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JHMI Transcriptomics and Deep Sequencing Core Publications

This is a list of publications that has either used data generated through the core or used assistance from the core data analysis unit. Names in bold indicates current and prior members of the core facility. This may not be a complete list. If you are a core user and has published a paper using data generated from the core and the paper is not listed here, we would appreciate if you can let us know. Thank you!

Total: 432

Core Member Co-Authored: 144

  • 2020(14/3)

  • 2019(28/9)

  • 2018(37/18)

  • 2017(35/9)

  • 2016 (44/10)

    • Horiuchi Y, Kondo MA, Okada K, Takayanagi Y, Tanaka T, Ho T, Varvaris M, Tajinda K, Hiyama H, Ni K, Colantuoni C, Schretlen D, Cascella NG, Pevsner J, Ishizuka K, and Sawa A.
      Molecular signatures associated with cognitive deficits in schizophrenia: a study of biopsied olfactory neural epithelium.
      Transl. Psychiatry. 2016. 6(10): e915. DOI: 10.1038/tp.2016.154. PMID: 27727244.
      [Affymetrix Human U133 Plus 2.0 array hybridization and processing]
    • Lee J, Choi J, Scafidi S, and Wolfgang MJ.
      Hepatic Fatty Acid Oxidation Restrains Systemic Catabolism during Starvation.
      Cell Rep. 16(1): 201-212. PMID: 27320917.
      [Affymetrix mouse Exon 1.0ST array and data analysis]
    • Lee J, Choi J, Aja S, Scafidi S, and Wolfgang MJ.
      Loss of Adipose Fatty Acid Oxidation Does Not Potentiate Obesity at Thermoneutrality.
      Cell Rep. 14(6): 1308-1316. PMID: 26854223.
      [Affymetrix mouse Exon 1.0 ST array and data analysis]
    • Paksa A, Bandemer J, Hoeckendorf B, Razin N, Tarbashevich K, Minina S, Meyen D, Biundo A, Leidel SA, Peyrieras N, Gov NS, Keller PJ, and Raz E.
      Repulsive cues combined with physical barriers and cell-cell adhesion determine progenitor cell positioning during organogenesis.
      Nat. Commun. 2016. 7: 11288. PMID: 27088892.
      [RNAseq and data analysis]
    • Edward DP, Mahale A, Hao H, Khan A, Hameed S, Al Jadaan I, Owaidhah O, Kondkar AA, Al Shamrani M, Shahwan SA, and Abu-Amero KK.
      Aqueous humor microRNA profiling in primary congenital glaucoma.
      J. Transl. Sci. DOI:10.15761/JTS.1000169.
      [Affymetrix miRNA v4 and data analysis]
    • Sido JM, Jackson AR, Nagarkatti PS, and Nagarkattis M.
      Marijuana-derived ∆-9-tetrahydrocannabinol suppresses Th1/Th17 cell-mediated delayed-type hypersensitivity through microRNA regulation.
      J Mol Med. 2016. 94(9):1039-51. PMID: 27038180.
      [Affymetrix miRNA 4.0 microarray]
    • Liang L, Gu X, Zhao J-Y, Wu S, Miao X, Xiao J, Mo K, Zhang J, Lutz BM, Bekker A, and Tao Y-X.
      G9a participates in nerve injury-induced Kcna2 downregulation in primary sensory neurons.
      Sci Rep. 6:37704. PMID: 27874088.
      [Affymetrix Mouse Exon 1.0ST array]
    • Benjamin JS, Pilarowski GO, Carosso GA, Zhang L, Huso DL, Goff LA, Vernon HJ, Hansen KD, and Bjornsson HT.
      A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome.
      Proc. Natl. Acad. Sci. USA. 2016 Dec. 20. pii:201611431. PMID: 27999180.
      [Affymetrix Mouse Gene 1.0 ST array]
    • van de Garde MDB, Movita D, van der Heide M, Herschke F, De Jonghe S, Gama L, Boonstra A, and Vanwolleghem T.
      Liver Monocytes and Kupffer Cells Remain Transcriptionally Distinct during Chronic Viral Infection.
      PLOS One. http://dx.doi.org/10.1371/journal.pone.0166094. PMID: 27812182.
      [Nanostring Assay]
    • Sharma N, LaRusch J, Sosnay P, Gottschalk LB, Lopez A, Pellicore MJ, Evans T, Davis E, Atalar M, Na CH, Rosson GD, Belchis D, Milewski M, Pandey A, and Cutting GR.
      A sequence upstream of canonical PDZ binding motif within CFTR C-terminus enhances NHERF1 interaction.
      Am J. Physiol Lung Cell Mol Physiol. [Epub ahead of print]. PMID: 27793802.
    • Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CRL, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, and Burns KH.
      Somatic retrotransposition is infrequent in glioblastomas.
      Mobile DNA 7,22. DOI:10.1186/s13100-016-0077-5. PMID: 27843500.
      [Illumina Sequencing and Affymetrix SNP 6.0]
    • Ladle BH, Li K-P, Phillips MJ, Pucsek AB, Haile A, Powell JD, Jaffee EM, Hildeman DA, and Gamper CJ.
      De novo DNA methylation by DNA methyltransferase 3a controls early effector CD8+ T-cell fate decisions following activation.
      Proc Natl Acad Sci USA. 113(38), 10631-6. PMID: 27582468.
      [Nanostring Gene Expression Assay]
    • Zimmerlin L, Park TS, Huo JS, Verma K, Pather SR, Talbot CC Jr., Agarwal J, Steppan D, Zhang YW, Considine M, Guo H, Zhong X, Gutierrez C, Cope L, Canto-Soler MV, Friedman AD, Baylin SB, and Zambidis ET.
      Tankyrase inhibition promotes a stable human naϊve pluripotent state with improved functionality.
      Development. 2016 Sep 22. pii:dev.138982. [Epub ahead of print]. PMID:27660325.
      [data analysis]
    • Bam M, Yang X, Zumbrun EE, Zhong Y, Zhou J, Ginsberg JP, Leyden Q, Zhang J, Nagarkatti PS, and Nagarkatti M.
      Dysregulated immune system networks in war veterans with PTSD is an outcome of altered miRNA expression and DNA methylation.
      Sci Rep. 6, 31209. PMID:27510991.
      [Affymetrix miRNA array]
    • Chaw RC, Arensburger P, Clarke III TH, Ayoub NA, and Hayashi CY.
      Candidate egg case silk genes for the spider Argiope argentata from differential gene expression analyses.
      Insect Mol Bio. 2016 Aug 8.doi:10.1111/imb.12260 [Epub ahead of print]. PMID: 27500384.
      [RNAseq library preparation]
    • Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, and Zelikovsky A.
      Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.
      in Research in Computational Molecular Biology. Volume 9649 of the series Lecture Notes in Computer Science. pp. 164-175.
      [PacBio Sequencing]
    • Sliva A, Kuang Z, Meluh PB, and Boeke JD.
      Barcode sequencing screen identifies SUB1 as a regulator of yeast pheromone inducible genes.
      G3(Bethesda). 2016. 6(4), 881-92. PMID: 26837954.
      [Deep Sequencing: barcode seq, ChIPseq, RNAseq]
    • Gottschalk LB, Vecchio-Pagan B, Sharma N, Han ST, Franca A, Wohler ES, Batista DAS, Goff LA, and Cutting GR.
      Creation and characterization of an airway epithelial cell line for stable expression of CFTR variants.
      J Cyst Fibros. 15, 285-94. PMID: 26694805.
    • Mvubu NE, Pillay B, Gamieldien J, Bishai W, and Pillay M.
      Canonical pathways, networks and trancriptional factor regulation by clinical strains of Mycobacterium tuberculosis in pulmonary alveolar epithelial cells.
      Tuberculosis. 97, 73-85. PMID:26980499.
    • Mvubu NE, Pillay B, Gamieldien J, Bishai W, and Pillay M.
      Mycobacterium tuberculosis strains exhibit differential and strain-specific molecular signatures in pulmonary epithelial cells.
      Dev Comp Immuolo. 65, 321-329. PMID: 27497873.
    • Kleensang A, Vantaangoli MM, Odwin-Dacosta S, Andersen ME, Boekelheide K, Bouhifd M, Fornace Jr AJ, Li H-H, Livi CB, Madnick S, Maertens A, Rosenberg M, Yager JD, Zhaog L, and Hartung T.
      Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function.
      Sci Rep 6, 28994. PMCID: PMC4960662.
      [Agilent miRNA and CGH/SNP arrays]
    • Foster DB, Liu T, Kammers K, O'Meally R, Yang N, Papanicolaou KN, Talbot CC Jr, Cole RN, and O'Rourke B.
      Integrated Omic Analysis of a Guinea Pig Model of Heart Failure and Sudden Cardiac Death.
      J Proteome Res. 2016 Aug. 3. [Epub ahead of print]. PMID: 27399916.
      [Affymetrix Guinea Pig GeneChip array and data analysis]
    • O'Grady T, Wang X, zu Bentrup KH, Baddoo M, Concha M, and Flemington EK.
      Global transcript structure resolution of high gene density genomes through multi-platform data integration.
      Nucl. Acids Res. 2016. 44(18),e145. PMID: 27407110.
      [PacBio Iso-Seq]
    • Williams DW, Engle EL, Shirk EN, Queen SE, Gama L, Mankowski JL, Zink MC, and Clements JE.
      Splenic Damage during SIV infection: Role of T-Cell Depletion and Macrophage Polarization and Infection.
      Am J. Pathol. 186(8), 2068-87. PMID: 27322772.
      [Nanostring Assay]
    • Campbell DP, Chrysostomou E, and Doetzlhofer A.
      Canonical Notch signaling plays an instructive role in auditory supporting cell development.
      Sci. Rep. 2016; 6: 19484. PMID: 26786414.
      [Affymetrxi mouse Exon 1.0ST arrays and data analysis]
    • Oh Y, Cho GS, Li Z, Hong I, Zhu R, Kim MJ, Kim YJ, Tampakakis E, Tung L, Huganir R, Dong X, Kwon C, Lee G.
      Functional Coupling with Cardiac Muscle Promotes Maturation of hPSC-Derived Sympathetic Neurons.
      Cell Stem Cell. Published Online ahead of Print 16 June, 2016. PMID:27320040.
      [Affymetrix Human PrimeView array]
    • Burr R, Stewart EV, Shao W, Zhao S, Hannibal-Bach HK, Ejsing CS, and Espenshade PJ.
      Mga2 Transcription Factor Regulates an Oxygen-responsive Lipid Homeostasis Pathway in Fission Yeast.
      JBC. 291, 12171-12183. PMID:27053105.
      [data analysis]
    • Salzberg SL, Breitwieser FP, Kumar A, Hao H, Burger P, Rodriguez FJ, Lim M, Quiñones-Hinojosa A, Gallia GL, Tornheim JA, Melia MT, Sears CL, and Pardo CA.
      Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system.
      Neuroimmunol. Neuroinflam. 2016. 3(4),e251. Published online June 13, 2016.
      [Nucleic Acid extraction, DNAseq, and RNAseq]
    • Heidecker B, Kittleson MM, Kasper EK, Wittstein IS, Champion HC, Russell ST, Baughman KL, and Hare JM.
      Transcriptomic Analysis Identifies the Effect of Beta-Blocking Agents on a Molecular Pathway of Contraction in the Heart and Predicts Response to Therapy.
      JACC:Basic to Translational Science. 2016. 1, 107-121.
      [Affymetrix Human U133Plus 2.0 GeneChip]
    • Zheng F, Kim YJ, Moran TH, Li H, and Bi S.
      Central transthyretin acts to decrease food intake and body weight.
      Sci Rep. 2016. 6:24238. PMID: 27053000.
      [Affymetrix Rat Genome 230 2.0 GeneChip]
    • Wu D, Talbot CC Jr, Liu Q, Jing ZC, Damico RL, Tuder R, Barnes KC, Hassoun PM, and Gao L.
      Identifying microRNAs targeting Wnt/&beta-catenin pathway in end-stage idiopathic pulmonary arterial hypertension.
      J Mol Med (Berl). 2016 [Epub ahead of print]. PMID: 27188753.
      [Agilent miRNA microarray and data analysis]
    • Choi IY, Lim HT, Estrellas K, Mula J, Cohen TV, Zhang Y, Donnelly CJ, Richard J-P, Kim YJ, Kim H, Kazuki Y, Oshimura M, Li HL, Hotta A, Rothstein J, Maragakis N, Wagner KR, and Lee G.
      Concordant but varied phenotypes among Duchenne muscular dystrophy patient-specific myoblasts derived using a huma iPSC-based model.
      Cell Reports. 2016. pii:S2211-1247(16)30584-8.[Epub ahead of print]. PMID: 27239027.
      [Microarray and Date Analysis]
    • Khan SY, Vasanth S, Kabir F, Gottsch JD, Khan AO, Chaerkady R, Lee MW, Leitch CC, Ma Z, Laux J, Villasmil R, Khan SN, Riazuddin S, Akram J, Cole RN, Talbot CC, Pourmand N, Zaghloul NA, Hejtmancik JF, and Riazuddin SA.
      FOXE3 contributes to Peters anomaly through transcriptional regulation of an autophagy-associated protein termed DNAJB1.
      Nat. Commun. 2016. 7, 10953. PMID: 27218149.
      [data analysis]
    • Kimura K and Huang RCC.
      Tetra-O-Methyl Nordihydroguaiaretic Acid Broadly Suppresses Cancer Metabolism and Synergistically Induces Strong Anticancer Activity in Combination with Etoposide, Rapamycin and UCN-01.
      PLoS One. 11(2): e0148685. PMID: 26886430.
      [RNAseq and data analysis]
    • Uosaki H, Cahan P, Lee DI, Wang S, Miyamoto M, Fernandez L, Kass DA, and Kwon C.
      Transcriptional Landscape of Cardiomyocyte Maturation.
      Cell Rep. 13(8), 1705-16. PMID: 26586429.
      [Affymetrix Mouse MOE430 2.0 array]
    • Tomaszkiewicz M, Rangavittal S, Cechova M, Sanchez RC, Fescemyer HW, Harris R, Ye D, O'Brien PC, Chikhi R, Ryder OA, Ferguson-Smith MA, Mevedev P, and Makova KD.
      A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.
      Genome Res. 26(4), 530-540. PMID: 26934921.
      [PacBio Sequencing]
    • Kim D, Hossain MZ, Nieves A, Gu L, Ratliff TS, Oh SM, Park A, Han S, Yang NB, Qi J, Taube JM, Kang S, and Garza LA.
      To Control Site-Specific Skin Gene Expression, Autocrine Mimics Paracrine Canonical Wnt Signaling and is Activated Ectopically in Skin Disease.
      Am J Pathol. 186(5), 1140-50. PMID: 27105735.
      [Affymetrix Human Exon 1.0ST]
    • de Melo J, Zibetti C, Clark BS, Hwang W, Miranda-Angulo AL, Qian J, and Blackshaw S.
      Lhx2 is an essential factor for retinal gliogenesis and Notch signaling.
      J. Neurosci. 36(8), 2391-405. PMID: 26911688.
    • Cheung KJ, Padmanaban V, Silvestri V, Schipper K, Cohen JD, Fairchild AN, Gorin MA, Verdone JE, Pienta KJ, Bader JS, and Ewald AJ.
      Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters.
      Proc. Natl. Acad. Sci. USA. 113(7): E854-63. PMID: 26831077.
    • Steinberg B, and Ostermeier M.
      Environmental changes bridge evolutionary valleys.
      Sci. Advances. 2(1):e1500921. PMID: 26844293.
      [PacBio RS II sequencing]
    • Rettig EM, Talbot C, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig E, Wheelan S, Marchionni L, Considine M, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, and Agrawal N.
      Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.
      Cancer Prev. Res. (Phila.). 2016 Feb. 9 [Epub ahead of print]. PMID: 26862087.
      [data analysis]
    • Wood LW, Cox NI, Phelps CA, Lai SC, Poddar A, Talbot C Jr, and Mu D.
      Thyroid Transcription Factor 1 Reprograms Angiogenic Activities of Secretome.
      Sci. Rep. 6,19587. PMID:26912193.
      [data analysis]
    • Guan H, Singh UP, Rao R, Mrelashvili D, Sen S, Hao H, Zumbrun EE, Singh NP, Nagarkatti PS, and Nagarkatti M.
      Inverse Correlation of Expression of miR-140-5p with Progression of Multiple Sclerosis and Differentiation of Encephalitogenic Th1 cells.
      Immunology. Accepted Article (published online first Jan 18, 2016). PMID: 26780721.
      [Affymetrix miRNA 4.0]
    • Loganathan R, Lee JS, Wells MB, Grevengoed E, Slattery M, and Andrew DJ.
      Ribbon regulates morphogenesis of the Drosophila embryonic salivary gland through transcriptional activation and repression.
      Dev Biol. 409(1),234-50. PMID: 26477561.
      [Affymetrix Drosophila genome 2.0 array and data analysis]
  • 2015 (28/10)

