https://oncinfo.org/ 2026-04-18T09:04:25+00:00 https://oncinfo.org/ https://oncinfo.org/_media/wiki:logo.png text/html 2018-11-01T13:41:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/aamirzainulabadeen?rev=1541079699&do=diff I am an undergraduate student in the Department of Computer Science at Princeton University. My other interests include poetry, distance running, and fitness swimming. I'll be participating once more in the REUSSA program at Texas State University during the summer of 2017 ( text/html 2023-04-21T18:31:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/amir_foroushani?rev=1682101894&do=diff [p1030127.jpg] ---------- I was a Postdoctoral Research Associate in Oncinfo lab from November 2014 until May 2016. I received my Ph.D. in Molecular Biology from the Simon Fraser University (SFU) and my M.Sc. in Computer Science from the University of Texas at Dallas ( text/html 2024-07-15T17:40:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/azad_khosh?rev=1721065256&do=diff Azad Khosh [Azad.jpg] With a multidisciplinary background spanning molecular and cellular biology, bioinformatics, and robotics, I am pursuing a PhD in the integrated biomedical sciences program at UTHealth Science Center at San Antonio. As a student researcher at the dynamic environment of the Oncinfo Lab and text/html 2024-12-11T20:24:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/bioinformatics_for_biologist_workshop?rev=1733948659&do=diff Bioinformatics for biologist workshop Objectives This workshop is a practical introduction to some basic bioinformatics tools for audience with little computational skills. The participants will have hands-on experience with simple, toy-example data. The following material was used in 2015 in two sections of the workshop in The University of Texas Health Science Center at San Antonio. text/html 2019-11-14T04:37:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/cave_2017?rev=1573706256&do=diff We (Aamir, Bryan, Gabriel, Hanie, Habil and Saba) went to Natural Bridge Caverns and Snake Farm on 2017-06-30. [oncinfo.org_lib_plugins_ckgedit_fckeditor_userfiles_image_wiki_public_cave2017.jpg] [img_20170630_121732077_hdr.jpg] [img_20170630_121648483_hdr.jpg] [img_20170630_121410395.jpg] [img_20170630_121338306_hdr.jpg] [img_20170630_120122781_hdr.jpg] [20170630_122501.jpg] [20170630_104417.jpg] [20170630_103914.jpg] [20170630_101944.jpg] [20170630_101915.jpg] text/html 2021-09-12T04:29:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/clonal_decomposition?rev=1631420944&do=diff Clonal decomposition Publications Zare, Habil, et al. “Inferring Clonal Composition from Multiple Sections of a Breast Cancer.” PLoS computational biology 10.7 (2014): e1003703. Alexander Gelfand, Cancer's heterogeneity: Modeling Tumors’ Diversity, Biomedical Computation Review2015. Software text/html 2025-12-06T17:49:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/for_members?rev=1765043372&do=diff How can I join the Oncinfo Lab? To join and be a good member of the Oncinfo Lab, you need to: * Be organized and disciplined, otherwise your efforts will be fruitless and lost even if you make important discoveries. Other lab members will enjoy working with you if your code is clean and you can clearly talk about your project. text/html 2020-05-27T03:00:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/gene_networks_inference?rev=1590548406&do=diff Gene networks inference Objectives Biological processes in a cell often require intricate coordination between multiple genes and proteins. The goal of this project is to infer useful biological and clinical information from large networks of thousands of genes. We develop an integrative approach to analyze co-expression and DNA methylation patterns in a single model. The results will be useful in pinpointing the cause and mechanism of complex diseases such as cancer. Our findings can potentia… text/html 2020-10-25T00:40:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/ghazal_ebrahimi?rev=1603586417&do=diff [photo_2018-03-31_11-16-28.jpg] I am an undergraduate student at Sharif University, and a guest member in the Oncinfo Lab. My CV Ghazal's lab notebook. Contact Details: Email : <mailto:ghazalebrahimi1997@gmail.com> text/html 2018-06-25T12:25:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/hanie_samimi?rev=1529929543&do=diff I am a graduate student at Texas State University. I obtained my Bachelor of Computer Science from University of Tehran, Iran in 2016. [My CV] Hanie's lab notebook. Contact Details: hanie.samimi@gmail.com h_s163@txstate.edu text/html 2020-12-16T00:03:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/hepatocellular_carcinoma?rev=1608076985&do=diff Hepatocellular carcinoma Objectives Hepatocellular carcinoma (HCC) is a the most common type of liver cancer and the third leading cause of cancer deaths in the world. Cirrhosis of the liver is a major risk and contributing factor for HCC. The goal of project one is to identify the genes that are associated with regressing tumors (regardless of type of treatment) vs. those that are growing from the C3HeB/FeJ mouse model. Normal liver is used as a control. The results will be useful in identi… text/html 2025-01-28T14:27:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/how_to?rev=1738074463&do=diff How to This is a collection of short answers and links to some miscellaneous questions that we have had while doing research in Oncinfo. This can also be a useful resource for other scholars in the field of computational biology with similar interests and challenges. text/html 2021-05-26T17:34:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/isha_mehta?rev=1622050463&do=diff Isha Mehta [fullsizeoutput_3.jpeg] Email: ishamehta25@gmail.com Location: School of Medicine, Room # 2.048V. [CV Link] Isha's lab notebook Isha's lab notebook-2 Isha's lab notebook-3 text/html 2019-05-15T20:02:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/jessica_zavadil?rev=1557950521&do=diff I was a PhD-MD student at the University of Texas Health Science Center in San Antonio. I collaborated with Oncinfo Lab in the Hepatocellular carcinoma project. Jessica's lab notebook text/html 2019-06-13T17:29:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/machine_learning_and_molecular_biology_requirements?rev=1560446972&do=diff Machine learning and molecular biology requirements These are two exemplar papers from the Oncinfo Lab, which illustrate the extend of biology and machine learning you need to know