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TAN LAB in Review: 2016 | 2015 |



  • Oct 17, 2017: Our collaborative project - PAGER 2.0: pathway, annotated-list, and gene-signature electronic repository for human network biology manuscript has been accepted in the 2018 Nucleic Acids Research Database Issue. This is a collaboration with Prof. Jake Chen and his team at the Informatics Institute, the University of Alabama at Birmingham. Congrats to Zongliang, Minjae, and Jimin! Check out the PAGER 2.0 web site.

  • Oct 16, 2017: Our lab will be going to the ROCKY 2017 Bioinformatics Conference in Snowmass/Aspen! Jihye, Jenn and Ilyssa have their abstracts accepted as both oral and poster presentation! Brian, Hyunmin and Shawna have their abstracts accepted as poster presentation! Congrats to all! See you all in ROCKY 2017! Stop by our posters and have a chat about our research!

  • Oct 16, 2017: Congrats to the Messersmith Lab for getting the Dasatinib paper accepted in PLoS ONE!.

  • Sept 29, 2017: CONGRATS TO JIHYE, Moumita and York, the DREAM team of winning the V Foundation for Translational Research 2017! Jihye is a co-PI for this award! Well deserved!!

  • Sept 13, 2017: Congrats to Casey and the Robinson lab for getting the ALK fusion in melanoma manuscript accepted in Molecular Cancer Therapeutics!

  • Aug 16, 2017: Congrats to Jenn, Minjae and Jihye! Our paper on IMPACT-WEB PORTAL has been accepted as Oral presentation in the 28th International Conference on Genome Informatics (GIW/BIOINFO 2017)! We are going to Seoul, South Korea!

  • Aug 2, 2017: Congrats to Kelsey for passing her comprehensive exam!

  • Aug 1, 2017: Congrats to Kelsey for receiving the T32 Cancer Biology training fellowship!

  • July 26, 2017: Congrats to Moumita Ghosh for receiving her R01! Jihye is part of this project! Yeah!

  • July 3, 2017: Congrats to Xuedong Liu and his team in getting the manuscript "Sorafenib Targets the Mitochondrial Electron Transport Chain Complexes and ATP Synthase to Activate the PINK1-Parkin Pathway and Modulate Cellular Drug Response" accepted in the Journal of Biological Chemistry! AC is a co-author of this manuscript.

  • June 30, 2017: Double Happiness in the lab! Congrats to Kelsey and Hyunmin!

  • June 30, 2017: Congrats to Hyunmin for receiving a research grant from the Cancer League of Colorado to develop a computational method for studying alternative splicing in cancer genomics data!

  • June 30, 2017: Congrats to Kelsey for receiving a TL1 Pre-doctoral Fellowship (T32) from the Colorado Clinical and Translational Sciences Institute (CCTSI)!

  • June 26, 2017: Congrats to Todd Hankinson and collaborators for getting the manuscript "Molecular analyses reveal inflammatory mediators in the solid component and cyst fluid of human adamantinomatous craniopharyngioma" accepted in the Journal of Neuropathology and Experimental Neurology! AC is a co-author of this paper!

  • June 1, 2017: A big welcome to Dr. Ilyssa Summer, joining us as a post-doctoral research fellow.

  • May 31, 2017: A big welcome to Georgia Phillips as a Cancer Center Summer Fellow working in our lab. Her research project will be drug-induced pathway expression changes.

  • May 15, 2017: Our paper on studying the molecular mechanisms of ENMD-2076 in triple negative breast cancer is published today in Frontiers in Oncology. Congrats to the Diamond Lab!

  • May 12, 2017: The NSCLC RET resistance paper is available online today in Molecular Cancer Therapeutics, check it out!

  • May 11, 2017: Jenn is the winner of the "I'm a Scientist USA"! Check out Five questions for Jenn Hintzsche by the CU Conections! Congrats Jenn!

  • Apr 24, 2017: Congrats to Diamond lab for getting the in vivo molecular study of ENMD-2076 in TNBC accepted in Frontiers in Oncology!