    • Sinclair SH, Yegnasubramanian S, and Dumler JS.
      Global DNA methylation changes and differential gene expression in Anaplasma phagocytophilum-infected human neutrophils.
      Clinical Epigenetics. 7, 77. PMID: 26225157.
      [data analysis]
    • Kremkow BG, Baik JY, MacDonald ML, and Lee KH.
      CHOgenome.org 2.0: Genome resources and website updates.
      Biotechnol. J. 10(7), 931-8. PMID:25923813.
      [PacBio RS II Sequencing]
    • Lee SS, Bohrson C, Pike AM, Wheelan SJ, and Greider CW.
      ATM Kinase Is Required for Telomere Elongation in Mouse and Human Cells.
      Cell Reports. 13(8), 1623-1632. PMID: 26586427.
      [PacBio RS II Sequencing]
    • Blum D, Hao H, McCarthy M, and Reproducibility Project: Cancer Biology.
      Registered report: Transcriptional amplification in tumor cells with elevated c-Myc.
      eLife. 2015; 4:e04024. DOI:http://dx.doi.org/10.7554/eLife.04024.001.>
      [Nanostring assay]
    • Drahos J, Schwameis K, Orzolek LD, Hao H, Birner P, Tayler PR, Pfeiffer RM, Schoppmann SF, and Cook MB.
      MicroRNA profiles of Barrett's esophagus and esophageal adenocarcinoma: differences in glandular non-native epithelium.
      Cancer Epidemiology, Biomarkers & Prevention. Published Online First November 24, 2015. PMID:26604271.
      [Nanostring human miRNA assay]
    • Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, and Zelikovsky A.
      2SNV: Quasispecies Reconstruction from PacBio Reads.
      Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on. DOI:10.1119/ICCABS.2015.7344730.
      [PacBio Sequencing]
    • Lee YS, Talbot CC Jr, and Lee SJ.
      Genome-wide expression analysis comparing hypertrophic changes in normal and dysferlinopathy mice.
      Genom Data. 6, 253-257. PMCID: PMID:26697388.
      [Affymetrix mouse Exon 1.0ST array and data analysis]
    • Mainigi M, Rosenzweig JM, Lei J, Mensah V, Thomaier L, Talbot Jr CC, Olalere D, Ord T, Rozzah R, Johnston MV, and Burd I.
      Peri-implantation hormonal Milieu: elucidating mechanisms of adverse neurodevelopmental outcomes.
      Reprod. Sci. Published online before print Nov. 26, 2015. PMID:26614264.
      [Affymetrix mouse Gene 1.0ST and miRNA 3.0, data analysis]
    • Gaykalova DA, Manola JB, Ozawa H, Zizkova V, Morton K, Bishop JA, Sharma R, Zhang C, Michailida C, Considine M, Tan M, Fertig EJ, Hennessey PT, Ahn J, Kock WM, Westra WH, Khan Z, Chung CH, Ochs MF, and Califano JA.
      NF-kB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma.
      IJC. 137(8), 1879-1889. PMID: 25857630.
      [Affymetrix Human Exon 1.0ST and SNP 6.0 array]
    • Truong DM, Hewitt FC, Hanson JH, Cui X, and Lambowitz AM.
      Retrohoming of a mobile group II intron in human cells suggests how eukaryotes limit group II intron proliferatioin.
      PLoS Genetics. Aug. 4, 2015. DOI:10.1371/journal.pgen.1005422. PMID:26241655.
      [PacBio RS II sequencing]
    • Khan SY, Hackett SF, Lee MW, Pourmand N, Talbot CC Jr, and Riazuddin SA.
      Transcriptome Profiling of Developming Muring Lens Through RNA Sequencing.
      Invest Ophthalmol Vis Sci. 2015 56(8), 4919-4926. PMID: 26225632.
      [RNAseq data analysis]
    • Periz G, Lu J, Zhang T, Kankel MW, Jablonski AM, Kalb R, McCampbell A, and Wang J.
      Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
      PLoS Biology. DOI:10.1371/journal.pbio.1002114. PMID:25837623.
      [Affymetrix Human Gene 1.0ST array, data analysis]
    • Lee Y-S, Lehar A, Sebald S, Liu M, Swaggart KA, Talbot Jr CC, Pytel P, Barton ER, McNally EM, and Lee S-J.
      Muscle hypertrophy induced by myostatin inhibition accelerates degeneration in dysferlinopathy.
      Hum. Mol. Genet. (2015). First published online: July 23, 2015. DOI: 10.1093/hmg/ddv228.
      [Affymetrix Mouse Exon 1.0ST and data analysis]
    • Clarke TH, Garb JE, Hayashi CY, Arensburger P, and Ayoub NA.
      Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.
      Genome Biol Evol. 7(7),1856-1870. DOI: 10.1093/gbe/evv110.
      [RNAseq library preparation]
    • Hosseini I. Gama L, Gabhann FM.
      Multiplexed component analysis to identify genes contributing to the immune response during acute SIV infection.
      PLOS One. May 18, 2015. DOI: 10.1371/journal.pone.0126843
      [Nanostring nCounter Assay]
    • Guan H, Singh U, Singh N, Hao H, Nagarkatti P, and Nagarkatti M.
      Unique gut commensal bacteria in CD44 deficient mice can ameliorate experimental autoimmune encephalomyelitis (THER7P.943).
      The Journal of Immunology. 194 (1 Supplement) 208.3.
      [16s rRNA gene metagenomic sequencing and data analysis]
    • Poirier JT, Gardner EE, Connis N, Moreira AL, de Stanchina E, Hann CL, and Rudin CM.
      DNA methylation in small cell lung cancer defines distinct disease subtypes and correlates with high expression of EZH2.
      Oncogene Mar. 9, 2015.[Epub ahead of print] PMID: 25746006.
      [RNA and DNA extraction]
    • Foley K, Rucki AA, Xiao Q, Zhou D, Leubner A, Mo G,Kleponis J, Wu AA, Sharma R, Jiang Q, Anders RA, Iacobuzio-Donahue CA, Hajjar KA, Maitra A, Jaffee EM, and Zheng L.
      Semaphorin 3D autocrine signaling mediates the metastatic role of annexin A2 in pancreatic cancer.
      Science Signaling 8(388), ra77. PMID:26243191.
      [Affymetrix mouse Exon 1.0ST]
    • Bazley FA, Liu CF, Yuan X, Hao H, All AH, De Los Angeles A, Zambidis ET, Gearhart JD, and Kerr CL.
      Direct Reprogramming of Human Primordial Germ Cells into Induced Pluripotent Stem Cells: Efficient Generation of Genetically Engineered Germ Cells.
      Stem Cells and Development 24(22), 2634-2648. PMID:26154167.
      [Affymetrix Human U133 Plus 2.0 and data analysis]
    • Nelson AM, Reddy SK, Ratliff TS, Hossain MZ, Katseff AS, Zhu AS, Chang E, Resnik SR, Page C, Kim D, Whittam AJ, Miller LS, and Garza LA.
      dsRNA released by tissue damage activates TLR3 to drive skin regeneration.
      Cell Stem Cell 17(2), 139-151. PMID: 26253200.
      [Affymetrix mouse Exon 1.0ST array and data analysis]
    • Ewing AD, Cacita A, Wood LD, Ma F, Xing D, Kim M-S, Manda SS, Abril G, Pereira G, Makohon-Moore A, Looijenga LHJ, Gillis AJM, Hruban RH, Anders RA, Romans KE, Pandey A, Iacobuzio-Donahue CA, Bogelstein B, Kinzler KW, Kazazian Jr HH, and Solyom S.
      Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution.
      Genome Research. 25:1-10.
      [Affymetrix SNP 6.0 and data analysis]
    • Liu S, Wang Y, Worley PF, Mattson MP, and Gaiano N.
      The canonical Notch pathway effector RBP-J regulates neuronal plasticity and expression of GABA transporters in hippocampal networks.
      Hipposampus. 25(5), 670-678. PMID:25515406.
      [Mouse Gene 1.0ST]
    • Alder JK, Barkauskas CE, Limjunyawong N, Stanley SE, Kembou F, Tuder RM, Hogan BLM, Mitzner W, and Armanios M.
      Telomere dysfunction causes alveolar stem cell failure.
      PNAS; 112(16), 5099-5104. PMID: 25840590.
      [Affymetrix mouse Exon 1.0ST]
    • Movita D, van de Garde MD, Biesta P, Kreefft K, Haagmans B, Zuniga E, Herschke F, De Jonghe S, Gama L, Boonstra A, and Vanwolleghem T.
      Inflammatory monocytes recruited to the liber within 24 hours after virus-induced inflammation resemble Kupffer cells but are functionally distinct.
      J. Virol. 89(9), 4809-4817. PMID:25673700.
      [Nanostring nCounter Assay]
    • Bol GM, Vesuna F, Xie M, Zeng J, Aziz K, Gandhi N, Levine A, Irving A, Korz D, Tantravedi S, Heerma van Voss MR, Gabrielson K, Bordt EA, Polster BM, Cope L, van der Groep P, Kondaskar A, Rudek MA, Hosmane RS, van der Wall E, van Diest PJ, Tran PT, Raman V.
      Targeting DDX3 with a small molecule inhibitor for lung cancer therapy.
      EMBO Molecular Medicine. DOI 10.15252/emmm.201404368
      [Affymetrix Human Gene 1.0ST array]
    • Kouo T, Huang L, Pucsek AB, Cao M, Solt S, Armstrong T, and Jaffee E.
      Galectin-3 shapes antitumor immune responses by suppressing CD8+ T cells via LAG-3 and inhibiting expansion of plasmacytoid dendritic cells.
      Cancer Immunol Res; 3(4), 412-423.
      [Affymetrix mouse Exon 1.0ST array and Nugen amplification]
    • Cai Y, Agmon N, Choi WJ, Ubide A, Stracquadanio G, Caravelli K, Hao H, Bader JS, and Boeke JD.
      Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes.
      PNAS January 26, 2015. Published online before print. doi:10.1073/pnas.1424704112
      [RNA isolation and RNAseq]
    • Deng K, Pertea M, Rongvaux A, Wang L, Durand CM, Gihaur G, Lai J, McHugh HL, Hao H, Zhang H, Margolick JB, Gurer C, Murphy AJ, Valenzuela DM, Yancopoulos GD, Deeks SG, Strowig T, Kumar P, Siliciano JD, Salzberg SL, Flavell RA, Shan L, and Siliciano RF.
      Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations.
      Nature. 517, 381-385 (15 January 2015) doi:10.1038/nature14053. PMID:25561180
      [PacBio RS II sequencing and Illumina MiSeq Sequencing, Sequence alignment]
  • 2014 (27/6)