to be successful here as a PhD student. The bars are lower for MSc studnets and higher for postdocs. text/html 2019-05-10T22:35:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/mcl-sll?rev=1557527716&do=diff This page contains supplementary material for the manuscript entitled: “Automated analysis of multidimensional flow cytometry data improves diagnostic accuracy between mantle cell lymphoma and small lymphocytic lymphoma.” Autors: Habil Zare, Ali Bashashati, Robert Kridel, Nima Aghaeepour, Gholamreza Haffari, Joseph M. Connors,Randy D. Gascoyne, Arvind Gupta, Ryan R. Brinkman, and text/html 2020-10-25T00:32:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/meghan_short?rev=1603585957&do=diff [profpic.jpg] Short, Meghan I am a biostatistician, and currently a postdoc at the Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases. My mentor is Dr. Sudha Seshadri and I am learning computational biology techniques in the Oncinfo Lab to analyze multiomics data in the context of Alzheimer's research. text/html 2024-07-24T19:53:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/multiomics_analysis_for_dementia?rev=1721850833&do=diff Multiomics analysis for dementia Objectives Determine biomarkers for Alzheimer's and other neurodegenerative diseases using comprehensive analysis of multi-omics data including genomics, epigenomics, metabolomics, proteomics, etc. Data Large cohorts with phenotype data on dementia are available through the following resources (incomplete text/html 2025-10-29T16:04:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/oncinfo?rev=1761753866&do=diff Welcome to the Oncinfo Lab! Oncinfo is a research lab at the University of Texas Health Science Center at San Antonio . The focus of our projects is on bioinformatics and computational biology. We develop and apply sophisticated machine learning algorithms to analyze large biological, or clinical, data sets. From these complex data, our goal is to infer useful information that provides insight into biology, or leads to clinical applications. Oncinfo contributes to neuroscience through collabo… text/html 2022-03-03T17:14:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/postdoctorial_fellowship_awards?rev=1646327685&do=diff Pre and postdoctoral award opportunities for research on cancer, aging, and computational biology The first 8 rows in following table was composed in April 2015 by searching in Pivot database. Newer rows were added later Award Deadline Amount Comment text/html 2021-10-14T20:08:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/r_test?rev=1634242130&do=diff An R test These simple questions are designed to test the applicants on their expertise in R, self learning, working under pressure, presenting their results, and explaining their work. If you get help from people and internet, please include the person's name and the link to the webpage in your answers. text/html 2023-04-21T18:27:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/raheleh_roudi?rev=1682101636&do=diff Raheleh Roudi I am a visiting scientist in the Oncinfo Lab. Since 2011, I have been designing and conducting wet lab experiments to investigate the cellular and molecular aspects of solid tumors. In the Oncinfo Lab, I learn and apply computational biology techniques in several studies on Alzheimer's disease and other text/html 2019-07-29T18:46:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/rapamycin?rev=1564425984&do=diff Rapamycin effects on aging-associated pathologies Objectives Rapamycin is an inhibitor of the mTOR pathway and it has been used in preventing rejection of solid organ allografts. In this multi-PI study on an older age healthy human cohort, we assess the usability and efficacy of Rapamycin in improving physical performance, cardiac and vascular health, and immune outcomes. This approach is motivated by the promising results that were observed in prior studies on mice models. Oncinfo contributes… text/html 2019-12-25T01:51:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/serum_biomarkers_for_neurodegeneration?rev=1577238675&do=diff Serum biomarkers for neurodegeneration Objectives Identify novel serum biomarkers for neurodegeneration that allow accurate diagnosis of Alzheimer's disease (AD) in Hispanic and non-Hispanic white populations (Specific [Aims] ). Data * Six proteins were measured in blood samples of ~1200 Hispanic and ~500 non-Hispanic white participants. Covariates include gender, education, and age. text/html 2024-03-12T04:00:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/shiva_kazempour?rev=1710216034&do=diff Shiva Kazempour [img_2023.jpg] I am a biostatistician, and currently a PhD candidate in the Integrated Biomedical Sciences (IBMS) at the Oncinfo Lab. My PhD focus is on developing new deep learning models for handling and exctracting the best features from spatial transcriptomics. text/html 2023-04-21T14:46:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/sogand_sajedi?rev=1682088393&do=diff Sogand Sajedi [sogand.jpg] I graduated from Vienna University of Technology with a Ph.D. in engineering sciences and a master's degree in biomedical engineering. My dissertation focused on computational modeling and developing algorithms for analyzing neurons in the cochlea, retina, and brain in response to electrical stimulation. I have the required programming skills, which are essential in computational biology. As a postdoctoral associate at the Oncinfo Lab, I expand my knowledge and use m… text/html 2018-06-25T12:26:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/the_list_of_computational_biology_papers_in_nature_methods?rev=1529929578&do=diff The following articles were published in Nature Methods in 2015 in anti-chronological order. Application notes, brief communications, and alike are mostly excluded. * Walzthoeni, Thomas, et al. “xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. text/html 2024-03-28T15:32:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://oncinfo.org/useful_tools_for_functional_and_pathway_analysis?rev=1711639978&do=diff Useful tools for functional and pathway analysis and target identification If you have a list of genes, and you want to know their functions, the diseases and pathways they might be associated with, and some known or candidate drug targets for them, you can use the following tools and databases. Your gene list might have been obtained from differential expression or other omics analyses, gene network analysis, a genome-wide association study (