{"id":17,"date":"2021-10-18T14:11:47","date_gmt":"2021-10-18T14:11:47","guid":{"rendered":"http:\/\/geiselmed2.dartmouth.edu\/whitfield-lab\/?page_id=17"},"modified":"2024-09-26T17:49:34","modified_gmt":"2024-09-26T17:49:34","slug":"publications","status":"publish","type":"page","link":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<p style=\"font-weight: 400\">Chakravarty EF, Martyanov V, Fiorentino D, Wood TA, Haddon DJ, Jarrell JA, Utz PJ, Genovese MC, Whitfield ML, Chung L.\u00a0A Pilot Randomized Placebo-Controlled study of Abatacept for the Treatment of Diffuse Cutaneous Systemic Sclerosis.\u00a0Arthritis research &amp; therapy.\u00a0Forthcoming.<\/p>\n<p style=\"font-weight: 400\">Taroni JN, Martyanov V, Wood TA, Choe S, Huang CC, Hirano I, Yang GY, Brenner D, Jung B, Carns M, Podluski S, Chang RW, Varga J, Whitfield ML, Hinchcliff M.\u00a0Genome-wide gene expression analysis of systemic sclerosis esophageal biopsies identifies disease-specific molecular subsets.\u00a0Arthritis research &amp; therapy.\u00a0Forthcoming.<\/p>\n<p style=\"font-weight: 400\">Torres GM, Jarnagin HC, Park C, Yang H, Kosarek NN, Bhandari R, Wang CY, Kolling FW, Whitfield ML, Turk MJ, Liby KT, Pioli PA.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/37577680\/\">CDDO-Methyl Ester Inhibits BRAF Inhibitor Resistance and Remodels the Myeloid Compartment in BRAF-mutant Melanoma.\u00a0<\/a>bioRxiv.\u00a02023 Aug 3;.\u00a0doi: 10.1101\/2023.08.01.551524.\u00a0PubMed PMID: 37577680; PubMed Central PMCID: PMC10418171.<\/p>\n<p style=\"font-weight: 400\">Richmond JM, Patel D, Watanabe T, Chen HW, Martyanov V, Werner G, Garg M, Haddadi NS, Refat MA, Mahmoud BH, Wong LD, Dresser K, Deng A, Zhu JL, McAlpine W, Hosler GA, Feghali-Bostwick CA, Whitfield ML, Harris JE, Torok KS, Jacobe HT.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/36708947\/\">CXCL9 Links Skin Inflammation and Fibrosis through CXCR3-Dependent Upregulation of Col1a1 in Fibroblasts.\u00a0<\/a>J Invest Dermatol.\u00a02023 Jul;143(7):1138-1146.e12.\u00a0doi: 10.1016\/j.jid.2022.11.025.\u00a0Epub 2023 Jan 25.\u00a0PubMed PMID: 36708947.<\/p>\n<p style=\"font-weight: 400\">Bhandari R, Yang H, Kosarek NN, Smith AE, Garlick JA, Hinchcliff M, Whitfield ML, Pioli PA.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/35946522\/\">Human dermal fibroblast-derived exosomes induce macrophage activation in systemic sclerosis.\u00a0<\/a>Rheumatology (Oxford).\u00a02023 Feb 6;62(SI):SI114-SI124.\u00a0doi: 10.1093\/rheumatology\/keac453.\u00a0PubMed PMID: 35946522; PubMed Central PMCID: PMC9910573.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/33654308\/\">Moving towards a molecular categorization of autoimmune disease.\u00a0<\/a>Nat Rev Rheumatol.\u00a02021 Apr;17(4):193-194.\u00a0doi: 10.1038\/s41584-021-00589-z.\u00a0PubMed PMID: 33654308.<\/p>\n<p style=\"font-weight: 400\">Franks JM, Martyanov V, Wang Y, Wood TA, Pinckney A, Crofford LJ, Keyes-Elstein L, Furst DE, Goldmuntz E, Mayes MD, McSweeney P, Nash RA, Sullivan KM, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/32933919\/\">Machine learning predicts stem cell transplant response in severe scleroderma.\u00a0<\/a>Ann Rheum Dis.\u00a02020 Dec;79(12):1608-1615.\u00a0doi: 10.1136\/annrheumdis-2020-217033.\u00a0Epub 2020 Sep 15.\u00a0PubMed PMID: 32933919; PubMed Central PMCID: PMC8582621.<\/p>\n<p style=\"font-weight: 400\">Bhandari R, Ball MS, Martyanov V, Popovich D, Schaafsma E, Han S, ElTanbouly M, Orzechowski NM, Carns M, Arroyo E, Aren K, Hinchcliff M, Whitfield ML, Pioli PA.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/32134204\/\">Profibrotic Activation of Human Macrophages in Systemic Sclerosis.