    • Le A, Stine ZE, Nguyen C, Afzal J, Sun P, Hamaer M, Siegel NM, Gouw AM, Kang B-h, Yu S-H, cochran RL, Sailor KA, Song H, and Dang CV.
      Tumorigenicity of hypoxic respiring cancer cells revealed by a hypoxia-cell cycle dual reporter.
      Proc Natl Acad Sci USA. 2014 Aug 26; 111(34): 12486-91. DOI: 10.1073/pnas.1402012111. PMID: 25114222.
      [Bioinformatic Analysis]
    • Yolken RH, Jones-Brando L, Dunigan DD, Kannan G, Dickerson F, Severance E, Sabunciyan S, Talbot CC Jr, Prandovszke E, Gurnon JR, Agarkova IV, Leister F, Gressitt KL, Chen O, Deuber B, Ma F, Pletnikov MV, and Van Etten JL.
      Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice.
      Proc. Natl. Acad. Sci. U.S.A. 2014. 111(45), 16106-11. PMID: 25349393.
      [Affymetrix Mouse Exon 1.0ST array and data analysis]
    • Zhou Y and Nathans J.
      Gpr124 controls CNS angiogenesis and blood-brain barrier integrity by promoting ligand-specific cannonical Wnt signaling.
      Dev. Cell. 2014. 31(2): 248-256. PMID:25373781.
    • Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AEE, and Wardle FC.
      Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression.
      BMC Biology 2014. 12:81. PMID: 25277163.
      [RNAseq and data analysis]
    • He X, Cao Y, Wang L, Han Y, Zhou G, Cai Y, Chang H, and Gao P.
      Human Fibroblast Reprogramming to Pluripotent Stem Cells Regulated by the miR19a/b-PTEN Axis.
      PLoS ONE 9(4): e95213. DOI: 10.1371/journal.pone.0095213.
      [Affymetrix miRNA 2.0 microarray]
    • Sun W, Gaykalova DA, Ochs MF, Mambo E, Arnaoutakis D, Liu Y, Loyo M, Agrawal N, Howard J, Li R, Ahn S, Fertig E, Sidransky D, Houghton J, Buddavarapu K, Sanford T, Chouldhary A, Darden W, Adai A, Latham G, Bishop J, Sharma R, Westra WH, Hennessey P, Chung CH, and Califano JA.
      Activation of the NOTCH Pathway in Head and Neck Cancer.
      Cancer Res. 74, 1091-1104. PMID: 24351288.
      [Affymetrix SNP 6.0 and Human Exon 1.0ST]
    • Huang X, Shah S, Wang J, Ye Z, Dowey SN, Tsang KM, Mendelsohn LG, Kato GJ, Kickler TS, and Cheng L.
      Extensive Ex Vivo Expansion of Functional Human Erythroid Precursors Established From Umbilical Cord Blood Cells by Defined Factors.
      Molecular Therapy. 22(2), 451-463. PMID: 24002691.
      [Affymetrix Human Gene 1.0ST array]
    • Guintivano J, Arad M, Gould TD, Payne JL, and Kaminsky ZA.
      Antenatal prediction of postpartum depression with blood DNA methylation biomarker.
      Molecular Psychiatry. 19-560-567. PMID: 23689534.
      [Affymetrix Mouse Tilling 1.0 array]
    • Lun S, Miranda D, Kubler A, Guo H, Maiga MC, Wingless K, Pelly S, and Bishai, WR.
      Synthetic lethality reveals mechanisms of Mycobacterium tuberculosis resistance to ß-lactams.
      mBio; 5(5):e01767-14. PMID: 25227469.
      [RNAseq data analysis]
    • Masuda T, Zhang X, Berlinicke C, Wan J, Yerrabelli A, Conner EA, Kjellstrom S, Bush R, Thorgeirsson SS, Swaroop A, Chen S, and Zack DJ.
      The transcription factor GTF21RD1 regulates the topology and function of photoreceptors by modulating photoreceptor gene expression across the retina.
      The Journal of Neuroscience; 34(46), 15356-15368. doi:10.1523/JNEUROSCI.2089-14.2014.
      [Affymetrix mouse Exon 1.0ST array]
    • Black CM, Armstrong TD, and Jaffee EM.
      Apoptosis-regulated low-avidity cancer-specific CD8+ T cells can be rescued to eliminate HER2/neu-expressing tumors by costimulatory agonists in tolerized mice.
      Cancer Immunol Res; 2(4), 307-319.
      [Affymetrix mouse Exon 1.0ST array and Nugen amplification]
    • Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, and Chandrasegaran S.
      Total synthesis of a functional designer eukaryotic chromosome.
      Science. 344(6179), 55-58. [PMCID: PMC4033833]
      [DNAseq, RNAseq]
    • Pike A, Vadlamani A, Sandiford SL, Gacita A, and Dimopoulos G.
      Characterization of the Rel2-regulated transcriptome and proteome of Anopheles stephensi identifies new anti-Plasmodium factors.
      Insect Biochem. Mol. Bio. 52, 82-93. PMID: 24998399.
      [Array Scan]
    • Zhou Y, Wang Y, Tischfield M, Williams J, Smallwood PM, Rattner A, Taketo MM, and Nathans J.
      Canonical WNT signaling components in vascular development and barrier formation.
      J. Clin. Invest. 124(9), 3825-46. PMID: 25083995.
    • Shamir ER, Pappalardo E, Jorgens DM, Coutinho K, Tsai W-T, Aziz K, Auer M, Tran PT, Bader JS, and Ewald AJ.
      Twist1-induced dissemination preserves epithelial identity and requires E-cadherin.
      JCB. 204(5), 839-856. PMID:24590176.
    • Haney RA, Ayoub NA, Clarke TH, Hayashi CY and Garb JE.
      Dramatic expansion of the black widow toxin arsenal uncovered by multi-tissue transcriptomics and venom proteomics.
      BMC Genomics. 15, 366. PMID:24916504.
      [RNAseq library preparation]
    • Clarke TH, Garb JE, Hayashi CY, Haney RA, Lancaster AK, Corbett S, and Ayoub NA.
      Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit.
      BMC Genomics. 15, 365. PMID: 24916340.
      [RNAseq library preparation]
    • Spivak JL, Considine M, Williams DM, Talbot Jr CC, Rogers O, Moliterno AR, Jie C, and Ochs MF.
      Two clinical phenotypes in polycythemia vera.
      N Engl J Med 2014; 371:808-817. PMID: 25162887.
      [Affymetrix U133A and data analysis]
    • Miskimon M, Han S, Lee JJ, Ringkamp M, Wilson MA, Petralia RS, Dong X, Worley PF, Baraban JM and Reti IM.
      Selective expression of Narp in primary nociceptive neurons: Role in microglia/macrophage activation following nerve injury.
      J. Neuroimmunol. (2014)
      [RNA QC]
    • Li R, Ochs MF, Ahn SM, Hennessey P, Tan M, Soudry E, Gaykalova DA, Uemura M, Brait M, Shao C, Westra W, Bishop J, Fertig EJ, and Califano, JA.
      Expression Microarray Analysis Reveals Alternative Splicing of LAMA3 and DST Genes in Head and Neck Squamous Cell Carcinoma.
      PLoS One 9(3): e91263.
      [Human Exon 1.0ST array]
    • Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, and Zelikovsky A.
      Reconstruction of Influenza A Virus Variants from PacBio Reads.
      ? 2014 IEEE
      [PacBio RS Sequencing]
    • Bai B, Liu H, and Laiho M.
      Small RNA expression and deep sequencing analyses of the nucleolus reveal the presence of nucleolus-associated microRNAs.
      FEBS Open Bio. (2014) 4, 441-449. PMID: 24918059.
      [Ncode miRNA Microarray]
    • Meulendyke KA, Ubaida-Mohien C, Drewes JL, Liao Z, Gama L, Witwer KW, Graham DR, and Zink MC.
      Elevated Brain Monoamine Oxidase Activity in SIV- and HIV-associated Neurological Disease.
      J. Infect Dis. (2014). doi: 10.1093/iinfdis/jiu194. PMID: 24688074.
    • Mahairaki V, Ryu J, Peters A, Chang Q, Li T, Park TS, Burridge PW, Conover Talbot Jr C, Asnaghi L, Martin LJ, Zambidis ET, and Koliatsos VE.
      Induced Pluripotent Stem Cells from Familial Alzheimer's Disease Patients Differentiate into Mature Neurons with Amyloidogenic Properties.
      Stem Cells Dev. [Epub ahead of print] (2014) PMID:25027006.
      [data analysis]
    • Wu H, Luo J, Yu H, Rattner A, Mo A, Wang Y, Smallwood PM, Erlanger B, Wheelan SJ, Nathans J.
      Cellular Resolution Maps of X Chromosome Inactivation: Implications for Neural Development, Function, and Disease.
      Neuron 81(1), 103-119.
      [Nugen RNAseq V2]
    • Yeo AS, Azhar NA, Yeow W, Talbot CC Jr, Khan MA, Shankar EM, Rathakrishnan A, Azizan A, Wang SM, Lee SK, Fong MY, Manikam R, Sekaran SD.
      Lack of clinical manifestations in asymptomatic dengue infection is attributed to broad down-regulation and selective up-regulation of host defence response genes.
      PLoS One 9(4): e92240
      [data analysis]
    • Xiao J, Li Y, Prandovszky E, Karuppagounder SS, Talbot CC Jr, Dawson VL, Dawson TM, Yolken RH.
      MicroRNA-132 dysregulation in toxoplasma gondii infection has implications for dopamine signaling pathway.
      Neuroscience, 268, 128-138.
      [Affymetrix miRNA 2.0 array and data analysis]
  • 2013 (22/3)

