{"id":644,"date":"2023-07-20T16:18:08","date_gmt":"2023-07-20T16:18:08","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/?page_id=644"},"modified":"2023-08-17T19:50:32","modified_gmt":"2023-08-17T19:50:32","slug":"caballero","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/caballero\/","title":{"rendered":"caballero"},"content":{"rendered":"<p>[et_pb_section fb_built=&#8221;1&#8243; admin_label=&#8221;Team Section&#8221; module_id=&#8221;team&#8221; module_class=&#8221;team-section&#8221; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221; background_color=&#8221;#f7fcff&#8221; parallax=&#8221;on&#8221;][et_pb_row column_structure=&#8221;1_4,3_4&#8243; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221;][et_pb_column type=&#8221;1_4&#8243; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221;][et_pb_image src=&#8221;https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-content\/uploads\/sites\/458\/2023\/02\/Madison-Caballero3.jpg&#8221; title_text=&#8221;Madison-Caballero3&#8243; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221; min_height=&#8221;240px&#8221; custom_padding=&#8221;4px|16px|24px|0px||&#8221; animation_style=&#8221;fade&#8221; hover_enabled=&#8221;0&#8243; border_radii=&#8221;on|5px|5px|5px|5px&#8221; box_shadow_style=&#8221;preset3&#8243; custom_margin=&#8221;|-10px|-50px|||&#8221; sticky_enabled=&#8221;0&#8243;][\/et_pb_image][\/et_pb_column][et_pb_column type=&#8221;3_4&#8243; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221;][et_pb_text admin_label=&#8221;MAdison&#8221; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221; text_font=&#8221;Open Sans||||||||&#8221; text_text_color=&#8221;#000000&#8243; text_font_size=&#8221;16px&#8221; text_line_height=&#8221;1.8em&#8221; min_height=&#8221;355.4px&#8221;]<\/p>\n<h4><strong>Madison Caballero<\/strong>, PhD<\/h4>\n<p><strong>Bioinformatician III<\/strong><br \/>Email: madison.caballero@mssm.edu<\/p>\n<p>Madison is a bioinformatician III at <a href=\"https:\/\/labs.icahn.mssm.edu\/mahjanilab\">Dr. Mahjani<\/a> lab\u00a0<span>with a primary focus on investigating the role of ultra-rare genetic variation in psychiatric disorders. With a background in genetics, she specializes in analyzing large-scale genomics data using innovative computational approaches. Outside of research, Madison enjoys theater and spending time with her cat.<\/span><\/p>\n<p><span>Madison earned her PhD in Genetics from Cornell University in 2022, where her research delved into the epigenetic phenomenon of DNA replication timing and its relationship to mutation rate. Additionally, she received a BSc in Cellular and Molecular Biology from the University of Connecticut, where she led plant genomics research, software development for protein annotation, and the successful design of a genotyping array for pines.<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><strong>Select publications:<\/strong><\/p>\n<ul>\n<li>Caballero, M. The Interplay Between DNA Replication Timing and Mutations. Cornell University (2022). [<a href=\"https:\/\/www.proquest.com\/docview\/2771090428?pq-origsite=gscholar&amp;fromopenview=true\">doctoral dissertation<\/a>]<\/li>\n<li>Caballero, M. &amp; Koren, A. The landscape of somatic mutations in lymphoblastoid cell lines. <em>Cell Genomics<\/em> 100305 (2023).<\/li>\n<li>Caballero, M., Boos, D. &amp; Koren, A. Cell-type specificity of the human mutation landscape with respect to DNA replication dynamics. <em>Cell Genom<\/em> <strong>3<\/strong>, 100315 (2023).<\/li>\n<li>Caballero, M. <em>et al.<\/em> Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation. <em>Hum Mol Genet<\/em> ddac082 (2022).<\/li>\n<li>Caballero, M. <em>et al.<\/em> Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome. <em>Applications in Plant Sciences<\/em> <strong>9<\/strong>, e11439 (2021).<\/li>\n<li>Caballero, M. <em>et al.<\/em> Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives. <em>PLOS Genetics<\/em> <strong>15<\/strong>, e1007979 (2019).<\/li>\n<li>Caballero, M. &amp; Wegrzyn, J. gFACs: Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks. <em>Genomics, Proteomics &amp; Bioinformatics<\/em> <strong>17<\/strong>, 305\u2013310 (2019).