_content_element wpb_raw_html" ><div class="wpb_wrapper"> <a id="infectious"></a></div></div><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div></div></div></div><div class="fw-section hb-fw-6746e8e61183e without-border no-overlay" style="margin-bottom:0px !important;margin-top:0px !important;"><div class="vc_row element-row row hb-animate-element fade-in vc_custom_1446758118760 fw-content-wrap"><div class="vc_col-sm-4 wpb_column vc_column_container"><div class="wpb_wrapper"><div class="shortcode-wrapper shortcode-title clearfix hb-animate-element left-to-right" data-delay="300"><p style="color:#ff3838!important;border-color:#ff3838" class="hb-text-large ">INFECTIOUS DISEASE</p></div></div></div><div class="vc_col-sm-8 wpb_column vc_column_container"><div class="wpb_wrapper"><div class="shortcode-wrapper shortcode-content-box clearfix hb-animate-element right-to-left" data-delay="400"><div class="hb-box-cont" style="background-color: #ffffff"><div class="hb-box-cont-body"><h1><span style="color: #ff3838;">Through resources at Harvard University and the Broad Institute, the Sabeti lab is applying next generation, high-throughput sequencing technologies to the creation of tailored sequencing pipelines for some of the world’s most deadly viruses and bacteria.</span></h1></div></div></div></div></div></div><div class="video-overlay no-overlay"></div></div><div class="vc_row element-row row vc_custom_1446758707069"><div class="vc_col-sm-12 wpb_column vc_column_container vc_custom_1445879645760"><div class="wpb_wrapper"><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div><div class="wpb_text_column wpb_content_element wpb_animate_when_almost_visible wpb_bottom-to-top bottom-to-top" ><div class="wpb_wrapper"><p>Working with other collaborators at Tulane University and USAMRIID, the Sabeti lab has obtained a vast repository of valuable clinical samples from patients with viral hemorrhagic fevers. Our hope is to carry out in-depth genomic analysis and diversity studies, elucidating regions of selection and identifying novel strains. The ability to generate full-length sequences will help in creating accurate phylogenies for both Lassa fever and Ebola viruses, as well as refine our ability to predict and identify regions of selection and high mutation within the genomes of these viruses.</p><p>Using both 454 and Illumina technologies, the Sabeti lab is developing novel approaches to full-length genome sequencing for both Lassa fever virus and Ebola virus. With the capacity to generate millions of base pairs of data from less than a teaspoon of blood, we are able to assemble complete viral genomes for identification and genetic analysis of known and unknown viruses.</p></div></div><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div><div class="vc_tta-container" data-vc-action="collapse"><div class="vc_general vc_tta vc_tta-tabs vc_tta-color-black vc_tta-style-outline vc_tta-shape-square vc_tta-spacing-2 vc_tta-gap-2 vc_tta-o-no-fill vc_tta-tabs-position-top vc_tta-controls-align-left"><div class="vc_tta-tabs-container"><ul class="vc_tta-tabs-list"><li class="vc_tta-tab vc_active" data-vc-tab><a href="#1446675102896-c14909a9-91cb" data-vc-tabs data-vc-container=".vc_tta"><span class="vc_tta-title-text">LASSA FEVER</span></a></li><li class="vc_tta-tab" data-vc-tab><a href="#1446675133018-ae460cdb-980c" data-vc-tabs data-vc-container=".vc_tta"><span class="vc_tta-title-text">CHOLERA</span></a></li><li class="vc_tta-tab" data-vc-tab><a href="#1446675103253-31a8554d-c2bf" data-vc-tabs data-vc-container=".vc_tta"><span class="vc_tta-title-text">MALARIA</span></a></li></ul></div><div class="vc_tta-panels-container"><div class="vc_tta-panels"><div class="vc_tta-panel vc_active" id="1446675102896-c14909a9-91cb" data-vc-content=".vc_tta-panel-body"><div class="vc_tta-panel-heading"><h4 class="vc_tta-panel-title"><a href="#1446675102896-c14909a9-91cb" data-vc-accordion data-vc-container=".vc_tta-container"><span class="vc_tta-title-text">LASSA FEVER</span></a></h4></div><div class="vc_tta-panel-body"><div class="vc_row element-row vc_inner row vc_custom_1446762784374 vc_row-has-fill"><div class="wpb_column vc_column_container vc_col-sm-4 vc_col-has-fill"><div class="vc_column-inner