    • Haberman RP, Colantuoni C, Koh MT, and Gallagher M.
      Behaviorally activated mRNA expression profiles produce signatures of learning and enhanced inhibition in aged rats with preserved memory.
      PLoS One. 2013. 8(12):e83674. DOI: 10.1371/journal.pone.0083674. PMID: 24349543.
      [Affymetrix Rat Genome 230 2.0 array]
    • Fertig EJ, Markovic A, Danilova LV, Gaykalova DA, Cope L, Chung CH, Ochs MF, and Califano JA.
      Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis.
      PLoS One. 2013; 8(11):e78127. PMID: 24223768.
      [Affymetrix Human Exon 1.0ST array]
    • Gerber JM, Gucwa JL, Esopi D, Gurel M, Haffner MC, Vala M, Nelson WG, Jons RJ, and Yegnasubramanian S.
      Genome-wide comparison of the trancriptomes of highly enriched normal and chronic myeloid leukemia stem and progenitor cell populations.
      Oncotarget. 4(5), 715-728. PMID: 23651669.
      [Affymetrix Human Exon 1.0ST]
    • Sim S, Jupatanakul N, Ramirez JL, Kang S, Romero-Vivas CM, Mohammed H, and Dimopoulos G.
      Transcriptomic Profiling of Diverse Aedes aegypti Strains Reveals Increased Basal-level Immune Activation in Dengue Virus-refractory Populations and Identifies Novel Virus-vector Molecular Interactions.
      PLoS Negl. Trop. Dis. 7(7), e2295. PMID:23861987.
      [Array Scan]
    • Kulkarni P.
      A Multiplex Cancer/Testis Antigen-Based Biomarker Panel to Predict the Aggressive Phenotype of Prostate Cancer.
      Annual rept. 30-Sep2012-29 Sep 2013. ADA590492.
    • Brebi P, Maldonado L, Noordhuis MG, Ili C, Leal P, Garcia P, Brait M, Ribas J, Michailidi C, Perez J, Soudry E, Tapia O, Guzman P, Muñoz S, Van Neste L, Van Criekinge W, Irizarry R, Sidransky D, Roa JC, Guerrero-Preston R.
      Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population.
      Epigenetics, 9(2),308-317.
      [data analysis]
    • Ho Y-C, Shan L, Hosmane NN, Wang J, Laskey SB, Rosenbloom DIS, Lai J, Blankson JN, Siliciano JD, and Siliciano RF.
      Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure.
      Cell 155(3), 540-551.
      [PacBio RS Sequencing: amplicon sequencing and Circular Consensus Sequencing]
    • Xin X, Rodrigues M, Umapathis M, Kashiwabuchi F, Ma T, Babapoor-Farrokhran S, Wang S, Hu J, Bhutto I, Welsbie DS, Juh EJ, Handa JT, Eberhart CG, Lutty G, Semenza GL, Montaner S, and Sodhi A.
      Hypoxic retinal Müller cells promote vascular permeability by HIF-1-dependent up-regulation of angiopoietin-like 4.
      PNAS,110(36), E3425-E3434.
      [Human Gene 1.0ST GeneChips]
    • Donnelly CJ, Zhang P-W, Pham JT, Haeusler AR, Mistry NA, Vidensky S, Daley EL, Poth EM, Hoover B, Fines DM, Maragakis N, Tienary PJ, Petrucelli L, Traynor BJ, Wang J, Rigo F, Bennett CF, Blackshaw S, Sattler R, and Rothstein JD.
      RNA Toxicity from the ALS/FTD C90RF72 Expansion Is Mitigated by Antisense Intervention.
      Neuron, 80(2), 415-428.
      [Human Exon 1.0ST GeneChips and Nanostring Assay]
    • Huang X, Shah S, Wang J, Ye Z, Dowey SN, Tsang KM, Mendelsohn LG, Kato GJ, Kickler TS, and Cheng L.
      Extensive Ex Vivo Expansion of Functional Human Erythroid Precursors Established From Umbilical Cord Blood Cells by Defined Factors.
      Molecular Therapy advance online publication 15 October 2013; doi:10.1038/mt.2013.201.
      [Human Gene 1.0ST GeneChip]
    • Rattner A, Yu H, Williams J, Smallwood PM, Nathans J.
      Endothelin-2 signaling in the neural retina promotes the endothelial tip cell state and inhibits angiogenesis.
      PNAS 2013 110:E3830-E3839.
      [RNAseq, Affymetrix Mouse 430 2.0 microarray]
    • Russell JN, Clements JE, Gama L.
      Quantitation of Gene Expression in Formaldehyde-Fixed and Fluorescence-Activated Sorted Cells.
      PLoS One 2013, 8(9): e73849.
      [NanoString Assay]
    • Demokan S, Chuang AY, Chang X, Khan T, Smith IM, Pattani KM, Dsgupta S, Begum S, Khan Z, Liegeois NJ, Westra WH, Sidransky D, Koch W, and Califano JA.
      Identification of guaninie nucleotide-binding protein γ-7 as an epigenetically silenced gene in head and neck cancer by gene expression profiling.
      Int. J. Oncol. 2013; 42(4), 1427-1436.
      [Affymetrix Human U133 Plus 2.0 array]
    • Yan G, Eller MS, Elm C, Larocca CA, Ryu B, Panova IP, Dancy BM, Bowers EM, Meyers D, Lareau L, Cole PA, Taverna SD, and Alani RM.
      Selective inhibition of p300 HAT blocks cell cycle progression, induces cellular senescence, and inhibits the DNA damage response in melanoma cells.
      J. Invest. Dermat. 2013; advance online publication 23 May, 2013; DOI: 10.1038/jid.2013.187
      [Affymetrix Human Exon 1.0ST array]
    • Guintivano J, Arad M, Gould TD, Payne JL, and Kaminsky ZA.
      Antenatal prediction of postpartum depression with blood DNA methylation biomarkers.
      Mol. Psychiatry. 2013. Advanced online publication 21 May 2013: doi: 10.1038/mp.2013.62.
      [Affymetrix mouse promoter 1.0R array]
    • Garcia TA, Ventura CL, Smith MA, Merrell DS, and O'Brien AD.
      Cytotoxic Necrotizing Factor 1 and Hemolysin from Uropathogenic Escherichia coli Elicit Different Host Responses in the Murine Bladder.
      Infect. Immun. 2013; 81(1), 99-109. DOI: 10.1128/IAI.oo605-12
      [Agilent 4X44k mouse whole genome array]
    • Guan H, Fan D, Mrelashvili D, Hao H, Singh NP, Singh UP, Nagarkatti PS, and Nagarkatti M.
      MicroRNA let-7e is associated with the pathogenesis of experimental autoimmune encephalomyelitis.
      Eur. J. Immunol. 2013; 43, 104-114. DOI: 10.1002/eji.201242702
      [miRNA array, data analysis]
    • Mor E, Kano S-I, Cloantuoni C, Sawa A, Navon R, and Shomron N.
      MicroRNA-382 expression is elevated in the olfactory neuroepithelium of schizophrenia patients.
      Neurobiology of Disease. 2013 55, 1-10.
      [Human U133 Plus 2.0 array]
    • Kondo MA, Tajinda K, Colantuoni C, Hiyama H, Seshadri S, Huang B, Pou S, Furukori K, Hookway C, Jaaro-Peled H, Kano S-I, Matsuoka N, Harada K, Ni K, Pevsner J, and Sawa A.
      Unique pharmacological actions of atypical neuroleptic quetiapine: possible role in cell cycle/fate control.
      Transl. Psychia. 2013 3,e243.
      [Mouse MOE 430 2.0 array]
    • Chen H, Wang N, Zhao X, Ross CA, O'Shea KS, and McInnis MG.
      Gene Expression alterations in bipolar disorder postmortem brains.
      Bipolar Disorders. 2013 15(2), 177-187.
      [Human U133 Plus 2.0 array]
    • Shah SN, Cope L, Poh W, Belton A, Roy S, Talbot Jr CC, Sukuar S, Huso DL, and Resar LM.
      HMGA1: a master regulator of tumor progression in triple-negative breast cancer cells.
      PLoS ONE, 8(5): e63419. doi 10.1371/journal.pone.0063419.
      [Human Exon 1.0ST array, data analysis]
    • Matthaei M, Hu J, Meng H, Lackner E-M, Eberhart CG, Qian J, Hao H, and Jun AS.
      Endothelial cell whole genome expression analysis in a mouse model of early-onset Fuchs' endothelial corneal dystrophy.
      IOVS. 54, 1931-1940.
      [Mouse Exon 1.0ST array, data analysis]
  • 2012 (20/7)

    • Menezes LF, Zhou F, Patterson AD, Piontek KB, Krausz KW, Gonzalez FJ, and Germino GG.
      Network analysis of a Pkd1-mouse model of autosomal dominant polycystic kidney disease identifies HNF4α as a disease modifier.
      PLoS Genet. 2012. 8(11): e1003053. DOI: 10.1371/journal.pgen.1003053. PMID: 23209428.
      [Agilent Mouse miRNA array]
    • Pattani KM, Soudry E, Glazer CA, Ochs MF, Wang H, Schussel J, Sun W, Hennessey P, Mydlarz W, Loyo M, Demokan S, Smith IM, and Califano JA.
      MAGEB2 is activated by promoter demethylation in head and neck squamous cell carcinoma.
      PLoS One. 2012. 7(9): e45534. DOI: 10.1371/journal.pone.0045534. PMID: 23029077.
      [Affymetrix Human U133 Plus 2.0]
    • Hu L, Gocke AR, Knapp E, Rosenzweig JM, Grishkan IV, Baxi EG, Zhang H, Margolick JB, Whartenby KA, and Calabresi PA.
      Functional blockade of the voltage-gated potassium channel Kv1.3 mediates reversion of T effector to central memory lymphocytes through SMAD3/p21cip1 signaling.
      J. Biol. Chem. 2012. 287(2): 1261-8. DOI: 10.1074/jbc.M111.296798. PMID: 22110135.
      [Affymetrix Human U133 Plus 2.0 array and data analysis]
    • Starrett JR.
      Molecular Evolution of Silk Genes in Mesothele and Mygalomorph Spiders, With Implications for the Early Evolution and Functional Divergence of Silk.
      Ph.D. Dissertation, University of California Riverside.
      [RNAseq library preparation]
    • Shah T, Stasinopoulos I, Wildes F, Kakkad S, Artemov D, and Bhujwalla ZM.
      Noninvasive imaging identifies new roles for cyclooxygenase-2 in choline and lipid metabolism of human breast cancer cells.
      NMR in Biomed. 2012 25(5), 746-754.
      [Human U133 Plus 2.0 array]
    • Yu H, Ye X, Guo N, and Nathans J.
      Frizzled 2 and frizzled 7 function redundantly in convergent extension and closure of the ventricular septum and palate: evidence for a network of interacting genes.
      Development. 139, 4383-4394.
      [Mouse MOE 430 2.0 array]
    • Gardner EJ, Nizami ZF, Talbot Jr. CC, and Gall JG.
      Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis.
      Genes & Dev. 2012. 26, 2550-2559.
      [RNAseq, Xenopus tropicalis Genome array, data analysis]
    • Maeda Y, Tsuchiya T, Hao H, Tompkins DH, Xu Y, Mucenski ML, Du L, Keiser AR, Fukazawa T, Naomoto Y, Nagayasu T, and Whitsett JA.
      KrasG12D and Nkx2-1 haploinsufficiency induce mucinous adenocarcinoma of the lung.
      J. Clin. Invest. 2012 Nov 12. pii: 64048. doi: 10.1172/JCI64048. [Epub ahead of print].
      [ChIPseq, data analysis]
    • Dasgupta S, Jang JS, Shao C, Mukhopadhyay ND, Sokhi UK, Das SK, Brait M, Talbot Jr. CC, Yung RC, Begum S, Westra WH, Hoque MO, Ping Y, Yi JE, Lam S, Gazdar AF, Fisher PB, Jen J, and Sidransky D.
      SH3GL2 is frequently deleted in non-small cell lung cancer and downregulates tumor growth by modulating EGFR signaling.
      J. Mol. Med. 2012 Sep 12. [Epub ahead of print]
      [Mapping 500K array, data analysis]
    • Park TS, Huo JS, Peters A, Talbot Jr. CC, Verma K, Zimmerlin L, Kaplan IM, and Zambidis ET.
      Growth factor-activated stem cell circuits and stromal signals cooperatively accelerate non-integrated iPSC reprogramming of human myeloid progenitors.
      PLoS One 7(8): e42838. doi:10.1371/journal.pone.0042838.
      [data analysis]
    • Haberman RP, Quigley CK, and Gallagher M.
      Characterization of CpG island DNA methylation of impairment-related genes in a rat model of cognitive aging.
      Epigenetics 2012, 7(9), 1-12.
      [Rat 230 2.0 array]
    • Munshaw S, Hwang HS, Torbenson M, Quinn J, Hansen KD, Astemborski J, Mehta SH, Ray SC, Thomas DL, and Galagopal A.
      Laser captured hepatocytes show association of butyrylcholinesterase gene loss and fibrosis progression in hepatitis C-infected drug users.
      Hepatology. 2012, 56(2), 544-554.
      [Human U133 Plus 2.0 array]
    • Pashai N, Hao H, All A, Gupta S, Chaerkady R, De Los Angeles A, Gearhart JD, and Kerr CL.
      Genome-wide profiling of pluripotent cells reveals a unique molecular signature of human embryonic germ cells.
      PLoS One 2012, 7(6): e39088. doi:10.1371/journal.pone.0039088
      [Human U133 Plus 2.0 array, data analysis]
    • Cooper CL, Hardy RR, Reth M, and Desiderio S.
      Non-cell-autonomous hedgehog signaling promotes murine B lymphopoiesis from hematopoietic progenitors.
      Blood. 2012 119(23), 5438-5448.
      [Mouse Exon 1.0ST array]
    • Tang HL, Tang HM, Mak KH, Hu S, Wang SS, Wong KM, Wong CST, Wu HY, Law HT, Liu K, Talbot Jr CC, Lau WK, Montell DJ, and Fung MC.
      Cell Survival, DNA Damage and Oncogenic Transformation Following a Transient and Reversible Apoptotic Response.
      Mol. Biol. Cell. 23(12), 2240-2252. doi:10.1091/mbc.E11-11-0926.
      [data analysis]
    • Zhang T, Hwang H-Y, Hao H, Talbot Jr C, and Wang J.
      Caenorhbaditis elegans RNA-processing protein TDP-1 regulates protein homeostasis and life span.
      JBC 2012, 287, 8371-8382. doi: 10.1074/jbc.M111.311977
      [C. elegans Genome array, data analysis]
    • Witwer KW, Watson AK, Blankson JN, and Clements JE.
      Relationships of PBMC MicroRNA Expression, Plasma Viral Load, and CD4+ T-Cell Count in HIV-1-infected Elite Suppressors and Viremic Patients.
      Retrovirology 2012, 9(1), 5.
      [Nanostring miRNA assay]
    • Gama L, Shirk EN, Russell JN, Carvalho KI, Li M, Queen SE, Kalil J, Zink MC, Clements JE, and Kallas EG.
      Expansion of a Subset of CD14highCD16negCCR2low/neg Monocytes Functionally Similar to Myeloid-derived Suppressor Cells During SIV and HIV Infection.
      J. Leukoc. Biol. 91(5), 803-816.
      [NanoString Gene Expression assay]
    • Dasgupta S, Soudry E, Mukhopadhyay N, Shao C, Yee J, Lam S, Lam W, Zhang W, Gazdar AF, Fisher PB, and Sidransky D.
      Mitochondrial DNA Mutations in Respiratory Complex-1 in Never-Smoker Lung Cancer Patients Contribute to Lung Cancer Progression and Associated with EGFR Gene Mutation.
      J. Cell. Physiol. 2012, 227(6), 2451-2460.
      [Mito Chip]
    • Sim S, Ramirez JL, and Dimopoulos G.
      Dengue Virus Infection of the Aedes aegypti Salivary Gland and Chemosensory Apparatus Induces Genes that Modulate Infection and Blood-Feeding Behavior.
      PLoS Pathog. 2012, 8(3), e1002631.
      [Agilent 4X44K Gene Expression array scan]
  • 2011 (40/15)

