http://denisdermadi.com/skills daily 0.75 2015-06-15 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432048351376-D2F9PSWF2216EA9S92J2/55H.jpg Skills https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432069737988-48PRTMOYSBSE2WKJ22IS/lab_skills.jpg Skills https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432070297955-ZW9WTSJCNFQDH18QV3DN/LV2IUQNTZ5.jpg Skills http://denisdermadi.com/blog-dna-mmr-cancer-life-science daily 0.75 2020-10-16 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/intestinal-stem-cells-and-colon-cancer-biology-to-therapy-conference-short-talk-and-poster-presentation monthly 0.5 2018-09-29 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1538198693281-8H5O4OIUF7G0PT3LA556/Poster+for+the+conference Blog - Presenting a short talk and poster on Intestinal Stem Cells and Colon Cancer: Biology to Therapy conference - Poster for the conference Poster for the AACR conference. Trajectory analysis of mouse large intestine. http://denisdermadi.com/blog-dna-mmr-cancer-life-science/single-cell-omics-stockholm-may-26th monthly 0.5 2017-05-26 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1495836336530-B8CSI3A0I8RHN8I3NSMB/Stockholm_poster.jpg Blog - Single Cell Omics, Stockholm May 26th Cancer immunotherapy has proven successful with new generations of drugs (e.g. checkpoint inhibitors) that target lymphocytes and their surface molecules, however only small fraction of the patients benefits from these drugs. Thus, it is important to uncover additional mechanisms of tumor immune evasion. Lymphocytes are recruited into tumor by endothelial cells (ECs), which are the interface between the tumor and circulating blood. Tumors induce specialized ECs, known as high endothelial venules (HEV). Induction of HEVs in tumors correlates with favorable prognosis, but many tumors use HEVs to recruit immune suppressive cells. Tumor microenvironment through conditioning of the local endothelium trafficking programs mediates recruitment of immune suppressive lymphocytes and enhances carcinogenesis. Interaction of tumors may also alter the imprinting of lymphocyte adhesion/trafficking programs in tumor draining lymph nodes (LN) either through effects on tumor derived dendritic cells or directly when the LN is invaded by metastatic cells. We take advantage of mass cytometry (CyTOF) and single cell RNA-Seq to monitor the induction and regulation of EC and leukocyte trafficking receptors in B16, B16 OVA (more immunogenic), 4T1 and colon mouse tumors. High dimensional data, rich in information, is analyzed using an innovative single cell analysis algorithm, which aligns cells in developmental trajectories using protein or gene expression(s) of single cells. This algorithm has the potential to reveal, for the first time in an unsupervised manner, complex branching and allows the detection of new functionally important cells or specific transient cell populations. http://denisdermadi.com/blog-dna-mmr-cancer-life-science/new-publication-in-cancer-research-western-diet-deregulates-bile-acid-homeostasis-cell-proliferation-and-tumorigenesis-in-colon monthly 0.5 2018-09-29 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/studying-effects-of-western-style-diet-on-colon-mucosa-part-i monthly 0.5 2015-06-13 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1433716589394-C1VX4Z2MDOIALRJ72DS8/Colon+crypt Blog - Studying effects of Western style diet on colon mucosa - part I Fig. 1 Schematic colon crypt. Differentiated cells in blue, transient amplifying cells in red, green cells are stem cells, and yellow are goblet/endocrine cells. http://denisdermadi.com/blog-dna-mmr-cancer-life-science/2015/5/20/mutator-phenotype-versus-growth-advantage-in-cancer monthly 0.5 2015-06-08 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432116384886-2ZSERMVQA4DA5RAVY0BQ/mismatch+repair Blog - Mutator phenotype versus growth advantage in cancer Mismatch repair mechanism consist of rather simple steps. First, MSH2-MSH6 detect mismatch. Second, MLH1-PMS2 is engaged and that signals EXOI to cut out mismatch. New gap in DNA strand is re-sythetized by DNA polymerase. http://denisdermadi.com/blog-dna-mmr-cancer-life-science/2015/5/26/amazing-cancer-race-2015-problematic-questions-pitstop monthly 0.5 2015-06-09 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1433711595005-SLP76PLDA7G6622OBNRM/Silent+killers Blog - Amazing Cancer Race 2015 - Provocative questions pit-stop Some teams were creative and made costumes for the race... https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1433711642440-5IS15BV8Z9ACPZRBW0Z9/IMG_1355.JPG Blog - Amazing Cancer Race 2015 - Provocative questions pit-stop ... inspired by their research. NHL or Non-Hodgkin lymphoma? http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/computational+biology monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/FXR monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/algorithms monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/endothelial+cells monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/single+cell+proteomic monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/mismatch+repair monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/apoptosis monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Activity monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Research monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/mutator+phenotype monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/H3K36me3 monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/epigenetics monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/sequencing monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Prevention monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/genome+instability monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Students monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/bile+acids monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/immunotherapy monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/cell+trafficking+programs monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Western+style+diet monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/intestine+development monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/advancing+science monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Amazing+Cancer+Race monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/proteomics monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/colon+cancer monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/developmental+biology monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/single+cell+sequencing monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Science+%26+community monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/histone+modifications monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/chromatin monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/machine+learning monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/active+trascription monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/metabolism+%26+cancer monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/mutation monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/single+cell monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Cancer+awareness monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/FABP6 monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/tumor monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/cancer+immunotherapy monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/cancer monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/growth monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Mass+spectrometry monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/CyTOF monthly 0.5 http://denisdermadi.com/blog-dna-mmr-cancer-life-science/tag/Cancer monthly 0.5 http://denisdermadi.com/denis-dermadi-phd-job daily 1.0 2022-11-01 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993464566-H8VP7C7ZGTV3EDAN1MUH/repair.jpg Denis Dermadi Bebek - Re-purposing old furniture https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993464726-Y8OIUQWA2CGQ71WVJP8J/renovation.jpg Denis Dermadi Bebek - Renovation and re-design of spaces https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993466920-P61TN4EFYVKJQ59HIRUE/10321488_1076222689074063_1769620858755632879_o.jpg Denis Dermadi Bebek - Astronomy Polar light in Helsinki | Winter 2015 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993465650-H3WF0A77QVPBQFX954KT/1484150_798222353540766_1607928023_n.jpg Denis Dermadi Bebek - Baking https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993465944-V7M0DVHARBO27YH2FTY6/941521_696606987035637_1822526954_n.jpg Denis Dermadi Bebek - Cooking https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993466396-1NGXAVA58J2SWO6CC2JB/942852_10151593156591208_582416559_n.jpg Denis Dermadi Bebek - Running After Helsinki City Run | Half marathon https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993467092-I2MJHX7WW5FZWC3IFWMJ/886994_652893511406985_995846877_o.jpg Denis Dermadi Bebek - Traveling San Francisco one of my favourite destinations. https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993468153-87225SZTK5RWD3HX3CQK/61429_424150806663_6163782_n.jpg Denis Dermadi Bebek - Excercising Gym, swimming but when weather allows I like beach volleyball https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993467555-GZRUR4S4J86M93CIACPX/63376_424142281663_907715_n.jpg Denis Dermadi Bebek - Relaxing https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993467972-JH9L4TRLO0SCTCSFGHIN/424032_368973809798958_1786648144_n.jpg Denis Dermadi Bebek - Biking I like bike trips. This one was 25 days long on Croatian islands. Similar trip I did on Cuba. https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993538767-52MW3H5S0EZLN4HGL8HM/543267_527778120585192_1529513217_n.jpg Denis Dermadi Bebek - Hiking & camping https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993538770-MILZZT6Q5Y97STI6D0IB/600327_524740340888970_1669270085_n.jpg Denis Dermadi Bebek - Quality time with friends https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993539377-JGB4O4SFTGCAQLWGK7UE/428470_516973184999019_525222603_n.jpg Denis Dermadi Bebek - Fund rising for Finnish Cancer Society https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431993539545-WAH6U6G95ZW1C7RHRWIV/430200_385695894793416_772785318_n.jpg Denis Dermadi Bebek - Writing & astronomy Hemingway's writing relaxation room - Cuba https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431988549827-7GIDSB3UCUNVIWKLDXU1/Denis_info.jpg Denis Dermadi Bebek https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431989971079-NMXRGEFELKV92D6QJ1U7/8597609828_ab32aba876_b.jpg Denis Dermadi Bebek https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431992250670-3VVUTMME4TBORPJ8ZLHQ/tumblr_nkjz52DksK1sfie3io1_1280.jpg Denis Dermadi Bebek https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1433692970326-S11UOFP0UWTYMPTMRO7R/blog+head.jpg