\u00a0<\/a>Arthritis Rheumatol.\u00a02020 Jul;72(7):1160-1169.\u00a0doi: 10.1002\/art.41243.\u00a0Epub 2020 May 31.\u00a0PubMed PMID: 32134204; PubMed Central PMCID: PMC7329566.<\/p>\n<p style=\"font-weight: 400\">Hinchcliff M, Toledo DM, Taroni JN, Wood TA, Franks JM, Ball MS, Hoffmann A, Amin SM, Tan AU, Tom K, Nesbeth Y, Lee J, Ma M, Aren K, Carns MA, Pioli PA, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29391252\/\">Mycophenolate Mofetil Treatment of Systemic Sclerosis Reduces Myeloid Cell Numbers and Attenuates the Inflammatory Gene Signature in Skin.\u00a0<\/a>J Invest Dermatol.\u00a02018 Jun;138(6):1301-1310.\u00a0doi: 10.1016\/j.jid.2018.01.006.\u00a0Epub 2018 Jan 31.\u00a0PubMed PMID: 29391252; PubMed Central PMCID: PMC6590516.<\/p>\n<p style=\"font-weight: 400\">Franks JM, Cai G, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29360996\/\">Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data.\u00a0<\/a>Bioinformatics.\u00a02018 Jun 1;34(11):1868-1874.\u00a0doi: 10.1093\/bioinformatics\/bty026.\u00a0PubMed PMID: 29360996; PubMed Central PMCID: PMC5972664.<\/p>\n<p style=\"font-weight: 400\">Messemaker TC, Chadli L, Cai G, Goelela VS, Boonstra M, Dorj\u00e9e AL, Andersen SN, Mikkers HMM, van 't Hof P, Mei H, Distler O, Draisma HHM, Johnson ME, Orzechowski NM, Simms RW, Toes REM, Aarbiou J, Huizinga TW, Whitfield ML, DeGroot J, de Vries-Bouwstra J, Kurreeman F.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29179949\/\">Antisense Long Non-Coding RNAs Are Deregulated in Skin Tissue of Patients with\u00a0Systemic Sclerosis.\u00a0<\/a>J Invest Dermatol.\u00a02018 Apr;138(4):826-835.\u00a0doi: 10.1016\/j.jid.2017.09.053.\u00a0Epub 2017 Nov 24.\u00a0PubMed PMID: 29179949.<\/p>\n<p style=\"font-weight: 400\">Gordon JK, Martyanov V, Franks JM, Bernstein EJ, Szymonifka J, Magro C, Wildman HF, Wood TA, Whitfield ML, Spiera RF.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29073351\/\">Belimumab for the Treatment of Early Diffuse Systemic Sclerosis: Results of a Randomized, Double-Blind, Placebo-Controlled, Pilot Trial.\u00a0<\/a>Arthritis Rheumatol.\u00a02018 Feb;70(2):308-316.\u00a0doi: 10.1002\/art.40358.\u00a0Epub 2017 Dec 29.\u00a0PubMed PMID: 29073351; PubMed Central PMCID: PMC6590997.<\/p>\n<p style=\"font-weight: 400\">Martyanov V, Kim GJ, Hayes W, Du S, Ganguly BJ, Sy O, Lee SK, Bogatkevich GS, Schieven GL, Schiopu E, Marangoni RG, Goldin J, Whitfield ML, Varga J.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29121645\/\">Novel lung imaging biomarkers and skin gene expression subsetting in dasatinib treatment of systemic sclerosis-associated interstitial lung disease.\u00a0<\/a>PLoS One.\u00a02017;12(11):e0187580.\u00a0doi: 10.1371\/journal.pone.0187580.\u00a0eCollection 2017.\u00a0PubMed PMID: 29121645; PubMed Central PMCID: PMC5679625.<\/p>\n<p style=\"font-weight: 400\">Taroni JN, Mahoney JM, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29520335\/\">The mechanistic implications of gene expression studies in SSc: Insights from Systems Biology.\u00a0<\/a>Curr Treatm Opt Rheumatol.\u00a02017 Sep;3(3):181-192.\u00a0doi: 10.1007\/s40674-017-0072-0.\u00a0Epub 2017 Jul 29.\u00a0PubMed PMID: 29520335; PubMed Central PMCID: PMC5837066.<\/p>\n<p style=\"font-weight: 400\">Derrett-Smith EC, Martyanov V, Chighizola CB, Moinzadeh P, Campochiaro C, Khan K, Wood TA, Meroni PL, Abraham DJ, Ong VH, Lafyatis R, Whitfield ML, Denton CP.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28676069\/\">Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature.\u00a0<\/a>Arthritis Res Ther.\u00a02017 Jul 4;19(1):156.\u00a0doi: 10.1186\/s13075-017-1360-7.