    • Shao C, Sun W, Tan M, Glazer CA, Bhan S, Zhong X, Fakhry C, Sharma R, Westra WH, Hoque MO, Moskaluk CA, Sidransky D, Califano JA, and Ha PK.
      Integrated, genome-wide screening for hypomethlated oncogenes in salivary gland adenoid cystic carcinoma.
      Clin. Cancer Res. 2011. 17(13): 4320-30. DOI: 10.1158/1078-0432.CCR-10-2992. PMID: 21551254.
      [Affymetrix Human U133 Plus 2.0 array]
    • Kim Y, Sharov AA, McDole K, Cheng M, Hao H, Fan C-M, Gaiano N, Ko MSH, Zheng Y.
      Mouse B-Type Lamins Are Required for Proper Organogenesis But Not by Embryonic Stem Cells.
      Science. 2011 Dec 23; 334(6063), 1706-1710. [DOI: 10.1126/science.1211222]
      [Nimblgen aCGH array]
    • Schuldenfrei A, Belton A, Kowalski J, Talbot Jr CC, Di Cello F, Poh W, Tsai HL, Shah SN, Huso TH, Huso DL, Resar LM.
      HMGA1 Drives Stem Cell, Inflammatory Pathways, and Cell Cycle Progression Genes During Lymphoid Tumorigenesis.
      BMC Genomics.2011, 12: 549
      [Affymetrix mouse 430 2.0 array and data analysis]
    • Creamer TJ, Darby MM, Jamonnak N, Schaughency P, Hao H, Wheelan SJ, Corden J.
      Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1.
      PLoS Genet. 2011, 7(10): e1002329. doi:10.1371/journal.pgen.1002329
      [Agilent aCGH/ChIP-on-chip arrays and data analysis]
    • Guo C, Gerasimova T, Hao H, Ivanova I, Chakraborty T, Selimyan R, Oltz EM, Sen R.
      Two Forms of Loops Generate the Chromatin Conformation of the Immunoglobulin Heavy-Chain Locus.
      Cell, 2011 (DOI:10.1016/j.cell.2011.08.049)
      [Affymetrix mouse Tiling 2.0R array and data analysis]
    • Arnaoutakis GJ, George TJ, Wang KK, Wilson MA, Allen JG, Robinson CW, Haggerty KA, Weiss ES, Blue ME, Talbot Jr CC, Troncoso JC, Johnston MV, Baumgartner WA
      Serum Levels of neuron-specific ubiquitin carboxyl-terminal esterase-L1 predict brain injury in a canine model of hypothermic circulatory arrest.
      J Thorac Cardiovasc Surg 2011. 142(4):902-910.e1.
      [Agilent Custom Canine Gene Expression Array]
    • Calvi CL, Podowski M, D'Alessio FR, Metzger SL, Misono K, Poonyagariyagorn H, Lopez-Mercado A, Ku T, Lauer T, Cheadie C, Talbot Jr CC, Jie C, McGrath-Morrow S, King LS. Walston J, Neptune ER.
      Critical Transition in Tissue Homeostasis Accompanies Murine Lung Senescence.
      PLoS One 2011. 6(6):e20712
      [Data Analysis]
    • Xiao Z, Mohamood AD, Uddin S, Gutfreund R, Nakata C, Marchall A, Kimura H, Caturegli P, Womer KL, Huang Y, Jie C, Chakravarti S, Schneck JP, Yagita H, Hamad AR.
      Inhibition of Fas ligand in NOD mice unmasks a protective role for IL-10 against insulitis development.
      Am. J. Pathol. 2011, 179(2), 725-732.
      [Data Analysis]
    • Hyland EM, Molina H, Poorey K, Jie C, Dai J, Qian J, Bekiranov S, Auble DT, Pandey A, Boeke JD.
      An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae.
      Genes Dev. 2011, 25(12), 1306-1319.
      [Affymetrix GeneChip Yeast Genome 2.0 array and data analysis]
    • Huang Y, Chuang A, Hao H, Talbot C, Sen T, Trink B, Sidransky D, Ratovitski E.
      Phosph-ΔNp63α is a key regulator of the cisplatin-induced microRNAome in cancer cells.
      Cell Death Differ. 2011. 18,1220-1230 [PMID:21274007]
      [Combimatrix miRNA array and data analysis]
    • Xiao J, Jones-Brando L, Talbot Jr CC, Yolken RH.
      Differential Effects of Three Canonical Toxoplasma Strains on Gene Expression in Human Neuroepithelial cells.
      Infect Immun 2011. 79(3):1363-1373.
      [Affymetrix Human Exon 1.0ST array and data analysis]
    • Halper-Stromberg E, Frelin L, Ruczinski I, Scharpf R, Jie C, Carvalho B, Hao H, Hetrick K, Jedlicka A, Dziedzic A, Doheny K, Scott AF, Baylin S, Pevsner J, Spencer F, and Irizarry RA.
      Performance assessment of copy number microarray platforms using a spike-in experiment.
      Bioinformatics. 2011. 27(8), 1052-1060.
      [Agilent aCGH array]
    • Yang Y, Vidensky S, Jin L, Jie C, Lorenzini I, Frankl M, Rothstein JD.
      Molecular comparison of GLT1+ and ALDH1L1+ astrocytes in vivo in astroglial reporter mice.
      Glia. 2011. 59(2), 200-207.
      [Affymetrix Mouse Exon 1.0ST array and data analysis]
    • Dalai SK, Khoruzhenko S, Drake CG, Jie CC, Sadegh-Nasseri S.
      Resolution of infection promotes a state of dormance and longsurvival of CD4 memory T cell.
      Immunol Cell Biol. 2011. 89(8), 870-881.
      [Affymetrix Mouse Genome 430 2.0 array and data analysis]
    • Loyo M, Brait M, Kim MS, Ostrow KL, Jie CC, Chuang AV, Califano JA, Liegeois NJ, Begum S, Westra WH, Hoque MO, Tao Q, Sidransky D.
      A survey of methylated candidate tumor suppressor genes in nasopharyngeal carcinoma.
      Int J Cancer. 2011. 128(6), 1393-1403.
      [data analysis]
    • Ying M, Sang Y, Li Y, Guerrero-Cazares H, Quinone-Hinojosa A, Vescovi AL, Eberhart CG, Xia S, Laterra J.
      Krüppel-Like Family of Transcription Factor 9, a Differentiation-Associated Transcription Factor, Suppresses Notch1 Signaling and Inhibits Glioblastoma-Initiating Stem Cells.
      Stem Cells 2011. 29(1), 20-31.
      [Affymetrix Human Exon 1.0ST array]
    • Ying M, Wang S, Sang Y, Sun P, Lal B, Goodwin CR, Guerrero-Cazares H, Quinones-Hinojosa A, Laterra J, and Xia S.
      Regulation of Glioblastoma Stem Cells By Retinoid Acid: Role for Notch Pathway Inhibition.
      Oncogene 2011. 30, 3453-3467.
      [Affymetrix Human Exon 1.0ST array]
    • Dymond JS, Richardson SM, Coobles CE, Babatz T, Muller H, Annalurus N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, and Boeke JD.
      Synthetic Chromosome Arms Function in Yeast and Generate Phenotypic Diversity By Design.
      Nature 2011. 477,471-476.
      [Affymetrix Yeast Genome 2.0 array]
    • Chung SY, Chavez C, and Andrew DJ.
      Trachealess (Trh) Regulates All Tracheal Genes During Drosophila Embryogenesis.
      Developmental Biology 2011. 360(1), 160-172.
      [Affymetrix Drosophila Genome 2.0 array]
    • Guo N, Parry EM, Li L-S, Kembou F, Lauder N, Hussain MA, Berggren P-O, and Armanios M.
      Short Telomeres Compromise ß-Cell Signaling and Survival.
      PLoS One 2011. 6(3), e17858.
      [Affymetrix Mouse Exon 1.0ST array]
    • Haberman RP, Colantuoni C, Stocker AM, Schmidt AC, Pedersen JT, and Gallagher M.
      Prominent Hippocampal CA3 Gene Expression Profile in Neurocognitive Aging.
      Neurobiology of Aging 2011. 32(9), 1678-1692.
      [Affymetrix Rat Genome 230 2.0 array]
    • Ji H, Wu G, Zhan X, Nolan A, Koh C, Marzo AD, Doan HM, Fan J, Cheadle C, Fallahi M, Cleveland JL, Dang CV, and Zeller KI.
      Cell-Type Independent MYC Target Genes Reveal a Primordial Signature Involved in Biomass Accumulation.
      PLoS One. 2011. 6(10), e26057.
      [Affymetix Human Genome U133 Plus 2.0 array, Affymetrix Human Exon 1.0ST array, and Agilent Human Genome 44K microarray]
    • Yegnasubramanian S, Wu Z, Haffner MC, Esopi D, Aryee MJ, Badrinath R, He TL, Morgan JD, Carvalho B, Zheng Q, De Marzo AM, Irizarry RA, and Nelson WG.
      Chromosome-Wide Mapping of DNA Methylation Patterns in Normal and Malignant Prostate Cells Reveals Pervasive Methylation of Gene-Associated and Conserved Intergenic Sequences.
      BMC Genomics. 2011. 12, 313.
      [Affymetrix Human Tilling array 1.0R]
    • Heidecker B, Kittleson MM, Kasper EK, Wittstein IS, Champion HC, Russell SD, Hruban RH, Rodriguez ER, Baughman KL, and Hare JM.
      Transcriptomic Biomarkers for the Accurate Diagnosis of Myocarditis.
      Circulation. 2011. 123, 1174-1184.
      [Human U133 Plus 2.0 array]
    • Guo JU, Ma DK, Mo H, Ball MP, Jang M-H, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming G-L, Gao Y, and Song H.
      Neuronal Activity Modifies the DNA Methylation Landscape in the Adult Brain.
      Nat. Neurosci. 2011. 14(10), 1345-1351.
      [Mouse Exon 1.0ST array]
    • Tootle TL, Williams D, Hubb A, Frederick R, and Spradling A.
      Drosophila Eggshell Production: Identification of New Genes and Coordination by Pxt.
      PLoS One. 2011. 6(5), e19943.
      [Affymetrix Drosophila Genome 2.0 array]
    • Stine MJ, Wang CJ, Morarty WF, Ryu B, Cheong R, Westra WH, Levchenko A, and Alani RM.
      Integration of Genotypic and Phenotypic Screening Reveals Molecular Mediators of Melanoma-Stromal Interaction.
      Cancer Res. 2011. 71(7), 2433-2444.
      [Affymetrix Human Genome U133 Plus 2.0 array]
    • McCall MN, Kent OA, Yu J, Fox-Talbot K, Zaiman AL, and Halushka MK.
      MicroRNA Profiling of Diverse Endothelial Cell Types.
      BMC Med. Genomics. 2011. 4, 78.
      [Agilent Human miRNA v3 array]
    • Guo T, Mandai K, Condie BG, Wickramasinghe SR, Capecchi MR, and Ginty DD.
      An Evolving NGF-Hoxd1 Signaling Pathway Mediates Development of Divergent Neural Circuits in Vertebrates.
      Nat. Neurosci. 2011. 14(1), 31-36.
      [Affymetrix Mouse Genome 430 2.0 array]
    • Ye X, Wang Y, Rattner A, and Nathans J.
      Genetic Mosaic Analysis Reveals a Major Role for frizzled 4 and frizzled 8 in Controlling Ureteric Growth in the Developing Kidney.
      Development. 2011. 138(6), 1161-1172.
      [Affymetrix Mouse Genome 430 2.0 array]
    • Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, Koch W, Califano J, and Sidransky D.
      NID2 and HOXA9 Promoter Hypermethylation as Biomarkers for Prevention and Early Detection in Oral Cavity Squamous Cell Carcinoma Tissues and Saliva.
      Cancer Prev. Res. 2011. 4, 1061.
      [data analysis]
    • Wan J, Masuda T, Hackler Jr L, Torres KM, Merbs SL, Zack DJ, and Qian J.
      Dynamic Usage of Alternative Splicing Exons During Mouse Retina Development.
      Nucl. Acids Res. 2011. 39(18), 7920-7930.
      [Affymetrix Mouse Exon 1.0ST array]
    • De Melo J, Peng G-H, Chen S, and Blackshaw S.
      The Spalt Family Transcription Factor Sall3 Regulates the Development of Cone Photoreceptors and Retinal Horizontal Interneurons.
      Development. 2011. 138(11), 2325-2336.
      [Affymetrix Mouse Exon 1.0ST array]
    • Mithani SK, Smith IM, and Califano JA.
      Use of Integrative Epigenetic and Cytogenetic Analyses to Identify Novel Tumor-Suppressor Genes in Malignant Melanoma.
      Melanoma Res. 2011. 21(4), 298-307.
      [Affymetrix Human Genome U133 array hybridization and scan]
    • Garrido-Laguna I, Uson M, Rajeshkumar NV, Tan AC, De Oliveira E, Karikari C, Villaroel MC, Salomon A, Taylor G, Sharma R, Hruban RH, Maitra A, Laheru D, Rubiio-Viqueira B, Jimeno A, and Hidalgo M.
      Tumor Engraftment in Nude Mice and Enrichment in Stroma-Related Gene Pathways Predict Poor Survival and Resistance to Gemcitabine in Patients with Pancreatic Cancer.
      Clin. Cancer Res. 2011. 17(17),5793-5800.
      [Affymetrix Human Genome U133 Plus 2.0 array]
    • Peltonen K, Colis L, Liu H, Jäämaa S, Moore HM, Enbäck J, Laakkonen P, Vaahtokari A, Jones RJ, af Hällström TM, and Laiho M.
      Identification of Novel p53 Pathway Activating Small-Molecule Compounds Reveals Unexpected Similarities with Known Therapeutic Agents.
      PLoS One. 2011. 5(9), e12996.
      [Affymetrix Human Genome U133 Plus 2.0 array]
    • LeBron C, Pal P, Brait M, Dasgupta S, Guerrero-Preston R, Looijenga LHJ, Kowalski J, Netto G, and Hoque M.
      Genome-Wide Analysis of Genetic Alterations in Testicular Primary Seminoma Using High Resolution Single Nucleotide Polymorphism Arrays.
      Genomics. 2011. 97(6), 341-349.
      [Affymetrix 250k Nsp1 SNP array]
    • Dasgupta S, Shao C, Keane TE, Duberow DP, Mathies RA, Fisher PB, Kiemneney LA, and Sidransky D.
      Detection of Mitochondrial Deoxyribonucleic Acid Alterations in Urine from Urothelial Cell Carcinoma Patients.
      Intern. J. Cancer. 2011. DOI:10.1002/ijc.26357 [Epub ahead of print].
      [Affymetrix Mitochip 2.0]
    • Dasgupta S, Koch R, Westra WH, Califano JA, Ha PK, Sidransky D, and Kock WM.
      Mitochondrial DNA Mutation in Normal Margins and Tumors of Recurrent Head and Neck Squamous Cell Carcinoma Patients.
      Cancer Prev Res. 2011. 3(9), 1205-1211.
      [Affymetrix Mitochip 2.0]
    • Ying M, Sang Y, Guerrero-Cazares H, Quinones-Hinojosa A, Vescovi AL, Eberhart CG, Xia S, and Laterra J.
      KLF9, a differentiation-associated transcription factor, suppresses Notch1 signaling and inhibits glioblastoma-initiating stem cells.
      Stem Cells. 2011 29(10, 20-31.
      [Affymetrix Human Exon 1.0ST array]

  • 2010 (21/6)