vc_custom_1446757057754"><div class="wpb_wrapper"><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div><div class="wpb_single_image wpb_content_element vc_align_center vc_custom_1446762078362"> <figure class="wpb_wrapper vc_figure"><div class="vc_single_image-wrapper vc_box_border_grey"><img class="vc_single_image-img " src="https://www.sabetilab.org/wp-website/wp-content/uploads/2015/09/Happi1.jpg" width="300" height="320" alt="Happi" title="Happi" /></div> </figure></div><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div></div></div></div><div class="wpb_column vc_column_container vc_col-sm-8"><div class="vc_column-inner "><div class="wpb_wrapper"><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div><div class="wpb_text_column wpb_content_element vc_custom_1446762049905" ><div class="wpb_wrapper"><p>In our work studying genetic susceptibility to Lassa, we have established strong collaborations with outstanding partners in Nigeria. Dr. Christian Happi, with whom we have worked for years on malaria, runs a thriving research program at the Redeemer’s University.<br /> We are also working closely with and have support from the Provost of the College of Medicine, University of Ibadan, the Chancellor of Ambrose Ali University, and the chief medical director (CMD) of ISTH in Irrua. We have the guidance and participation of arguably the world’s leading expert on Lassa fever, Joe McCormick, former chief of special pathogens at the CDC.</p></div></div><div class="wpb_text_column wpb_content_element " ><div class="wpb_wrapper"><p><a href="/wp-website/wp-content/uploads/2015/09/ISTH-copy.png"><img class="size-full wp-image-4910 alignright" src="/wp-website/wp-content/uploads/2015/09/ISTH-copy.png" alt="ISTH copy" width="234" height="198" srcset="https://www.sabetilab.org/wp-website/wp-content/uploads/2015/09/ISTH-copy.png 234w, https://www.sabetilab.org/wp-website/wp-content/uploads/2015/09/ISTH-copy-100x85.png 100w" sizes="(max-width: 234px) 100vw, 234px" /></a>We are working with The Specialist Teaching Hospital in Irrua (ISTH), Nigeria, an ideal location for our study. The hospital, with its 140 physicians and ~16,000 annual patients (80% of which have febrile illness), is located in a rural area in Nigeria where Lassa is endemic with yearly outbreaks.</p><p>The hospital has a commitment to research and has collaborated with researchers at the Berhnardt-Nocht Institute (BNI) in Hamburg in one of the best recent epidemiological studies on Lassa. Their 2003-2004 study laid the ground work for our research. It examined 31 febrile patients, 17 healthy contacts, and 12 hospital staff, and got basic rates of infection and exposure for the site.</p></div></div></div></div></div></div><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div><div class="wpb_raw_code wpb_content_element wpb_raw_html" ><div class="wpb_wrapper"> <a id="functional"></a></div></div><div class="vc_separator wpb_content_element vc_separator_align_center vc_sep_width_100 vc_sep_border_width_2 vc_sep_pos_align_left vc_separator_no_text" ><span class="vc_sep_holder vc_sep_holder_l"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span><span class="vc_sep_holder vc_sep_holder_r"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span></div></div></div><div class="vc_tta-panel" id="1446675133018-ae460cdb-980c" data-vc-content=".vc_tta-panel-body"><div class="vc_tta-panel-heading"><h4 class="vc_tta-panel-title"><a href="#1446675133018-ae460cdb-980c" data-vc-accordion data-vc-container=".vc_tta-container"><span class="vc_tta-title-text">CHOLERA</span></a></h4></div><div class="vc_tta-panel-body"><div class="wpb_text_column wpb_content_element " ><div class="wpb_wrapper"><p>Cholera is a devastating illness caused by the bacillus Vibrio cholerae, which triggers a severe, dehydrating and occasionally fatal diarrhea. We are investigating the genetics of cholera resistance in Bangladesh, where the disease is endemic, to understand how the human immune system responds to cholera infection. Because cholera has a long history in Bangladesh, any person carrying a gene version protecting them from this devastating disease will have had a significant evolutionary advantage. Thus, these genes should show exceptionally strong natural selection signals. By applying powerful new computational techniques for detecting natural selection to genome-wide genotyping data from the Bangladeshi population, we are identifying genes that likely confer cholera resistance. By then integrating these tests with gene transcription profiling and proteomic analysis, we can learn how these genes alter an individual’s response to cholera infection. As part of this project, we are also researching the evolutionary history of the Bangladeshis by comparing them to the populations from around the world included in the Human Haplotype Map project.