  • Apr 21, 2017: Congrats to Sarah and the Doebele lab for getting the RET resistant in NSCLC manuscript accepted in Molecular Cancer Therapeutics!

  • Apr 15, 2017: Congrats to Peter Kabos and his lab for getting the April 15 COVER of Clinical Cancer Research! This is the paper about fibroblast subtypes regulate responsiveness of luminal breast cancer to estrogen. Check it out!

  • Apr 14, 2017: Congrats to Jimin and Minjae for having their second baby boy - Jonathan Jinho Yoo - born this morning!

  • Apr 7, 2017: Kelsey presented her update talk at the Cancer Biology Seminar.

  • Apr 7, 2017: 4th Annual Mini-Symposium on the Power of Informatics to Advance Health. AC is chairing the last session before keynote.

  • Apr 3, 2017: Congrats to Mary Reyland's lab for the co-dependency of KRAS and PKC-delta paper is online today in Oncogene. Check it out!

  • Apr 3, 2017: AC has been invited to present our research in the Global Congress on Molecular Pathology (AMP Global 2017) in Berlin, Germany (Apr 3-5).

  • Mar 27, 2017: Congrats to Kelsey for being selected as an awardee for the International Visiting Scientist Award from the Graduate school. She will be visiting Dr. Rachael Natrajan, our collaborator in the Institute of Cancer Research London. Congrats!

  • Mar 15, 2017: Our paper on characterizing the mutational landscape of mucosal melanoma that identifies SF3B1 mutation is now published online in Melanoma Research. Congrats to Jenn, Kelsey, Jihye and team!

  • Mar 8, 2017: Congrats to Lynn Heasley and his team on being awarded a DoD CDMRP award entitied "Identifying TME-derived Pathways for co-targeting with FGFR1 in mesothelioma"! AC is Co-PI and we will partipate in this project! Yeah!

  • Feb 15, 2017: Congrats to Jihye of being promoted to Assistant Research Professor in the Division of Medical Oncology, Department of Medicine! Now we can call her Prof. Kim!

  • Feb 15, 2017: Please welcome Dr. Hyunmin Kim in joining our lab as a Senior Research Instructor. Hyunmin is an expert in RNA sequencing and alternative splicing, and he will contribute to a lot of our ongoing projects! Welcome Hyunmin!

  • Jan 20, 2017: Our paper on identifying recurrent mutations in mucosal melanoma has been accepted in Melanoma Research! Congrats to Jenn, Jihye and Kelsey!

  • Jan 20, 2017: Our genome-wide loss-of-function screen paper that identifies SLC26A2 as a novel mediator of TRAIL resistance is available online now in Molecular Cancer Research!

  • Jan 16, 2017: Our collaborative paper on determine the context-dependent role for chromatin remodeling component PBRM1/BAF180 in ccRCC has been published today in Oncogenesis!

  • Jan 11, 2017: Congrats to the Reyland lab! Our collaborative paper of investigating the co-dependency of PKCδ and KRAS in lung cancer has been accepted in Oncogene! Yeah!

  • Jan 9, 2017: Congrats to the Ford lab! Our collaborative paper of using functional genomics screen in identifying SLC26A2 as a novel mediator of TRAIL resistance has been accepted in Molecular Cancer Research! Yeah!

  • Jan 1, 2017: HAPPY NEW YEAR! I wish you and your family a healthy and fulfilling new year! Check out our 2016 Lab Review. Thanks for your support to our research!



  • Dec 29, 2016: Our editorial piece on intratumoral heterogeneity in hepatocellular carcinoma is published today in Translational Cancer Research. Check it out!

  • Dec 26, 2016: Congrats to Donna Zhang and her group, our collaborative paper has been accepted and published online today in Molecular Carcinogenesis [PDF].

  • Dec 22, 2016: Our big data mining of adverse events from ClinicalTrials.gov has been published in ASSAY and Drug Development Technologies today, and our paper has been selected to be the cover of this issue! Check out the COVER!