    • Lau WM, Weber KL, Doucet M, Chou YT, Brady K, Kowalski J, Tsai HL, Yang J, and Kominsky SL.
      Identification of prospective factors promoting osteotropism in breast cancer: a potential role for CITED2.
      Int. J. Cancer. 2010. 126(4): 876-84. DOI: 10.1002/ijc.24780. PMID: 19642106.
      [Affymetrix Mouse Genome MOE 430 2.0 array]
    • Kang TH, Noh KH, Kim JH, Bae HC, Lin KY, Monie A, Pai SI, Hung CF, Wu TC, and Kim TW.
      Ectopic expression of X-linked lymphocyte-regulated protein pM1 renders tumor cells resistant to antitumor immunity.
      Cancer Res. 2010. 70(8), 3062-3070. doi: 10.1158/0008-5472.CAN-09-3856. PMID: 20395201.
      [Affymetrix Mouse Genome 430 2.0 arrays]
    • Allen JG, Weiss ES, Wilson MA, Arnaoutakis GJ, Blue ME, Talbot Jr CC, Jie C, Lange MS, Troncoso JC, Johnston MV, Baumgartner WA.
      Hawley H. Seiler Resident Award. Transcriptional Profile of Brain Injury in Hypothermic Circulatory Arrest and Cardiopulmonary Bypass.
      Ann Thorac Surg 2010. 89(6): 1965-1971
      [Agilent Canine 44K gene expression array]
    • Henderson-Macleannan NK, Papp JC, Talbot Jr CC, McCabe ER, Presson AP.
      Pathway Analysis Software: annotation errors and solutions.
      Mol Genet Metab. 2010. 101(2-3): 134-140.
      [data analysis]
    • Yustein JT, Liu YC, Gao P, Jie C, Le A, Vulca-Ross M, Chng WJ, Eberhart CG, Bergsagel PL, Dang CV.
      Induction of ectopic Myc target genes JAG2 augments hypoxic growth and tumorigenesis in a human B-cell model.
      Proc Natl Acad Sci U.S.A. 2010. 107(8), 3534-3539.
      [Affymetrix Human U133 Plus 2.0 Genome array and data analysis]
    • Kedziorek DA, Muja N, Walczak P, Ruiz-Cabello J, Gilad AA, Jie CC, Bulte JW.
      Gene expression profiling reveals early cellular responses to intracellular magnetic labelling with superparamagnetic iron oxide nanoparticles.
      Magn Reson Med. 2010. 63(4), 1031-1043.
      [Affymetrix Mouse Genome 430 2.0 array and data analysis]
    • Vivekanandan P, Daniel HD, Kannangai R, Martinez-Murillo F, Torbenson M.
      Hepatitis B virus replication induces methylation of both host and viral DNA.
      J Virol. 2010 May; 84(9), 4321-4329.
      [HCGI12K array (UHN, Ontario, Canada) and data analysis]
    • Dai J, Hyland EM, Norris A, and Boeke JD.
      Yin and Yang of Histone H2B Roles in Silencing and Longevity: A Tale of Two Arginines.
      Genetics. 2010. 186(3), 813-828.
      [Affymetrix Yeast Genome 2.0 array]
    • Fox RM, Hanlon CD, and Andrew DJ.
      The CrebA/Creb3-like Trnascription Factors Are Major and Direct Regulators of Secretory Capacity.
      JCB 2010. 191(3), 479-492.
    • Shimogori T, Lee DA, Miranda-Angulo A, Yang Y, Wang H, Jiang L, Yoshida AC, Kataoka A, Mashiko H, Avetisyan M, Qi L, Qian J, and Blackshaw S.
      A Genomic Atlas of Mouse Hypothalamic Development.
      Nat. Neurosci. 2010. 13(6), 767-775.
    • Rao A, Zhang Y, Muend S, and Rao R.
      Mechanism of Antifungal Activity of Terpenoid Phenols Resembles Calcium Stress and Inhibition of the TOR Pathway.
      Antimicrob. Agents Chemother. 2010. 54(12), 5062-5069.
    • Sharrow AC, Ronnett BM, Thoburn CJ, Barber JP, Giuntoli II RL, Armstrong DK, Jones RJ, and Hess AD.
      Identification and Characterization of a Spontaneous Ovarian Carcinoma in Lewis Rats.
      J. Ovarian Res. 2010. 3(1), 9-16.
    • De Biase LM, Nishiyama A, and Bergles DE.
      Excitability and Synaptic Communication Within the Oligodendrocyte Lineage.
      J. Neurosci. 2010. 30(10), 3600-3611.
    • Bennett MK, Kulaga HM, and Reed RR.
      Odor-Evoked Gene Regulation and Visualization in Olfactory Receptor Neurons.
      Mol. Cel. Neurosci. 2010. 43(4), 353-362.
    • Yu H, Smallwood PM, Wang Y, Vidaltamayo R, Reed R, and Nathans J.
      Frizzled 1 and Frizzled 2 Genes Function in Palate, Ventricular Septum and Neural Tube Closure: General Implications for Tissue Fusion Processes.
      Development. 2010. 137(21), 3707-3717.
    • Kakkad SM, Solaiyappan M, O'Rourke B, Stasinopoulos I, Ackerstaff E, Raman V, Bhujwalla ZM, and Glunde K.
      Hypoxic Tumor Microenvironments Reduce Collagen I Fiber Density.
      Neoplasia. 2010. 12(8), 608-617.
    • Vidal-Cardenas S, and Greider CW.
      Comparing Effects of mTR and mTERT Deletion on Gene Expression and DNA Damage Response: a Critical Examination of Telomere Length Maintenance-Independent Roles of Telomerase.
      Nucl. Acids Res. 2010. 38(1), 60-71.
    • Garrido-Laguna I, Tan AC, Uson M, Angenendt M, Ma WW, Villaroel MC, Zhao M, Rajeshkumar NV, Jimeno A, Donehower R, Iacobuzio-Donahue C, Barrett M, Rudek MA, Rubio-Viqueira B, Laheru D, and Hidalgo M.
      Integrated Preclinical and Clinical Development of mTOR Inhibitors in Pancreatic Cancer.
      Br. J. Cancer. 2010. 103(5), 649-655. [Affymetrix Human U133 Plus 2.0 array]
    • Scharpf RB, Iacobuzio-Donahue CA, Cope L, Ruczinski I, Garrett-Mayer E, Lakkur S, Campagna D, and Parmigian G.
      Cross-Platform Comparison of Two Pancreatic Cancer Phenotypes.
      Cancer Inform. 2010. 9, 257-264.
    • Walter K, Omura N, Hong S-M, Griffith M, Vincent A, Borges M, and Goggins M.
      Overexpression of Smoothened Activates the Sonic Hedgehog Signaling Pathway in Pancreatic Cancer - Associated Fibroblasts.
      Clin Cancer Res 2010 16, 1781.
    • Davidson B, Stavnes HT, Holth A, Chen X, Yang Y, Shih L-M, and Wang T-L.
      Gene expression signatures differentiate ovarian/peritoneal serous carcinoma from breast carcinoma in effusions.
      J. of Cell. and Mol. Med. 2010 15, 535-544.
  • 2009 (26/6)

    • Metzger MB and Michaelis S.
      Analysis of quality control substrates in distinct cellular compartments reveals a unique role for Rpn4p in tolerating misfolded membrane proteins.
      Mol. Biol. Cell. 2009. 20(3): 1006-1019. DOI: 10.1091/mbc.e08-02-0140. PMID: 19073890.
      [Affymetrix Yeast Genome 2.0 array]
    • Cox RT and Spradling AC.
      Clueless, a conserved Drosophila gene required for mitochondrial subcellular localization, interacts genetically with parkin.
      Dis Model Mech. 2009. 2(9-10): 490-9. DOI: 10.1242/dmm.002378. PMID 19638420.
      [Affymetrix Drosophila Genome 2.0 array]
    • Garcia-Ortiz JE, Pelosi E, Omari S, Nedorezov T, Piao Y, Karmazin J, Uda M, Cao A, Cole SW, Forabosco A, Schlessinger D, and Ottolenghi C.
      Foxl2 functions in sex determination and histogenesis throughout mouse ovary development.
      BMC Dev. Biol. 2009. 9:36. DOI: 10.1186/1471-213X-9-36. PMID: 19538736.
      [Affymetrix Mouse MOE 430 2.0 array hybridization and processing]
    • Smith IM, Glazer CA, Mithani SK, Ochs MF, Sun W, Bhan S, Vostrov A, Adbullaev Z, Lobanenkov V, Gray A, Liu C, Chang SS, Ostrow KL, Westra WH, Begum S, Dhara M, and Califano J.
      Coordinated activation of candidate proto-oncogenes and cancer tests antigens via promoter demethylation in head and neck cancer and lung cancer.
      PLoS One. 2009. 4(3): e4961. DOI: 10.1371/journal.pone.0004961. PMID: 19305507.
      [Affymetrix Human U133 Plus 2.0 array hybridization and scan]
    • Smith IM, Mithani SK, Liu C, Chang SS, Begum S, Dhara M, Westra W, Sidransky D, Califano JA.
      Novel integrative methods for gene discovery associated with head and neck squamous cell carcinoma development.
      Arch. Otolaryngol. Head Neck Surg. 2009. 135(5): 487-495. DOI: 10.1001/archoto.2009.43. PMID: 19451471.
      [Affymetrix Human U133 Plus 2.0 array hybridization and scan]
    • Choi KH, Higgs BW, Weis S, Song J, Llenos IC, Dulay JR, Yolken RH, and Webster MJ.
      Effects of typical and atypical antipsychotic drugs on gene expression profiles in the liver of schizophrenia subjects.
      BMC Psychiatry. 2009 9, 57.
    • Pletneva M, Fan H, Park JJ, Radojcic V, Jie C, Yu Y, Chan C, Redwood A, Pardoll D, Housseau F.
      IFN-producing killer dendritic cells are antigen-presenting cells endowed with T-cell cross-priming capacity.
      Cancer Res. 2009 Aug 15; 69(16), 6607-6614.
    • Liang Y, Jiang H, Ratovitski T, Jie C, Nakamura M, Hirschhorn RR, Wang X, Smith WW, Hai T, Poirier MA, Ross CA.
      ATF3 plays a protective role against toxicity by N-terminal fragment of mutant huntingtin in stable PC12 cell line.
      Brain Res. 2009 Aug 25; 1286, 221-229.
    • Getnet D, Maris CH, Hipkiss EL, Grosso JF, Harris TJ, Yen HR, Bruno TC, Wada S, Adler A, Georgantas RW, Jie C, Goldberg MV, Pardoll DM, Drake CG.
      Tumor recognition and self-recognition induce distinct transcriptional profiles in antigen-specific CD4 T cells.
      J Immunol. 2009 Apr 15; 182(8), 4675-4685.
    • den Dunnen JT, Sijmons RH, Andersen PS, Vihinen M, Beckmann JS, Rossetti S, Talbot Jr CC, Hardison RC, Povey S, Cotton RG.
      Sharing data between LSDBs and central repositories.
      Hum Mutat. 2009 Apr; 30(4), 493-495.
    • Inoue T, Maeno A, Talbot Jr CC, Zeng Y, Yeater DB, Leman ES, Kulkarni P, Ogawa O, Getzenberg RH.
      Purine-rich element binding protein (PUR) alpha induces endoplasmic reticulum stress response and cell differentiation pathways in prostate cancer cells.
      Prostate. 2009 Jun 1; 69(8), 861-873.
    • Doi A, Park I-H, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, and Feinberg AP.
      Differential Methylation of Tissue- and Cancer-Specific CpG Island Shores Distinguishes Human Induced Pluripotent Stem Cells, Embryonic Stem Cells and Fibroblasts.
      Nat. Genet. 2009. 41(12), 1350-1353.
    • Kanashiro-Takeuchi RM, Heidecker B, Lairault G, Dharamsi JW, and Hare JM.
      Sex-Specific Impact of Aldosterone Receptor Antagonism on Ventricular Remodeling and Gene Expression after Myocardial Infarction.
      Clin. Transl. Sci. 2009. 2(2), 134-142.
    • Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, and Feinberg AP.
      The Human Colon Cancer Methylome Shows Similar Hypo- and Hypermethylation at Conserved Tissue-Specific CpG Island Shores.
      Nat. Genet. 2009. 41(2), 178-186.
    • Keefe MJ.
      Global Assessment of Melanoma-Endothelial Cell Communication Identifies Neuropilin-2 as a Mediator of Melanoma Cell Proliferation.
      Johns Hopkins Press. 2009. (Dissertation, ISBN:0549938265).
    • Jiang T, Collins BJ, Jin N, Watkins DN, Brock MV, Matsui W, Nelkin BD, and Ball DW.
      Achaete-Scute Complex Homologue 1 Regulates Tumor-Initiating Capacity in Human Small Cell Lung Cancer.
      Cancer Res. 2009. 69(3), 845-854.
    • Mandai K, Guo T, Hillaire CS, Meabon JS, Kanning KC, Bothwell M, and Ginty DD.
      LIG Family Receptor Tyrosine Kinase-Associated Proteins Modulate Growth Factor Signals during Neural Develpment.
      Neuron. 2009. 63(6), 614-627.
    • Rodriguez-Pla A, Martinez-Murrilo F, Savino PJ, Eagle Jr RC, Seo P, Soloski MJ.
      MMP-12, a novel matrix metalloproteinase associated with giant cell arteritis.
      Rheumatology. 2009; 48(11), 1460-1461.
    • Choi JH, Sheu JJ-C, Guan B, Jinawath N, Markowski P, Wang T-L, and Shih I-M.
      Functional Analysis of 11q13.5 Amplicon Identifies Rsf-1 (HBXAP) as a Gene Involved in Paclitaxel Resistance in Ovarian Cancer.
      Cancer Res. 2009. 69(4), 1407-1415.
    • Stasinopoulos I, O'Brien DR, and Bhujwalla ZM.
      Inflammation, but not Hypoxia, Mediated HIF-1α Activation Depends on COX-2.
      Cancer Biol. Ther. 2009. 8(1), 31-35.
    • Wang Z, Sarje A, Che P-L, and Yarema KJ.
      Moderate Strength(0.23-0.28 T) Static Magnetic Fields (SMF) Modulate Signaling and Differentiation in Human Embryonic Cells.
      BMC Genomics. 2009. 10,356.
    • Ye X, Wang Y, Cahill H, Yu M, Badea TC, Smallwood PM, Peachey NS, and Nathans J.
      Norrin, Frizzled-4, and Lrp5 Signaling in Endothelial Cells Controls a Genetic Program for Retinal Vescularization.
      Cell. 2009. 139(2), 285-298.
    • Mithani SK, Shao C, Tan M, Smith IM, Califano JA, El-Naggar AK, and Ha PK.
      Mitochondrial Mutations in Adenoid Cystic Carcinoma of the Salivary Glands.
      PLoS One. 2009. 4(12), e8493.
    • Dasgupta S, Yung RC, Westra WH, Rini DA, Brandes J, and Sidransky D.
      Following Mitochondrial Footprints through a Long Mucosal Path to Lung Cancer.
      PLoS One. 2009. 4(8), e6533.
    • Tan AC, Jimeno A, Lin SH, Wheelhouse J, Chan F, Solomon A, Rajeshkumar NV, Rubio-Viqueira B, and Hidalgo M.
      Characterizing DNA Methylation Patterns in Pancreatic Cancer Genome.
      Mol. Oncol. 2009. 3(5-6), 425-438.
    • Elmouelhi N, Aich U, Paruchuri VDP, Meledel MA, Campbell CT, Wang JJ, Srinivas R, Khanna HS, and Yarema KJ.
      The Hexosamine Template - A Platform for Modulating Gene Expression and for Sugar-Based Drug Discovery.
      J. Med. Chem. 2009. 52(8), 2515-2530.

