Publications

 

2018

Couts KL, Bemis J, Turner JA, Bagby SM, Murphy D, Christiansen J, Hintzsche JD, Le A, Pitts TM, Wells K, Applegate A, Amato C, Multani P, Chow-Maneval E, Tentler JJ, Shellman YG, Rioth MJ, Tan AC, Gonzalez R, Medina T, Doebele RC, Robinson WA.  ALK Inhibitor response in melanomas expressing EML4-ALK fusions and alternate ALK isoforms.  Mol Cancer Ther 17: 222-231, 2018.  PMID: 29054983 / PMC5752582

Goldstein NB, Koster MI, Jones KL, Gao B, Hoaglin LG, Robinson SE, Wright MJ, Birlea SI, Luman A, Lambert KA, Shellman YG, Fujita M, Robinson WA, Roop DR, Norris DA, Birlea SA.  Repigmentation of human vitiligo skin by NBUVB is controlled by transcription of GLI1 and activation of the beta-catenin pathway in the hair follicle bulge stem cells.  J Invest Dermatol 138: 657-668, 2018.  PMID: 29054607 / PMC6135256

Hintzsche JD, Yoo M, Kim J, Amato CM, Robinson WA, Tan AC.  IMPACT web portal: Oncology database integrating molecular profiles with actionable therapeutics.  BMC Med Genomics 11: 26, 2018.  PMID: 29697364 / PMC5918430

Keysar S, Eagles J, Miller B, Jackson BC, Chowdhury FN, Reisinger J, Chimed TS, Le PN, Morton JJ, Somerset H, Varella-Garcia M, Tan AC, Song JI, Bowles DW, Reyland ME, Jimeno A.  Salivary gland cancer patient-derived xenografts enable characterization of cancer stem cells and new gene events associated with tumor progression.  Clin Cancer Res 24: 2935-2943, 2018.  PMID: 29555661 / PMC6004240

Kim J, Yoo M, Shin J, Kim H, Kang J, Tan AC.  Systems pharmacology-based approach of connecting disease genes in genome-wide association studies with traditional Chinese medicine.  Int J Genomics 2018: 7697356, 2018.  PMID: 29765977 / PMC5885494

Kim S, Park D, Choi Y, Lee K, Kim B, Jeon M, Kim J, Tan AC, Kang J.  A pilot study of biomedical text comprehension using an attention-based deep neural reader: Design and experimental analysis.  JMIR Med Inform 6: e2, 2018.  PMID: 29305341 / PMC5783222

Klauck PJ, Bagby SM, Capasso A, Bradshaw-Pierce EL, Selby HM, Spreafico A, Tentler JJ, Tan AC, Kim J, Arcaroli JJ, Purkey A, Messersmith WA, Kuida K, Eckhardt SG, Pitts TM.  Antitumor activity of the polo-like kinase inhibitor, TAK-960, against preclinical models of colorectal cancer.  BMC Cancer 18: 136, 2018.  PMID: 29402316 / PMC5800287

Kogut I, McCarthy SM, Pavlova M, Astling DP, Chen X, Jakimenko A, Jones KL, Getahun A, Cambier JC, Pasmooij AMG, Jonkman MF, Roop DR, Bilousova G.  High-efficiency RNA-based reprogramming of human primary fibroblasts.  Nat Commun 9: 745, 2018.  PMID: 29467427 / PMC5821705

Lee K, Kim B, Choi Y, Kim S, Shin W, Lee S, Park S, Kim S, Tan AC, Kang J.  Deep learning of mutation-gene-drug relations from the literature.  BMC Bioinformatics 19: 21, 2018.  PMID: 29368597 / PMC5784504

Pilling AB, Kim J, Estrada-Bernal A, Zhou Q, Le AT, Singleton KR, Heasley LE, Tan AC, DeGregori J, Doebele RC.  ALK is a critical regulator of the MYC-signaling axis in ALK positive lung cancer.  Oncotarget 9: 8823-8835, 2018.  PMID: 29507657 / PMC5823650

Ross BC, Boguslav M, Weeks H, Costello JC.  Simulating heterogeneous populations using Boolean models.  BMC Syst Biol 12: 64, 2018.  PMID: 29879983 / PMC5992775

Vartuli RL, Zhou H, Zhang L, Powers RK, Klarquist J, Rudra P, Vincent MY, Ghosh D, Costello JC, Kedl RM, Slansky JE, Zhao R, Ford HL.  Eya3 promotes breast tumor-associated immune suppression via threonine phosphatase-mediated PD-L1 upregulation.  J Clin Invest 128: 2535-2550, 2018.  PMID: 29757193 / PMC5983346

Yue Z, Zheng Q, Neylon MT, Yoo M, Shin J, Zhao Z, Tan AC, Chen JY.  PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.  Nucleic Acids Res 46: D668-D676, 2018.  PMID: 29126216 / PMC5753198

 

2017

Astling DP, Heft IE, Jones KL, Sikela JM.  High resolution measurement of DUF1220 domain copy number from whole genome sequence data.  BMC Genomics 18: 614, 2017.  PMID: 28807002 / PMC5556342