  • Dec 14, 2016: Our review paper on computational methods for Whole Exome Sequencing (WES) analysis is published today in International Journal of Genomics.

  • Dec 1, 2016: Congrats to Cheng-Jun Hu's lab ! Our collaborative paper on identying the role of PBRM1/BAF180 in clear cell renal cell carcinoma has been accepted in Oncogenesis.

  • Nov 30, 2016: Congrats to Todd Hankinson on receiving the R03 from NCI! AC is a co-Investigator for this project.

  • Nov 29, 2016: Congrats to Kelsey! Her Editorial comments on intratumoral heterogeneity has been accepted in Translational Cancer Research.

  • Nov 19, 2016: The detection of kinase gene fusions in melanoma is available online today Pigment Cell Melanoma Research.

  • Nov 18, 2016: AC visited Moffitt Cancer Center and gave a talk there! Thanks for hosting me, Dr. Ann Chen!

  • Oct 31, 2016: Congrats to Jackie and Kasey for getting the "Kinase gene fusions in defined subsets of melanoma" paper accepted in Pigment Cell and Melanoma Research! Yeah!

  • Oct 26, 2016: Our survey paper on bioinformatics tools for whole-exome sequencing data has been accepted in International Journal of Genomics! Congrats Jenn!

  • Oct 25, 2016: Our collaborative Cell Reports paper on exploiting RTK coactivation dependencies as therapeutic approach in cancers with SWI/SNF definicies is now published! Check it out.
  • Oct 19, 2016: BEST: Next-generation Biomedical Entity Search Tool is now published in PLoS ONE.

  • Oct 18, 2016: Our collaborative paper on using networks to identify candidate genes that could sensitize lung cancer cells to ALK inhibitors is now published in Science Signaling.

  • Oct 10, 2016: The PNAS paper on ATM/G6PD-driven redox metabolism promotes FLT3 inhibitor resistance in acute myeloid leukemia is available online today, Check it out!

  • Oct 10, 2016: Congrats to Kit, our paper on evaluating MLN4924 in preclinical melanoma models has been accepted in Investigational New Drugs.

  • Sept 30, 2016: Happy day! Two papers accepted, one paper published and a pilot grant awarded in the same day!

  • Sept 30, 2016: Our JoVE video on the development and maintenance of patient derived tumor xengoraft (PDX) models is now available online! Check out the cool video!!

  • Sept 30, 2016: We received a pilot grant from the RNA Bioscience Initiative to study circulating miRNAs in predicting the rate of Autosomal Dominant Polycystic Kidney Disease (ADPKD). This is a collaborative project with Profs. Bernie Gitomer and Michel Chonchol in the Renal Division!

  • Sept 30, 2016: Our collaborative paper with Jaewoo Kang and his team in developing BEST: Biomedical Entity Search Tool has been accepted in PLoS ONE today! Congrats to Sunwon! Check out the BEST web site.

  • Sept 30, 2016: Our collaborative paper with Peter Kabos and his team in studying the role of fibroblast in regulating estrogen response in ER-positive breast cancer has been accepted in Clinical Cancer Research today!

  • Sept 29, 2016: Our collaborative paper with Eric Haura and his team in Moffitt Cancer Center on identifying synthetic lethality partners in ALK inhibitors has been accepted in Science Signaling today! Congrats to Jihye and the DeGregori lab!

  • Sept 23, 2016: Combining AZ1366 and EGFR inhibitors in NSCLC paper is now available online in Clinical Cancer Research. Check it out here!

  • Sept 19, 2016: Mindy Szeto (MSTP) joins lab for a rotation. Welcome, Mindy!

  • Sept 16, 2016: DSigDB is now included as a data source in ChemSpider - a free chemical structure database providing fast access to >57 million structures, properties, and associated information. ChemSpider is owned by the Royal Society of Chemistry.