  • 2008 (21/6)

    • Munugalavadla V, Vemula S, Sim EC, Krishnan S, Chen S, Yan J, Li H, Niziolek PJ, Takemoto C, Robling AG, Yang F-C, and Kapur R.
      The p85α subunit of class IA phosphatidylinositol 3-kinase regulates the expression of multiple genes involved in osteoclast maturation and migration.
      Mol. Cell Biol. 2008. 28(23): 7182-98. DOI: 10.1128/MCB.00920-08. PMID: 18809581.
      [Affymetrix Mouse Genome MOE 430 2.0 array]
    • Gao Z, Barth AS, DiSilvestre D, Akar FG, Tian Y, Tanskanen A, Kass DA, Winslow RL, Tomaselli GF.
      Key pathways associated with heart failure development revealed by gene networks correlated with cardiac remodeling.
      Physiol. Genomics. 2008. 35(3): 222-230. DOI: 10.1152/physiolgenomics.00100.2007. PMID: 18780759.
      [Affymetrix Canine Genome Array]
    • Wheelan SJ, Martinez Murillo F, Boeke JD.
      The incredible shrinking world of DNA microarrays.
      Mol Biosyst. 2008 Jul; 4(7), 726-732.
    • Mohamood AS, Bargatze D, Xiao Z, Jie C, Yagita H, Ruben D, Watson J, Chakravarti S, Schneck JP, Hamad AR.
      Fas-mediated apoptosis regulates the composition of peripheral alphabeta T cell repertoire by constitutively purging out double negative T cells.
      PLoS One. 2008; 3(10):e3465.
    • Farrar JE, Nater M, Caywood E, McDevitt MA, Kowalski J, Takemoto CM, Talbot Jr CC, Meltzer P, Esposito D, Beggs AH, Schneider HE, Graboswka A, Ball SE, Niewiadomska E, Sieff CA, Vlachos A, Atsidaftos E, Ellis SR, Lipton JM, Gazda HT, Arceci RJ.
      Abnormalities of the large ribosomal subunit protein, Rpl35a, in Diamond-Blackfan anemia.
      Blood. 2008 Sep 1; 112(5), 1582-1592.
    • Sedaght AR, German J, Teslovich TM, Cofrancesco J Jr, Jie CC, Talbot Jr CC, Siliciano RF.
      Chronic CD4+ T-cell activation and depletion in human immunodeficiency virus type 1 infection: type 1 interferon-mediated disruption of T-cell dynamics.
      J Virol. 2008 Feb; 82(4), 1870-1883.
    • Christoforou N, Miller RA, Hill CM, Jie CC, McCallion AS, Gearhart JD.
      Mouse ES cell-derived cardiac precursor cells are multipotent and facilitate identification of novel cardiac genes.
      J Clin Invest. 2008 Mar; 118(3), 894-903.
    • Celic I, Verreault A, and Boeke JD.
      Histone H3K56 Hyperacetylation Perturbs Replisomes and Causes DNA Damage.
      Genetics. 2008. 179(4), 1769-1784.
    • Miller RA, Christoforou N, Pevsner J, McCallion AS, and Gearhart JD.
      Efficient Array-Based Identification of Novel Cardiac Genes through Differentiation of Mouse ESCs.
      PLoS One. 2008. 3(5), e2176.
    • Heidecker B, Kasper EK, Wittstein IS, Champion HC, Breton E, Russell ST, Kittleson MM, Baughman KL, and Hare JM.
      Transcriptomic Biomarkers for Individual Risk Assessment in New-Onset Heart Failure.
      Circulation. 2008. 118(3), 238-246.
    • Sfanos KS, Bruno TC, Maris CH, Xu L, Thoburn CJ, DeMarzo AM, Meeker AK, Issacs WB, and Drake CG.
      Phenotypic Analysis of Prostate-Infiltrating Lymphocytes Reveals TH17 and Treg Skewing.
      Clin. Cancer Res. 2008. 14(11), 3254-3261.
    • Deppmann CD, Mihalas S, Sharma N, Lonze BE, Niebur E, and Ginty DD.
      A Model for Neuronal Competition During Development.
      Science. 2008. 320(5874), 369-373.
    • Song D, Chaerkady R, Tan AC, Garcia-Garcia E, Nalli A, Suárez-Gauthier A, López-Ríos F, Zhang XF, Solomon A, Tong J, Read M, Fritz C, Jimeno A, Pandey A, and Hidalgo M.
      Antitumor Activity and Molecular Effects of the Novel Heat Shock Protein 90 Inhibitor, IPI-504, in Pancreatic Cancer.
      Mol. Cancer Ther. 7(10),3275-3284.
    • Haberman RP, Lee HJ, Colantuoni C, Koh MT, and Gallagher M.
      Rapid Encoding of New Information Alters the Profile of Plasticity-related mRNA Transcripts in the Hippocampal CA3 Region.
      PNAS.2008. 105(30), 10601-10606.
    • Makita T, Sucov HM, Gariepy CE, Yanagisawa M, and Ginty DD.
      Endothelins Are Vascular-Derived Axonal Guidance Cues for Developing Sympathetic Neurons.
      Nature. 2008. 452(7188), 759-763.
    • Rattner A, Toulabi L, Williams J, Yu H, and Nathans J.
      The Genomic Response of the Retinal Pigment Epithelium to Light Damage and Retinal Detachment.
      J. Neurosci. 2008. 28(39), 9880-9889.
    • Liu C, Wang Y, Smallwood PM, and Nathans J.
      An Essential Role for Frizzled5 in Neuronal Survival in the Parafascicular Nucleus of the Thalamus.
      J. Neurosci. 2008. 28(22), 5641-5653.
    • Liu J-W, Nagpal JK, Sun W, Lee J, Kim MS, Ostrow KL, Zhou S, Jeronimo C, Henrique R, Criekinge WV, Moon CS, Califano JA, Trink B, and Sidransky D.
      ssDNA-Binding Protein 2 Is Frequently Hypermethylated and Suppresses Cell Growth in Human Prostate Cancer.
      Clin Cancer Res. 2008. 14(12), 3754-3760.
    • Campagna D, Cope L, Lakkur SS, Henderson C, Laheru D, and Iacobuzio-Donahue CA.
      Gene Expression Profiles Associated with Advanced Pancreatic Cander.
      Int. J. Clin. Exp. Pathol. 2008. 1(1), 32-43.

    • Singh OV, Pollard HB, and Zeitlin PL.
      Chemical Rescue of ΔF508-CFTR Mimics Genetic Repair in Cystic Fibrosis Bronchial Epithelial Cells.
      Mol. Cell. Proteom. 2008. 7(6), 1099-1100.
    • Allen AK and Spradling AC.
      The Sf1-Related Nuclear Hormone Receptor Hr39 R egulates Drosophila Female Reproductive Tract Development and Function.
      Devel opment. 2008. 135(2), 311-321.

  • 2007 (16/6)

    • Jimeno A, Rubio-Viqueira B, Amado ML, Grunwald V, Maitra A, Iacobuzio-Donahue C, and Hidalgo M.
      Dual mitogen-activated protein kinase and epidermal growth factor receptor inhibition in biliary and pancreatic cancer.
      Mol. Cancer Ther. 2007. 6(3): 1079-88. DOI:10.1158/1535-7163.MCT-06-0448. PMID: 17363501.
      [Affymetrix Human Genome U133A array]
    • Peterson NC and Servinsky MD.
      Development of molecular and cellular biomarkers of pain.
      Comp. Med. 2007. 57(6): 554-562. PMID: 18246867.
      [Affymetrix Mouse Genome U74Av2 and MOE 430 2.0 arrays]
    • Zhang L, Jie C, Obie C, Abidi F, Schwartz CE, Stevenson RE, Valle D, Wang T.
      X chromosome cDNA microarray screening identifies a functional PLP2 promoter polymorphism enriched in patients with X-linked mental retardation.
      Genome Res. 2007 May; 17(5), 641-648.
    • Lin KY, Lu D, Hung CF, Peng S, Huang L, Jie C, Murillo F, Rowley J, Tsai YC, He L, Kim DJ, Jaffee E, Pardoll D, Wu TC.
      Ectopic expression of vascular cell adhesion molecule-1 as a new mechanism for tumor immune evasion.
      Cancer Res. 2007 Feb 15; 67(4), 1832-1841.
    • Shahlee A, Branda S, Lee Y, Jie C, Takemoto C.
      Distinct and Shared transcriptomes are regulated by Microphthalmia-associated transcription factor isoforms in mast cells.
      J Immunol. 2007 Jan 1; 178(1):378-388
    • Weis S, Llenos IC, Dulay JR, Elashoff M, Martinez-Murillo F, Miller CL.
      Quality control for microarray analysis of human brain samples: The impact of postmortem factors, RNA characteristics, and histopathology.
      J Neurosci Methods. 2007 Sep 30; 165(2), 198-209.
    • Horaitis O, Talbot Jr CC, Phommarinh M, Philips KM, Cotton RG.
      A database of locus-specific databases.
      Nat Genet. 2007 Apr; 39(4), 425.
    • Kannangai R, Vivekanandan P, Martinez-Murillo F, Choti M, and Torbenson M.
      Fibrolamellar carcinomas show overexpression of genes in the RAS, MAPK, PIK3, and xenobiotic degradation pathways.
      Human Pathology 2007 Apr; 38(4), 639-644.
    • Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell J.
      Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.
      Mol. Cell. 2007. 26(5), 745-752.
    • Kaur R, Ma B, and Cormack BP.
      A Family of Glycosylphosphatidylinositol-Linked Aspartyl Proteases Is Required for Virulence of Candida glabrata.
      PNAS. 2007. 104(18), 7628-7633.
    • Yang Z, Quigley HA, Pease ME, Yang Y, Qian J, Valenta D, and Zack DJ.
      Changes in Gene Expression in Experimental Glaucoma and Optic Nerve Transection: The Equilibrium between Protective and Detrimental Mechanisms.
      Invest. Ophthalmol. Vis. Sci. 2007. 48(12), 5539-5548.
    • Zhang Y-Q and Rao R.
      Global Disruption of Cell Cycle Progression and Nutrient Response by the Antifungal Agent Amiodarone.
      JBC. 2007. 282(52), 37844-37853.
    • Mori N, Glunde K, Takagi T, Raman V, and Bhujwalla ZM.
      Choline Kinase Down-Regulation Increases the Effect of 5-Fluorouracil in Breast Cancer Cells.
      Cancer Res. 2007. 67(23),11284-11290.
    • Stasinopoulos I, O'Brien DR, Wildes F, Glunde K, and Bhujwalla ZM.
      Silencing of Cyclooxygenase-2 Inhibits Metastasis and Delays Tumor Onset of Poorly Differentiated Metastatic Breast Cancer Cells.
      Mol. Cancer Res. 2007. 5(5),435-442.
    • Chen J and Nathans J.
      Estrogen-Related receptor ß/NR3B2 Controls Epithelial Cell Fate and Endolymph Production by the Stria Vascularis.
      Developmental Cell. 2007. 13(3), 325-337.
    • Ackerstaff E, Artemov D, Gillies RJ, and Bhujwalla ZM.
      Hypoxia and the Presence of Human Vascular Endothelial Cells Affect Prostate Cancer Cell Invasion and Metabolism.
      Neoplasia. 2007. 9(12), 1138-1151.