</p><p>This project is a collaboration with <a href="http://www2.massgeneral.org/id/labs/larocque/">Dr. Regina LaRocque</a>, an Infectious Disease Specialist at MGH, and <a href="http://www.icddrb.org/">ICDDRB</a>, an international health research institution and hospital located in Dhaka, Bangladesh that treats tens of thousands of patients every year.</p></div></div><div class="vc_separator wpb_content_element vc_separator_align_center vc_sep_width_100 vc_sep_border_width_2 vc_sep_pos_align_left vc_separator_no_text" ><span class="vc_sep_holder vc_sep_holder_l"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span><span class="vc_sep_holder vc_sep_holder_r"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span></div></div></div><div class="vc_tta-panel" id="1446675103253-31a8554d-c2bf" data-vc-content=".vc_tta-panel-body"><div class="vc_tta-panel-heading"><h4 class="vc_tta-panel-title"><a href="#1446675103253-31a8554d-c2bf" data-vc-accordion data-vc-container=".vc_tta-container"><span class="vc_tta-title-text">MALARIA</span></a></h4></div><div class="vc_tta-panel-body"><div class="wpb_text_column wpb_content_element " ><div class="wpb_wrapper"><p><a href="/wp-content/uploads/2015/09/mosquito-e1446759477153.jpg"><img class=" wp-image-5034 alignright" src="/wp-content/uploads/2015/09/mosquito-e1446759477153.jpg" alt="mosquito" width="280" height="258" srcset="https://www.sabetilab.org/wp-website/wp-content/uploads/2015/09/mosquito-e1446759477153.jpg 301w, https://www.sabetilab.org/wp-website/wp-content/uploads/2015/09/mosquito-e1446759477153-300x276.jpg 300w, https://www.sabetilab.org/wp-website/wp-content/uploads/2015/09/mosquito-e1446759477153-100x92.jpg 100w" sizes="(max-width: 280px) 100vw, 280px" /></a>Plasmodium falciparum malaria is a major public health challenge that significantly contributes to global morbidity and mortality. Efforts to control and eliminate malaria combine antimalarial drugs, bed nets and indoor residual spraying, with vaccine development a longer-term goal. Genetic variation in the parasite population threatens to undermine these efforts, as the parasite evolves rapidly to evade host immune systems, drugs and vaccines.</p><p>Working with the <a href="http://www.broadinstitute.org/">Broad Institute</a>, the <a href="http://www.hsph.harvard.edu/">Harvard School of Public Health</a>, and the <a href="http://www.ucad.sn/">University of Cheikh Anta Diop</a>, Dakar, Senegal, we have been studying genetic variation in parasite populations to help expand our understanding of basic parasite biology and allow us to track parasites as they evolve in response to interventions.</p></div></div><div class="vc_separator wpb_content_element vc_separator_align_center vc_sep_width_100 vc_sep_border_width_2 vc_sep_pos_align_left vc_separator_no_text" ><span class="vc_sep_holder vc_sep_holder_l"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span><span class="vc_sep_holder vc_sep_holder_r"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span></div></div></div></div></div></div></div><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div></div></div></div><div class="vc_row element-row row vc_custom_1446758043223"><div class="vc_col-sm-4 wpb_column vc_column_container vc_custom_1446835789747"><div class="wpb_wrapper"><div class="shortcode-wrapper shortcode-title clearfix hb-animate-element left-to-right" data-delay="300"><p style="color:#ff3838!important;border-color:#ff3838" class="hb-text-large ">FUNCTIONAL ANALYSIS</p></div></div></div><div class="vc_col-sm-8 wpb_column vc_column_container vc_custom_1446835798434"><div class="wpb_wrapper"><div class="shortcode-wrapper shortcode-content-box clearfix hb-animate-element right-to-left" data-delay="400"><div class="hb-box-cont"><div class="hb-box-cont-body"><h1><span style="color: #ff3838;">Genome-wide scans, such as those our lab develops, generate lists of loci that are probable candidates for recent natural selection. In order to create a case for selection of a candidate gene, we perform follow-up studies to determine the allele’s biological function, using methods such as case/control association studies, the development of cell cultures containing the gene of interest, and in vivo transgenic studies.