Donson AM, Apps J, Griesinger AM, Amani V, Witt DA, Anderson RCE, Niazi TN, Grant G, Souweidane M, Johnston JM, Jackson EM, Kleinschmidt-DeMasters BK, Handler MH, Tan AC, Gore, Virasami A, Gonzalez-Meljem JM, Jacques TS, Martinez-Barbera JP, Foreman NK, Hankinson, for the Advancing Treatment for Pediatric Craniopharyngioma Consortium.  Molecular analyses reveal inflammatory mediators in the solid component and cyst fluid of human adamantinomatous craniopharyngioma.  J Neuropathol Exp Neurol 76: 779-788, 2017.  PMID: 28859336 / PMC6005018

Gehring AM, Astling DP, Matsumi R, Burkhart BW, Kelman Z, Reeve JN, Jones KL, Santangelo TJ.  Genome replication in Thermococcus kodakarensis independent of Cdc6 and an origin of replication.  Front Microbiol 8: 2084, 2017.  PMID: 29163389 / PMC5663688

Griesinger AM, Witt DA, Grob ST, Georgio Westover SR, Donson AM, Sanford B, Mulcahy Levy JM, Wong R, Moreira DC, DeSisto JA, Balakrishnan I, Hoffman LM#, Handler MH, Jones KL, Vibhakar R, Venkataraman S, Foreman NK.  NF-kappaB upregulation through epigenetic silencing of LDOC1 drives tumor biology and specific immunophenotype in Group A ependymoma.  Neuro Oncol 19: 1350-1360, 2017.  PMID: 28510691 / PMC5596179

Lummus SC, Donson AM, Gowan K, Jones KL, Vibhakar R, Foreman NK, Kleinschmidt-DeMasters BK.  p16 Loss and E2F/cell cycle deregulation in infant posterior fossa ependymoma.  Pediatr Blood Cancer 64: e26656, 2017.  PMID: 28548702 / PMC5647247

Mitra S, Schiller D, Anderson C, Gamboni F, D'Alessandro A, Kelher M, Silliman CC, Banerjee A, Jones KL.  Hypertonic saline attenuates the cytokine-induced pro-inflammatory signature in primary human lung epithelia.  PLoS One 12: e0189536, 2017.  PMID: 29253007 / PMC5734749

Nelson-Taylor SK, Le AT, Yoo M, Schubert L, Mishall KM, Doak A, Varella-Garcia M, Tan AC, Doebele RC.  Resistance to RET-inhibition in RET-rearranged NSCLC is mediated by reactivation of RAS/MAPK signaling.  Mol Cancer Ther 16: 1623-1633, 2017.  PMID: 28500237 / PMC5544556

Ohm AM, Tan AC, Heasley L, Reyland ME.  Co-dependency of PKCdelta and K-Ras: Inverse association with cytotoxic drug sensitivity in KRAS mutant lung cancer.  Oncogene 36: 4370-4378, 2017.  PMID: 28368426 / PMC5532068

Scott AJ, Song EK, Bagby S, Purkey A, McCarter M, Gajdos C, Quackenbush KS, Cross B, Pitts TM, Tan AC, Eckhardt SG, Fenton H, Arcaroli J, Messersmith WA.  Evaluation of the efficacy of dasatinib, a Src/Abl inhibitor, in colorectal cancer cell lines and explant mouse model.  PLoS One 12: e0187173, 2017.  PMID: 29091939 / PMC5665512

Stern JL, Paucek RD, Huang FW, Ghandi M, Nwumeh R, Costello JC, Cech TR.  Allele-specific DNA methylation and its Interplay with repressive histone marks at promoter-mutant TERT genes.  Cell Rep 21: 3700-3707, 2017.  PMID: 29281820 / PMC5747321

Zhang C, Liu Z, Bunker E, Ramirez A, Lee S, Peng Y, Tan AC, Eckhardt SG, Chapnick DA, Liu X.  Sorafenib targets the mitochondrial electron transport chain complexes and ATP synthase to activate the PINK1-Parkin pathway and modulate cellular drug response.  J Biol Chem 292: 15105-15120, 2017.  PMID: 28673964 / PMC5592685

Zhou K, Spillman MA, Behbakht K, Komatsu JM, Abrahante JE, Hicks D, Schotl B, Odean E, Jones KL, Graner MW, Bemis LT.  A method for extracting and characterizing RNA from urine: For downstream PCR and RNAseq analysis.  Anal Biochem 536: 8-15, 2017.  PMID: 28803886 / PMC - In Process (NIHMS #964083)

             

Contact Information

For consultation requests, general questions, or new project requests, please use our request services form through our iLab site. Alternatively, you may email the Core Manager.

Andrew Goodspeed, PhD
Core manager and Data Analyst
Andrew.Goodspeed@cuanschutz.edu
(303) 724 6582

James Costello, PhD
Director
James.Costello@cuanschutz.edu
(303) 724 8619