  • 2006 (15/9)

    • Kim JW, Tchernyshyov I, Semenza GL, Dang CV.
      HIF-1-mediated expression of pyruvate dehyfrogenase kinase: a metabolic switch required for cellular adaptation to hypoxia.
      Cell Metab. 2006. 3(3): 177-85. DOI: 10.1016/j.cmet.2006.02.002. PMID: 16517405.
      [Affymetrix Human Genome HU-U133A array]
    • Wang X, Bo J, Bridges T, Dugan KD, Pan TC, Chodosh LA, and Montell DJ.
      Analysis of cell migration using whole-genome expression profiling of migratory cells in the Drosophila ovary.
      Dev. Cell. 2006. 10(4): 483-95. DOI: 10.1016/j.devcel.2006.02.003. PMID: 16580993.
      [Affymetrix Drosophila Genome array]
    • Wheelan SJ, Scheifele LZ, Martinez-Murillo F, Irizarry RA, Boeke JD.
      Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposon insertion site profiling chip (TIP-chip).
      Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17632-7.
    • Wheelan SJ, Martinez-Murillo F, Irizarry RA, Boeke JD.
      Stacking the deck: double-tiled DNA microarrays.
      Nat Methods. 2006 Nov;3(11):903-7.
    • Xu Y, Zhang W, Klaus J, Young J, Koerner I, Sheldahl LC, Hurn PD, Martinez-Murillo F, Alkayed NJ.
      Role of cocaine- and amphetamine-regulated transcript in estradiol-mediated neuroprotection.
      Proc Natl Acad Sci U S A. 2006 Sep 26;103(39):14489-94.
    • Glunde K, Jie C, Bhujwalla ZM.
      Mechanisms of indomethacin-induced alterations in the choline phospholipid metabolism of breast cancer cells.
      Neoplasia. 2006 Sep;8(9):758-71.
    • Mohamood AS, Trujillo CJ, Zheng D, Jie C, Murillo FM, Schneck JP, Hamad AR.
      Gld mutation of Fas ligand increases the frequency and up-regulates cell survival genes in CD25+CD4+ TR cells.
      Int Immunol. 2006 Aug;18(8):1265-77.
    • Turchan-Cholewo J, Liu Y, Gartner S, Reid R, Jie C, Peng X, Chen KC, Chauhan A, Haughey N, Cutler R, Mattson MP, Pardo C, Conant K, Sacktor N, McArthur JC, Hauser KF, Gairola C, Nath A.
      Increased vulnerability of ApoE4 neurons to HIV proteins and opiates: protection by diosgenin and L-deprenyl.
      Neurobiol Dis. 2006 Jul;23(1):109-19.
    • Song J, Jie C, Polk P, Shridhar R, Clair T, Zhang J, Yin L, Keppler D.
      The candidate tumor suppressor CST6 alters the gene expression profile of human breast carcinoma cells: down-regulation of the potent mitogenic, motogenic, and angiogenic factor autotaxin.
      Biochem Biophys Res Commun. 2006 Feb 3; 340(1), 175-182.
    • Arigo JT, Eyler DE, Carroll KL, and Corden JL.
      Termination of Cryptic Unstable Transcripts Is Directed by Yeast RNA-Binding Proteins Nrd1 and Nab3.
      Molecular Cell. 2006. 23(6), 841-851.
    • Davidson B, Zhang Z, Kleinberg L, Li M, Flørenes VA, Wang T-L, and Shih I-M.
      Gene Expression Signatures Differentiate Ovarian/Peritoneal Serous Carcinoma from Diffuse Malignant Peritoneal Mesothelioma.
      Clin. Cancer Res. 2006. 12(20), 5944-5950.
    • Tang L, Liu X, and Clarke ND.
      Inferring Direct Regulatory Targets from Expression and Genome Location Analysis: A Comparison of Transcription Factor Deletion and Overexpression.
      BMC Genomics. 2006. 7,215.
    • Dunn CD, Lee MS, Spencer FA, and Jensen RE.
      A Genomewide Screen for Petite-Negative Yeast Strains Yields a New Subunit of the i-AAA Protease Complex.
      Mol. Biol. Cell. 2006. 17(1), 213-226.
    • Takahashi H, McCaffery JM, Irizary RA, and Boeke JD.
      Nucleocytosolic Acetyl-Coenzyme A Synthetase Is Required for Histome Acetylation and Global Transcription.
      Mol. Cell. 2006. 23(2), 207-217. [Affymetrix Yeast Genome 2.0 array]
    • O'Donnell KA, Yu D, Zeller KI, Kim J-W, Racke F, Thomas-Tikhonenko A, and Dang CV.
      Activation of Transferrin Receptor 1 by c-Myc Enhances Cellular Proliferation and Tumorigenesis.
      Mol. Cell. Biol. 2006. 26(6), 2373-2386.

  • 2005 (17/7)

    • Kannangai R, Diehl AM, Sicklick J, Rojkind M, Thomas D, and Torbenson M.
      Hepatic angiomyolipoma and hepatic stellate cells share a similar gene expression profile.
      Hum. Pathol. 2005. 36(4): 341-7. DOI: 10.1016/j.humpath.2005.01.002. PMID: 15891994.
      [Affymetrix Human Genome U133A array]
    • Wang K, Xue T, Tsang SY, Van Huizen R, Wong CW, Lai KW, Ye Z, Cheng L, Au KW, Zhang J, Li GR, Lau CP, Tse HF, and Li RA.
      Electrophysiological properties of pluripotent human and mouse embryonic stem cells.
      Stem Cells. 2005. 23(10), 1526-34. DOI: 10.1634/stemcells.2004-0299. PMID: 16091557.
      [Affymetrix Human Genome U133A array]
    • Denkin S, Byrne S, Jie C, Zhang Y.
      Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate.
      Arch Microbiol. 2005 Nov; 184(3), 152-157.
    • Peyser BD, Irizarry RA, Tiffany CW, Chen O, Yuan DS, Boeke JD, Spencer FA.
      Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools.
      Nucleic Acids Res. 2005 Sep 15;33(16):e140.
    • Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, Irizarry RA, Boeke JD.
      Improved microarray methods for profiling the Yeast Knockout strain collection.
      Nucleic Acids Res. 2005 Jul 1;33(12):e103.
    • Chen H, Rubin E, Zhang H, Chung S, Jie C, Garrett E, Biswal S, Sukumar S.
      Identification transcriptional targets of HOXA5.
      J Biol Chem. 2005 May 13; 280(19):19373-80
    • Ren J-G, Jie C, Talbot Jr CC.
      How PEDF Prevents Angiogenesis: A Hypothesized Pathway.
      Medical Hypotheses 2005. 64(1): 74-78.
    • Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S,Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino F, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W.
      Multiple-laboratory comparison of microarray platforms.
      Nat Methods. 2005 May; 2(5), 345-350.
    • Yang R, Murillo FM, Delannoy MH, Blosser RL, Yutzy WH 4th, Uematsu S, Takeda K, Akira S, Viscidi RP, Roden RB.
      B lymphocyte activation by human papillomavirus-like particles directly induces Ig class switch recombination via TLR4-MyD88.
      J Immunol. 2005 Jun 15; 174(12), 7912-7919.
    • Mao R, Wang X, Spitznagel EL, Frelin LP, Ting JC, Ding H, Kim J-W, Ruczinski I, Downey TJ, and Pevsner J.
      Primary and Secondary Transcriptional Effects in the Developing Human Down Syndrome Brain and Heart.
      Genome Biology. 2005. 6(13), R107.
    • Rattner A and Nathans J.
      The Genomic Response to Retinal Disease and Injury: Evidence for Endothelin Signaling from Photoreceptors to Glia.
      J. Neurosci. 2005. 25(18), 4540-4549.
    • Chen J, Rattner A, and Nathans J.
      The Rod Photoreceptor-Specific Nuclear Receptor Nr2e3 Represses Transcription of Multiple Cone-Specific Genes.
      J. Neurosci. 2005. 25(1), 118-129.
    • Chou W-C, Chen H-Y, Yu S-L, Cheng L, Yang P-C, and Dang CV.
      Arsenic Suppresses Gene Expression in Promyelocytic Leukemia Cells Partly through Sp1 Oxidation.
      Blood. 2005. 106(1),304-310.
    • Li F, Wang Y, Zeller KI, Potter JJ, Wonsey DR, O'Donnell KA, Kim J-W, Yustein JT, Lee LA, and Dang CV.
      Myc Stimulates Nuclearly Encoded Mitochondrial Genes and Mitochondrial Biogenesis.
      Mol. Cell. Biol. 2005. 25(14), 6225-6234.
    • Safford M, Collins S, Lutz MA, Allen A, Huang C-T, Kowalski J, Blackford A, Horton MR, Drake C, Schwartz RH, and Powell JD.
      Egr-2 and Egr-3 Are Negative Regulators of T Cell Activation.
      Nat. Immunol. 2005. 6(5), 472-480.
    • Jimeno A, Rubio-Viqueira B, Amador ML, Oppenheimer D, Bouraoud N, Kulesza P, Sebastani V, Maitra A, and Hidalgo M.
      Epidermal Growth Factor Receptor Dynamics Influences Response to Epidermal Growth Factor Receptor Targeted Agents.
      Cancer Res. 2005. 65(8), 3003-3010.
    • Hansel DE, Dhara S, Huang RC, Ashfaq R, Deasel M, Shimada Y, Bernstein HS, Harmon J, Brock M, Forastiere A, Washington MK, Maitra A, and Montgomery E.
      CDC2/CDK1 Expression in Esphageal Adenocarcinoma and Precursor Lesions Serves as a Diagnostic and Cancer Progression Marker and Potential Novel Drug Target.
      Am. J. Surg. Pathol. 2005. 29(3), 390-399.

  • 2004 (16/14)

    • Yung CK, Halperin VL, Tomaselli GF, and Winslow RL.
      Gene expression profiles in end-stage human idiopathic dilated cardiomyopathy: altered expression of apoptotic and cytoskeletal genes.
      Genomics. 2004. 83(2), 281-297. doi: https://doi.org/10.1016/j.ygeno.200308.007. PMID:14706457.
      [Affymetrix Human Genome GeneChip HG-U133A array]
    • Vine AM, Heaps AG, Kaftantzi L, Mosley A, Asquith B, Witkover A, Thompson G, Saito M, Goon PK, Carr L, Martinez-Murillo F, Taylor GP, Bangham CR.
      The role of CTLs in persistent viral infection: cytolytic gene expression in CD8+ lymphocytes distinguishes between individuals with a high or low proviral load of human T cell lymphotropic virus type I.
      J Immunol. 2004 Oct 15; 173(8), 5121-5129.
    • Chou W, Jie C, Kenedy A, Jones R, Trush M, Dang C.
      Role of NADPH oxidase in arsenic-induced reactive oxygen species formation and cytotoxicity in myeloid leukemia cells.
      Proc Natl Acad Sci 2004 101:4578-4583.
    • Glunde K, Jie C, Bhujwalla ZM.
      Molecular Causes for the Abberant Choline Phospholipid Metabolism of Breast Cancer Cells.
      Cancer Research. 2004 64(12): 4270-6.
    • Warren C, Eckley M, Lee M, Hanna J, Hughes A, Peyser B, Jie C, Irizarry R, Spencer F.
      The S Phase Checkpoint Safeguards High Fidelity Sister Chromatid Cohesion.
      Mol Biol Cell. 2004 15: 1724-1735.
    • Yin X, Zhou J, Jie C, Xing D, Zhang Y.
      Anticancer Activity Mechanism of Scutellaria barbata extract on human lung cancer cell line A549.
      Life Sci. 2004 17;75(18):2233-44.
    • Ng CM, Cheng A, Myers LA, Martinez-Murillo F, Jie C, Hausladen JMW, Mecham RP, Judge DP, Dietz HC.
      TGF-beta-dependent pathogenesis of mitral valve prolapse in a mouse model of Marfan syndrome.
      J Clin Invest, 2004 Dec;114 (11):1586-92.
    • Yang R, Martinez-Murillo F, Cui H, Blosser R, Uematsu S, Takeda K, Akira S, Viscidi R, and Roden R.
      Papillomavirus-like particles stimulate murine bone marrow-derived dendritic cells to produce alpha interferon and Th1 immune responses via MyD88.
      J Virol. 2004 Oct;78(20):11152-60.
    • Abounader R, Reznik T, Colantuoni C, Martinez-Murillo F, Rosen EM, Laterra J.
      Regulation of c-Met-dependent gene expression by PTEN.
      Oncogene. 2004 Dec 9;23(57):9173-82.
    • Yang R, Murillo FM, Lin KY, Yutzy WH 4th, Uematsu S, Takeda K, Akira S, Viscidi RP, Roden RB.
      Human papillomavirus type-16 virus-like particles activate complementary defense responses in key dendritic cell subpopulations.
      J Immunol. 2004 Aug 15;173(4):2624-31.
    • Wu Z, Irizarry R, Gentleman R, Martinez Murillo F, Spencer F.
      A model based background adjustment for oligonucleotide expression arrays.
      Journal of the American Statistical Association 2004, vol. 99, no. 468, pp. 909 917.
    • Georgantas RW 3rd, Tanadve V, Malehorn M, Heimfeld S, Chen C, Carr L, Martinez-Murillo F, Riggins G, Kowalski J, Civin CI.
      Microarray and serial analysis of gene expression analyses identify known and novel transcripts overexpressed in hematopoietic stem cells.
      Cancer Res. 2004 Jul 1;64(13):4434-41.
    • Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC.
      Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise.
      Nat Genet. 2004 Oct;36(10):1073-8.
    • Maxwell PH, Coombes C, Kenny AE, Lawlwer JF, Boeke JD, and Curcio MJ.
      Ty1 Mobilizes Subtelomeric Y'Elements in Telomerase-Negative Saccharomyces cerevisiae Survivors.
      Mol. Cell. Biol. 2004. 24(22), 9887-9898.
    • Kowalski J, Drake C, Schwartz RH, and Powell J.
      Non-Parametric, Hypothesis-Based Analysis of Microarrays for Comparison of Several Phenotypes.
      Bioinformatics. 2004. 20(3), 364-373.
    • Lee MS and Spencer FA.
      Bipolar Orientation of Chromosomes in Saccharomyces cerevisiae Is Monitored by Mad1 and Mad2, but Not by Mad3.
      Proc. Natl. Acad. Sci. USA. 2004. 102(29), 10655-10660.
  • 2003 (2)

  • 2002 (1)

Last modified: Mon Aug 24 2020