Denis Dermadi Bebek https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432117347523-SD50H87UNWDVJZEW4S5T/photo-1420708392410-3c593b80d416.jpeg Denis Dermadi Bebek http://denisdermadi.com/denis-dermadi-drawings-life-science-portfolio daily 0.75 2015-05-20 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072541658-5V8MOT386VIHCEFGSS30/CancerBio_Summer_School_poster.jpg Drawings - Amazing Cancer Race poster Photoshop https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432118636357-EHQEIBHE1VZWHMBFYKJY/mous+goes+popart.jpg Drawings https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072485833-T81AD0PJOXW7WCM1F8KR/GENEmania.jpg Drawings - Network analysis in GeneMANIA An example of network analysis. For more finished work look at publications.An example of network analysis. For more finished work look at publications. https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072485857-THAW7LJI43L5VCCMW12G/mous+goes+popart.jpg Drawings - Mouse goes PopArt Photoshop, cover image for my PhD dissertation https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072546282-I212K088TOY43WP9Q3H6/POster_FCS.jpg Drawings - Amazing Cancer Race poster Photoshop https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072486493-NGCAGIT2OG77ETYXBT91/Colon_crypt.jpg Drawings - Colon crypt This figure was drawn in Photoshop for purposes of illustration in my PhD dissertation. Stem cells are at the bottom of the crypt: green, proliferative cells are found in the lower third of the crypt: red, and differentiated cells are in the remaining two thirds of the crypt: blue. Yellow cells are goblet cells. The cells at the top of the crypt undergo apoptosis and shredded. https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072487859-YNC7ISAKU2QSNI1Z8XR9/Stages_CRC.jpg Drawings - Colorectal cancer development This figure was drawn in Photoshop for purposes of illustration in my PhD dissertation. Abnormalities in APC and mismatch repair genes are early changes in normal epithelium leading to an early adenoma. Increase of epigenetic abnormalities is postulated to be one of the first changes in colon cancer development. additional mutations are needed for more advanced stages of colon cancer. https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072488544-EGDWF5WY8B9N3YKM5VBN/Proteomics.jpg Drawings - Proteomics experiment overview This figure was drawn in Photoshop for purposes of illustration in my PhD dissertation. After laborious wet lab, and calculation of relative protein expressions, more interesting data analysis is done: identification of differentially expressed proteins, advanced analyses e.g. hierarchical clustering and principal component analysis and systems biology - network analysis. https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072488753-2K23SR356PGRC3QSIE0Q/Cell.jpg Drawings - Effects of Western diet on cell metabolism This figure was drawn in Photoshop for purposes of illustration in my PhD dissertation. Western diet shifts energy metabolism towards fatty acid oxidation (FAO) and fatty acids become primary source of energy, which leads to upregulated oxidative phosphorylation (OXPHOS) and results in increased levels of reactive oxygen species (ROS). Increased levels of ROS damage proteins and DNA. Cellular mechanisms for reduction of ROS toxicity are activated https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432072489543-EK8IQUNUAMN3LUAKVKQA/Colon_bile_A.jpg Drawings - Bile acid metabolism Work in progress, Adobe Illustrator. http://denisdermadi.com/publications daily 0.75 2020-10-16 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1432114831074-BIBQG45CJ7X5VNBGM3SQ/VL01D336R8.jpg Publications http://denisdermadi.com/contact daily 0.75 2020-07-14 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1431994955717-YTRMS0SUDDZ4UTUTN833/contact.jpg Contact http://denisdermadi.com/tspacealgorithm daily 0.75 2019-02-16 https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550019367881-E0A8DZQL4Q2W6PILJ4GM/tspace.jpg tSpace | Trajectory Inference Algorithm - tSpace trajectory inference algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550020121828-4V7TDNX3D3QUPAH504OJ/tSpace-heatmap-7-1.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550019940399-C9VYD2EYEF1ANTKNT1JZ/tSpace-4-3.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550020259049-TH7U61EUTJ8COQNI3SPA/UMAP-tSpace-8-1.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550020056200-L0LZ550YTROTHBJ9MQIV/tSpace-6-2.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550295581990-6T33UUJ5X8FYIALK6B8U/tspace-2-1.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550019642719-0F1D4XB9J1LZE99D1XU4/tSpace-3-1.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550019686170-OVZB40VEPQKY3YI0I8UF/tSpace-4-2.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550019966957-2MZN8R3RYR25S0DEEW6U/tSpace-6-1.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550019580062-HLXPSADI57IFE1GBHVWZ/tSpace-2-2.png tSpace | Trajectory Inference Algorithm https://images.squarespace-cdn.com/content/v1/555990f2e4b07b37133d1edb/1550019669725-KFBRH9AOZRXEOWLRQ2D6/tSpace-4-1.png tSpace | Trajectory Inference Algorithm http://denisdermadi.com/read-me-marquee daily 0.75 2025-04-23 https://images.squarespace-cdn.com/content/v1/515c7b5ae4b0875140c3d94a/1373494866621-8L8TJSL19SCJDJ7JYPHM/index-collection-read-me-1.jpg Read Me https://images.squarespace-cdn.com/content/v1/515c7b5ae4b0875140c3d94a/1373494887029-4AXRW743FMOYDJKF3T3M/index-collection-read-me-2.jpg Read Me