  • Sept 16, 2016: Congrats to Hannah and the DeGregori lab! Our collaborative paper of combining AZ1366 with EGFR inhibitors in non-small cell lung cancer overcomes resistance mechanisms has been accepted by the Clinical Cancer Research! Yeah! Preliminary data was generated from the SLuG genes! Congrats Jihye!

  • Sept 15, 2016: Our big data mining and adverse event pattern analysis in ClinicalTrials.gov paper is online today! Check it out at ASSAY and Drug Development Technologies.

  • Sept 15, 2016: Jimeno lab's paper on describing regualtion of head and neck squamous cancer stem cells by PI3K and SOX2 is online today! Check it out at Journal of the National Cancer Institute.

  • Sept 13, 2016: Congrats to Mark, Jihye and DeGreogri lab! Our collaborative paper of identifying ATM/G6PD-driven redox metabolism in FLT3 inhibitor resistance to AML has been accepted in PNAS!

  • Sept 7, 2016: Congrats to Paul Huang and team! Our collaborative paper "Dual targeting of PDGFRα and FGFR1 displays synergistic efficacy in malignant rhabdoid tumours" has been accepted in Cell Reports! Congrats to Karen!

  • Aug 22, 2016: Our visitor, Dr. Paul Huang will be presenting a special seminar on "New Ways to Target Tumor Suppressor Signaling Networks for Cancer Therapy", RC1S 8th Floor Conference Room from 10am - 11am. Please come and join us, and learn some new research ideas from Dr. Huang!

  • Aug 21, 2016: Congrats to Callie and Minjae! Our paper on big data mining and pattern analysis of adverse events in ClinicalTrials.gov has been accepted in ASSAY and Drug Development Technologies! Yeah!!

  • Aug 18, 2016: We have received an award of R21 from the National Cancer Institute (NCI/NIH) to study "Kinase Dependent Chemotherapy Resistance Mechanisms in Small Cell Lung Cancer"! This is a collaborative project with Drs. Jeff Kern and James Finigan in the National Jewish Health, and Dr. Charles Rudin in the Memorial Sloan Kettering Cancer Center! Yeah!!

  • Aug 17, 2016: Our paper on identifying prognostic genes in breast cancer in now available online in Oncotarget. This is a collaborative research with Paul Huang and his team in the Institute of Cancer Research, London. Karen is the co-first author of this work.

  • Aug 15, 2016: Our collaborator, Prof. Jaewoo Kang (Korea University), is visiting our lab. (8/15 - 8/22). Welcome Jaewoo!

  • Aug 11, 2016: Our collaborator, Dr. Paul Huang (The Institute of Cancer Research, London), is visiting our lab. (8/11 - 8/29). Welcome Paul!

  • Aug 5, 2016: Our paper on evaluating barasertib (AZD1152) against SCLC cell lines is now available online in Molecular Cancer Therapeutics.

  • Aug 2, 2016: HiPub is available online in Bioinformatics!

  • July 28, 2016: Congrats to Kyubum and the HiPub team! Our paper of HiPub, a seamless Chrome plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for knowledge discovery has been accepted in Bioinformatics! Yeah! Try it out today HiPub webpage.

  • July 27, 2016: Two papers were accepted today in Molecular Cancer Therapeutics and Oncotarget!! Yeah!

  • July 27, 2016: Congrats to Barb in the Bunn lab for getting the paper of evaluating barasertib (AZD1152), a novel aurora kinase B inhibitor, in small cell lung cancer accepted in Molecular Cancer Therapeutics!

  • July 27, 2016: Congrats to Karen, working together with Paul Huang and his ICR team for getting the paper "Systematic analysis of tumour cell-extracellular matrix adhesion identifies independent prognostic factors in breast cancer" accepted in Oncotarget!

  • July 25, 2016: Congrats to Bernard and Sok Ching, our collaborators at the Cancer Research Malaysia! Our collaborative paper - DESIGN - a computational pipeline to predict drug sensitivity has been accepted in the 27th International Conference on Genome Informatics (GIW2016)! This paper has been invitied to submit to BMC Genomics! Check out the DESIGN web resource!