</span></h1></div></div></div></div></div></div><div class="vc_row element-row row vc_custom_1446841163807"><div class="vc_col-sm-12 wpb_column vc_column_container"><div class="wpb_wrapper"><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div><div class="wpb_raw_code wpb_content_element wpb_raw_html" ><div class="wpb_wrapper"> <a id="computational"></a></div></div><div class="vc_separator wpb_content_element vc_separator_align_center vc_sep_width_100 vc_sep_border_width_2 vc_sep_pos_align_left vc_separator_no_text" ><span class="vc_sep_holder vc_sep_holder_l"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span><span class="vc_sep_holder vc_sep_holder_r"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span></div><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div></div></div></div><div class="vc_row element-row row vc_custom_1446758225765"><div class="vc_col-sm-5 wpb_column vc_column_container"><div class="wpb_wrapper"><div class="shortcode-wrapper shortcode-title clearfix hb-animate-element left-to-right" data-delay="300"><p style="color:#ff3838!important;border-color:#ff3838" class="hb-text-large "><a id="#"></a>COMPUTATIONAL BIOLOGY</p></div></div></div><div class="vc_col-sm-7 wpb_column vc_column_container"><div class="wpb_wrapper"><div class="shortcode-wrapper shortcode-content-box clearfix hb-animate-element right-to-left" data-delay="400"><div class="hb-box-cont"><div class="hb-box-cont-body"><h1><span style="color: #ff3838;">In the era of genomics, we can now probe information buried in the millions of sequence variations that have occurred and persisted in the human genome, in search of signatures of genome evolution. </span></h1></div></div></div><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div></div></div></div><div class="vc_row element-row row vc_custom_1446758254049"><div class="vc_col-sm-12 wpb_column vc_column_container"><div class="wpb_wrapper"><div class="vc_tta-container" data-vc-action="collapse"><div class="vc_general vc_tta vc_tta-tabs vc_tta-color-black vc_tta-style-outline vc_tta-shape-square vc_tta-spacing-2 vc_tta-gap-2 vc_tta-o-no-fill vc_tta-tabs-position-top vc_tta-controls-align-left vc_custom_1489121579210"><div class="vc_tta-tabs-container"><ul class="vc_tta-tabs-list"><li class="vc_tta-tab vc_active" data-vc-tab><a href="#1446676645680-453c2bd8-f9dc" data-vc-tabs data-vc-container=".vc_tta"><span class="vc_tta-title-text">GENOME-WIDE SCANS FOR SELECTION</span></a></li><li class="vc_tta-tab" data-vc-tab><a href="#1446676646015-d513dadd-b394" data-vc-tabs data-vc-container=".vc_tta"><span class="vc_tta-title-text">VISUALIZATION SOFTWARE</span></a></li></ul></div><div class="vc_tta-panels-container"><div class="vc_tta-panels"><div class="vc_tta-panel vc_active" id="1446676645680-453c2bd8-f9dc" data-vc-content=".vc_tta-panel-body"><div class="vc_tta-panel-heading"><h4 class="vc_tta-panel-title"><a href="#1446676645680-453c2bd8-f9dc" data-vc-accordion data-vc-container=".vc_tta-container"><span class="vc_tta-title-text">GENOME-WIDE SCANS FOR SELECTION</span></a></h4></div><div class="vc_tta-panel-body"><div class="wpb_text_column wpb_content_element " ><div class="wpb_wrapper"><p>We have developed computational methods, such as the LRH, XP-EHH, and CMS tests, to detect genetic variants under positive selection. These methods identify variants that have recently emerged and spread through populations, relying on the breakdown of recombination as a clock for estimating the ages of alleles. We have applied these methods to large datasets of human genetic variation finding many novel candidates for selection.