<\/li>\n<\/ul>\n<ul>\n<li><a title=\"Google Scholar\" href=\"https:\/\/scholar.google.com\/citations?user=KRum9JQAAAAJ&amp;hl=en\">Google Scholar<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Education:<\/strong><\/p>\n<ul>\n<li>PhD, 2022, Genetics, University of Cornell University<\/li>\n<li>BSc, 2018, Molecular and Cellular Biology, University of Connecticut<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=&#8221;1&#8243; admin_label=&#8221;Projects Section &#8211; Part 2&#8243; module_id=&#8221;projects&#8221; module_class=&#8221;projects-section&#8221; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221; background_color=&#8221;#f9f9f9&#8243; background_image=&#8221;https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-content\/uploads\/sites\/458\/2023\/03\/vector-feb-2021-83_generated.jpg&#8221; parallax=&#8221;on&#8221; parallax_method=&#8221;off&#8221; locked=&#8221;off&#8221;][et_pb_row _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221;][et_pb_column type=&#8221;4_4&#8243; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221;][et_pb_text admin_label=&#8221;Title&#8221; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221; text_font=&#8221;Open Sans|600|||||||&#8221; text_text_color=&#8221;#0C71C3&#8243; text_font_size=&#8221;22px&#8221; text_line_height=&#8221;1.8em&#8221;]<\/p>\n<p><span style=\"color: #000000\"><strong>Research Projects &#8211; Computational Genetics<\/strong><\/span><\/p>\n<p>[\/et_pb_text][et_pb_accordion _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221; border_radii=&#8221;on|6px|6px|6px|6px&#8221; border_width_all=&#8221;0px&#8221; box_shadow_style=&#8221;preset3&#8243;][et_pb_accordion_item title=&#8221;Genetic Architecture of Autism Spectrum Disorder&#8221; open=&#8221;on&#8221; open_toggle_text_color=&#8221;#000000&#8243; open_toggle_background_color=&#8221;#FFFFFF&#8221; closed_toggle_background_color=&#8221;#FFFFFF&#8221; icon_color=&#8221;#0C71C3&#8243; use_icon_font_size=&#8221;on&#8221; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221; border_radii=&#8221;on|6px|6px|6px|6px&#8221; border_width_all=&#8221;0px&#8221; box_shadow_style=&#8221;preset3&#8243; toggle_text_color=&#8221;#000000&#8243; toggle_font=&#8221;Open Sans||||||||&#8221;]<\/p>\n<p><span style=\"font-size: 15px\">Our efforts encompass a range of projects aimed at unraveling the genetic risk architecture of autism spectrum disorder, encompassing both common and rare variation:\u00a0<\/span><\/p>\n<ol>\n<li><span style=\"font-size: 15px\">Investigating genetic variants with a moderate effect size in ASD.<\/span><\/li>\n<li><span style=\"font-size: 15px\">Exploring tandem repeat expansions in the context of ASD.<\/span><\/li>\n<li><span style=\"font-size: 15px\">Analyzing differential gene mutations associated with ASD.<\/span><\/li>\n<li>Examining the interplay between gene-environment interactions and the heterogeneity of ASD.<\/li>\n<li>Assessing how ancestral differences contribute to the heterogeneity of ASD.<\/li>\n<li><span style=\"font-size: 15px\">Uncovering the impact of common genetic variations on ASD risk, particularly through the autoimmunity pathway.<\/span><\/li>\n<\/ol>\n<p>[\/et_pb_accordion_item][et_pb_accordion_item title=&#8221;Model Development: Variant effect prediction using deep learning &#8221; open_toggle_text_color=&#8221;#000000&#8243; open_toggle_background_color=&#8221;#FFFFFF&#8221; closed_toggle_background_color=&#8221;#FFFFFF&#8221; icon_color=&#8221;#0C71C3&#8243; use_icon_font_size=&#8221;on&#8221; _builder_version=&#8221;4.9.0&#8243; _module_preset=&#8221;default&#8221; border_radii=&#8221;on|6px|6px|6px|6px&#8221; border_width_all=&#8221;0px&#8221; box_shadow_style=&#8221;preset3&#8243; toggle_text_color=&#8221;#000000&#8243; toggle_font=&#8221;Open Sans||||||||&#8221; open=&#8221;off&#8221;]<\/p>\n<p>We are in the process of developing an innovative model utilizing deep learning methods to effectively differentiate between deleterious and non-deleterious mutations, including non-coding variants.<\/p>\n<p>[\/et_pb_accordion_item][\/et_pb_accordion][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Madison Caballero, PhD Bioinformatician IIIEmail: madison.caballero@mssm.edu Madison is a bioinformatician III at Dr. Mahjani lab\u00a0with a primary focus on investigating the role of ultra-rare genetic variation in psychiatric disorders. With a background in genetics, she specializes in analyzing large-scale genomics data using innovative computational approaches. Outside of research, Madison enjoys theater and spending time with [&hellip;]<\/p>\n","protected":false},"author":572,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-644","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-json\/wp\/v2\/pages\/644","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-json\/wp\/v2\/users\/572"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-json\/wp\/v2\/comments?post=644"}],"version-history":[{"count":14,"href":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-json\/wp\/v2\/pages\/644\/revisions"}],"predecessor-version":[{"id":804,"href":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-json\/wp\/v2\/pages\/644\/revisions\/804"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/mahjanilab\/wp-json\/wp\/v2\/media?parent=644"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}