  • July 21, 2016: Our review paper on exploiting RTK co-activation for cancer therapy is now available online Drug Discovery Today!

  • July 19, 2016: Congrats to Stephen Keysar in the Jimeno Lab for getting the paper "Regulation of head and neck squamous cancer stem cells by PI3K and SOX2" accepted in JNCI: Journal of the National Cancer Institute! Great work!

  • July 3 2016: Our collaboratorative paper on "Treating experimental arthritis with the innate inflammation inhibitor IL 37 reduces joint and systemic inflammation" has been accepted by Rheumatology. Congrats Giulio and co-authors!

  • July 1, 2016: Our paper on evaluating alisertib (MLN8237) against preclinical colorectal cancer is now available in Oncotarget. Check it out!

  • July 1, 2016: Welcoming new member to the Tan Lab. Kelsey Wuensch will be starting her Ph.D. research in our lab. Kelsey is a Cancer Biology graduate student and she will be researching in melanoma. Welcome Kelsey!

  • July 1, 2016: Welcoming new member to the Tan Lab. Paul Francoeur will be joining us as a research assistant in the lab. Paul has a background in molecular biology and biochemistry, he will be helping us with the wet experiments, as well as learning some bioinformatics projects! Welcome Paul!

  • July 1, 2016: IMPACT Whole Exome Sequencing Pipeline is published today in JAMIA. Check it out. [IMPACT paper]. It was selected as part of the JAMIA Intelligent Systems Collection to commemorate ISMB 2016 conference. Articles are freely accessible through Oct 1, 2016.

  • June 29, 2016: We received a team research grant from the Cancer League of Colorado to develop computational methods for immune-signatures. This is a collaborative grant with Gail. Thanks for the support CLC!

  • June 16, 2016: Two papers were accepted today in Drug Discovery Today and Oncotarget!! Yeah!

  • June 16, 2016: Congratulations to Todd and PETT team! Our paper on Alisertib (MLN8237) testing in preclinical colorectal cancer models has been accepted by Oncotarget!

  • June 16, 2016: Our review paper "Exploiting receptor tyrosine kinase co-activation for cancer therapy" has been accepted by Drug Discovery Today. AWESOME! This is a collaboration with Paul Huang in ICR, London.

  • June 14, 2016: Our paper "Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies" is now available online in Oncotarget.

  • June 6, 2016: AC visited Prof. Cheong's group at the Cancer Research Malaysia. Thanks Sok Ching for hosting the event.

  • June 3, 2016: AC visited the Molecular Pathology unit at the Institute of Medical Reserach Malaysia. Thanks Alan for hosting the event.

  • May 28, 2016: Congrats to Nikita! The paper that describes a new adjusted AUC metric for integrating heterogeneous pharmacogenomic studies is accepted by Oncotarget! This is an integration analysis of CCLE, GDSC and CTRP drug sensitivity data. Check out the accompanying QAPC website for results and code.

  • May 25-26, 2016: AC attended the Big Data in Biomedicine Conference in Stanford! Great line-up of speakers and a lot of interesting topics. See Presentations.

  • May 24, 2016: TJ's paper on MAPK pathway mediates resistance to Dasatinib in thyroid cancer is available online at Molecular Cancer Therapeutics today!

  • May 13, 2016: Congrats to TJ and Rebecca! The paper that identified MAPK pathway mediates resistance to Dasatinib in thyroid cancer is accepted by Molecular Cancer Therapetuics!

  • May 11, 2016: AC is giving a talk at the Institute of Cancer Research London. Thanks Paul for hosting the seminar.

  • May 6, 2016: AC is giving a talk at the Department of Chemistry, University of Cambridge. Thanks Andreas for hosting the visit.

  • May 1-14, 2016: AC is visiting Paul Huang at the Institute of Cancer Research London.