</p><p>We are developing methods to further refine the signals from large candidate regions to localize the underlying selected polymorphism. We have developed software to make detection of selection, by these and other methods, possible for the rapidly expanding empirical data on genetic variation in humans and other species.</p><p>The lab continues to refine existing, and develop novel, methods and tools to detect and localize signals of selection in humans and other organisms. We are using approaches that take advantage of rapidly expanding datasets of genetic variation and larger population sampling, increasingly affordable full-genome sequencing, and new insights into the structure of genetic variation in the genome. We will apply our methods to look for instances of natural selection, using our own data and data collected for human in 2 international efforts: The International Haplotype Map Consortium (1000 individuals genotyped for 1 million polymorphisms) and the 1000 Genomes Consortium (full genome sequences from 1000 individuals).</p></div></div><div class="vc_separator wpb_content_element vc_separator_align_center vc_sep_width_100 vc_sep_border_width_2 vc_sep_pos_align_left vc_separator_no_text" ><span class="vc_sep_holder vc_sep_holder_l"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span><span class="vc_sep_holder vc_sep_holder_r"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span></div><div class="vc_empty_space" style="height: 50px" ><span class="vc_empty_space_inner"></span></div></div></div><div class="vc_tta-panel" id="1446676646015-d513dadd-b394" data-vc-content=".vc_tta-panel-body"><div class="vc_tta-panel-heading"><h4 class="vc_tta-panel-title"><a href="#1446676646015-d513dadd-b394" data-vc-accordion data-vc-container=".vc_tta-container"><span class="vc_tta-title-text">VISUALIZATION SOFTWARE</span></a></h4></div><div class="vc_tta-panel-body"><div class="wpb_text_column wpb_content_element " ><div class="wpb_wrapper"><p>Mirador is a software tool for visual exploration of complex biomedical data sets, specifically designed to find correlations between variables of interest, to propose new hypothesis of association, and to build predictive models. Its interface allows navigation of data sets with thousands of variables and up to millions of individual records. It uses a Mutual Information-based measure of correlation to rapidly quantify the significance of pairwise associations. Mirador has been used to find <a href="http://fathom.info/latest/9779" target="_blank" rel="noopener">correlations patterns</a> in several public health, survey, and country databases, to construct <a href="http://fathom.info/mirador/ebola/prognosis" target="_blank" rel="noopener">clinical prediction models</a> in Ebola Virus Disease and other infectious diseases, and received <a href="http://www.hhsvizrisk.org/" target="_blank" rel="noopener">innovation and scientific excellence awards</a> from the U.S. Department of Health and Human Services. It continues a line of work initiated in the lab by David Reshef and his <a href="http://video.mit.edu/watch/inventor-david-reshef-4778/" target="_blank" rel="noopener">project Visualyzer</a>, and it is freely available for download at <a href="http://fathom.info/mirador/" target="_blank" rel="noopener">http://fathom.info/mirador/</a>. Mirador has been developed in collaboration with Fathom Information Design, and was initially funded by the <a href="http://ccdd.hsph.harvard.edu/" target="_blank" rel="noopener">Center of Communicable Disease Dynamics</a> and the <a href="http://www.epimodels.org/drupal/" target="_blank" rel="noopener">MIDAS</a> network funded by the National Institutes of Health.</p></div></div><div class="vc_separator wpb_content_element vc_separator_align_center vc_sep_width_100 vc_sep_border_width_2 vc_sep_pos_align_left vc_separator_no_text" ><span class="vc_sep_holder vc_sep_holder_l"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span><span class="vc_sep_holder vc_sep_holder_r"><span style="border-color:#ff3838;" class="vc_sep_line"></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><aside id="contact-panel"><h4 class="hb-focus-color">Contact Us</h4><p>Send us an email and we'll get back to you, asap.</p><form 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