  • Apr 13, 2016: One of our papers "Antitumor Activity of the MEK Inhibitor TAK-733 against Melanoma Cell Lines and Patient-Derived Tumor Explants" published in Molecular Cancer Therapeutics 2015 was selected in the "Must Read Collections" of the journal. This collection features the most impactful article(s) published in MCT 2015. Congrats! Check it out!

  • Apr 13, 2016: BRONCO paper is published today in DATABASE. Go BRONCO! [PDF]

  • Apr 4, 2016: GenomeWeb published an article describing our IMPACT pipeline. [NEWS].

  • Apr 1, 2016: The Oncotarget paper that describes the establishment of a novel panel of oral cancer cell lines for drug development is now available online. [PDF].

  • Mar 29, 2016: The IMPACT whole-exome sequencing analysis paper is now available online in JAMIA!
  • Mar 29, 2016: Congrats to Brian as he was selected as a trainee for the NIH Ruth L. Kirschstein National Research Service Award T32CA174648 in Translational Lung, Head and Neck Cancer! Great job Brian!

  • Mar 28, 2016: Tan lab alumni, Heather Selby, now a Ph.D. candidate in the Bioinformatics Graduate Program at Boston University is visiting us from Mar 28 - Apr 1, come and say hi to her! She is giving an informal talk on Mar 30 (11am - 12pm, RC1S 8108) about her ongoing research work, come and join the talk.

  • Mar 17, 2016: Congrats to Sok Ching and her team in Cancer Research Malaysia! The paper describing a panel of newly established oral cancer cell lines for drug development has been accepted in Oncotarget!

  • Mar 9, 2016: Congrats to Kyubum! His paper that describes the BRONCO (Biomedical entity Relation ONcology COrpus) for extracting gene-variant-disease-drug relations has been accepted in DATABASE - The Journal of Biological Databases and Curation! This project started when Kyubum was a visiting student in our lab (Aug 2014 - Feb 2015) from Prof. Kang's lab (Korea University). GO BRONCO!

  • Feb 26, 2016: AC is visiting Prof. Kang's lab at Korea University, lots of research and teaching! (2/26 - 3/12).

  • Feb 24, 2016: Congrats to Stacey and John for getting the PDX method development paper accepted in The Journal of Visualized Experiments. This is the only peer-reviewed, PubMed-indexed video journal! Video is in production, stay tuned!

  • Feb 21, 2016: The Oncotaret paper from the Reyland lab is now available onlie. [PDF]

  • Feb 9, 2016: Congrats to Reyland lab for having the PKCδ regulates integrin αVβ3 expression and transformed growth of KRAS dependent lung cancer cells paper accepted by Oncotarget!!

  • Feb 1, 2016: Congrats to Jenn for her IMPACT paper has been accepted by the Journal of the American Medical Informatics Association (JAMIA)!! Yeah!

  • Jan 21, 2016: Congrats to Dillon Le for being accepted into the School of Medicine Research Track for the Class of 2019. Dillon will be developing computational tools on drug-induced gene expression changes for drug repurposing and repositoning. Welcome Dillon and Congrats!

  • Jan 21, 2016: Congrats to Jimeno lab for publishing the XactMice model today in Oncogene. [PDF] [PubMed].

  • Jan 13, 2016: Congrats to Schedin lab for publishing the study of Mammary epithelial cell phagocytosis downstream of TGF-B3 is characterized by adherens junction reorganization in Cell Death and Differentiation.[PDF] [PubMed]

  • Jan 4, 2016: Congrats to Jimeno lab for publishing the pilot study of combining cetuximab and IPI-926 in recurrent/metastatic head and neck cancer in Oral Oncology.[PubMed]

  • Jan 1, 2016: Two papers were published today:

  • Jan 1, 2016: Prof. Jaewoo Kang from the Korea University is visiting us until Jan 15, 2016. Welcome Jaewoo!

  • Jan 1, 2016: Happy New Year 2016! Our lab 2015 in review is out now, thanks for your support to our research!