\u00a0PubMed PMID: 28676069; PubMed Central PMCID: PMC5496265.<\/p>\n<p style=\"font-weight: 400\">Taroni JN, Martyanov V, Mahoney JM, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28011145\/\">A Functional Genomic Meta-Analysis of Clinical Trials in Systemic Sclerosis: Toward\u00a0Precision Medicine and Combination Therapy.\u00a0<\/a>J Invest Dermatol.\u00a02017 May;137(5):1033-1041.\u00a0doi: 10.1016\/j.jid.2016.12.007.\u00a0Epub 2016 Dec 21.\u00a0PubMed PMID: 28011145; PubMed Central PMCID: PMC8190797.<\/p>\n<p style=\"font-weight: 400\">Cai G, Xiao F, Cheng C, Li Y, Amos CI, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28426704\/\">Population effect model identifies gene expression predictors of survival outcomes in lung adenocarcinoma for both Caucasian and Asian patients.\u00a0<\/a>PLoS One.\u00a02017;12(4):e0175850.\u00a0doi: 10.1371\/journal.pone.0175850.\u00a0eCollection 2017.\u00a0PubMed PMID: 28426704; PubMed Central PMCID: PMC5398559.<\/p>\n<p style=\"font-weight: 400\">Steinberg SM, Shabaneh TB, Zhang P, Martyanov V, Li Z, Malik BT, Wood TA, Boni A, Molodtsov A, Angeles CV, Curiel TJ, Whitfield ML, Turk MJ.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28202513\/\">Myeloid Cells That Impair Immunotherapy Are Restored in Melanomas with Acquired Resistance to BRAF Inhibitors.\u00a0<\/a>Cancer Res.\u00a02017 Apr 1;77(7):1599-1610.\u00a0doi: 10.1158\/0008-5472.CAN-16-1755.\u00a0Epub 2017 Feb 15.\u00a0PubMed PMID: 28202513; PubMed Central PMCID: PMC5380540.<\/p>\n<p style=\"font-weight: 400\">Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann RB, Farber HW, Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28330499\/\">A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis.\u00a0<\/a>Genome Med.\u00a02017 Mar 23;9(1):27.\u00a0doi: 10.1186\/s13073-017-0417-1.\u00a0PubMed PMID: 28330499; PubMed Central PMCID: PMC5363043.<\/p>\n<p style=\"font-weight: 400\">Lofgren S, Hinchcliff M, Carns M, Wood T, Aren K, Arroyo E, Cheung P, Kuo A, Valenzuela A, Haemel A, Wolters PJ, Gordon J, Spiera R, Assassi S, Boin F, Chung L, Fiorentino D, Utz PJ, Whitfield ML, Khatri P.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28018971\/\">Integrated, multicohort analysis of systemic sclerosis identifies robust transcriptional signature of disease severity.\u00a0<\/a>JCI Insight.\u00a02016 Dec 22;1(21):e89073.\u00a0doi: 10.1172\/jci.insight.89073.\u00a0PubMed PMID: 28018971; PubMed Central PMCID: PMC5161207.<\/p>\n<p style=\"font-weight: 400\">Lyons SM, Cunningham CH, Welch JD, Groh B, Guo AY, Wei B, Whitfield ML, Xiong Y, Marzluff WF.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27402160\/\">A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues.\u00a0<\/a>Nucleic Acids Res.\u00a02016 Nov 2;44(19):9190-9205.\u00a0doi: 10.1093\/nar\/gkw620.\u00a0Epub 2016 Jul 8.\u00a0PubMed PMID: 27402160; PubMed Central PMCID: PMC5100578.<\/p>\n<p style=\"font-weight: 400\">Sargent JL, Li Z, Aliprantis AO, Greenblatt M, Lemaire R, Wu MH, Wei J, Taroni J, Harris A, Long KB, Burgwin C, Artlett CM, Blankenhorn EP, Lafyatis R, Varga J, Clark SH, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26945694\/\">Identification of Optimal Mouse Models of Systemic Sclerosis by Interspecies Comparative Genomics.\u00a0<\/a>Arthritis Rheumatol.\u00a02016 Aug;68(8):2003-15.\u00a0doi: 10.1002\/art.39658.\u00a0PubMed PMID: 26945694; PubMed Central PMCID: PMC5695038.<\/p>\n<p style=\"font-weight: 400\">Johnson ME, Grassetti AV, Taroni JN, Lyons SM, Schweppe D, Gordon JK, Spiera RF, Lafyatis R, Anderson PJ, Gerber SA, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26801089\/\">Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis.\u00a0<\/a>Arthritis Res Ther.\u00a02016 Jan 22;18:27.\u00a0doi: 10.1186\/s13075-016-0914-4.\u00a0PubMed PMID: 26801089; PubMed Central PMCID: PMC4724133.<\/p>\n<p style=\"font-weight: 400\">Martyanov V, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26555452\/\">Molecular stratification and precision medicine in systemic sclerosis from genomic and proteomic data.\u00a0<\/a>Curr Opin Rheumatol.\u00a02016 Jan;28(1):83-8.\u00a0doi: 10.1097\/BOR.0000000000000237.\u00a0Review.\u00a0PubMed PMID: 26555452; PubMed Central PMCID: PMC4722537.<\/p>\n<p style=\"font-weight: 400\">Iwamoto N, Vettori S, Maurer B, Brock M, Pachera E, J\u00fcngel A, Calcagni M, Gay RE, Whitfield ML, Distler JH, Gay S, Distler O.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25384965\/\">Downregulation of miR-193b in systemic sclerosis regulates the proliferative vasculopathy by urokinase-type plasminogen activator expression.\u00a0<\/a>Ann Rheum Dis.\u00a02016 Jan;75(1):303-10.\u00a0doi: 10.1136\/annrheumdis-2014-205326.\u00a0Epub 2014 Nov 10.\u00a0PubMed PMID: 25384965.<\/p>\n<p style=\"font-weight: 400\">Brooks L 3rd, Lyons SM, Mahoney JM, Welch JD, Liu Z, Marzluff WF, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26377992\/\">A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs.\u00a0<\/a>RNA.\u00a02015 Nov;21(11):1943-65.\u00a0doi: 10.1261\/rna.053389.115.\u00a0Epub 2015 Sep 16.\u00a0PubMed PMID: 26377992; PubMed Central PMCID: PMC4604434.<\/p>\n<p style=\"font-weight: 400\">Rice LM, Ziemek J, Stratton EA, McLaughlin SR, Padilla CM, Mathes AL, Christmann RB, Stifano G, Browning JL, Whitfield ML, Spiera RF, Gordon JK, Simms RW, Zhang Y, Lafyatis R.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26240058\/\">A longitudinal biomarker for the extent of skin disease in patients with diffuse cutaneous systemic sclerosis.\u00a0<\/a>Arthritis Rheumatol.\u00a02015 Nov;67(11):3004-15.\u00a0doi: 10.1002\/art.39287.\u00a0PubMed PMID: 26240058; PubMed Central PMCID: PMC5522178.<\/p>\n<p style=\"font-weight: 400\">Johnson ME, Pioli PA, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26223504\/\">Gene expression profiling offers insights into the role of innate immune signaling in SSc.\u00a0<\/a>Semin Immunopathol.\u00a02015 Sep;37(5):501-9.\u00a0doi: 10.1007\/s00281-015-0512-6.\u00a0Epub 2015 Jul 30.\u00a0Review.\u00a0PubMed PMID: 26223504; PubMed Central PMCID: PMC4722533.<\/p>\n<p style=\"font-weight: 400\">Gordon JK, Martyanov V, Magro C, Wildman HF, Wood TA, Huang WT, Crow MK, Whitfield ML, Spiera RF.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26283632\/\">Nilotinib (Tasigna\u2122) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial.\u00a0<\/a>Arthritis Res Ther.\u00a02015 Aug 18;17(1):213.\u00a0doi: 10.1186\/s13075-015-0721-3.\u00a0PubMed PMID: 26283632; PubMed Central PMCID: PMC4538758.<\/p>\n<p style=\"font-weight: 400\">Taroni JN, Martyanov V, Huang CC, Mahoney JM, Hirano I, Shetuni B, Yang GY, Brenner D, Jung B, Wood TA, Bhattacharyya S, Almagor O, Lee J, Sirajuddin A, Varga J, Chang RW, Whitfield ML, Hinchcliff M.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26220546\/\">Molecular characterization of systemic sclerosis esophageal pathology identifies inflammatory and proliferative signatures.\u00a0<\/a>Arthritis Res Ther.\u00a02015 Jul 29;17:194.\u00a0doi: 10.1186\/s13075-015-0695-1.\u00a0PubMed PMID: 26220546; PubMed Central PMCID: PMC4518531.<\/p>\n<p style=\"font-weight: 400\">Rice LM, Padilla CM, McLaughlin SR, Mathes A, Ziemek J, Goummih S, Nakerakanti S, York M, Farina G, Whitfield ML, Spiera RF, Christmann RB, Gordon JK, Weinberg J, Simms RW, Lafyatis R.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26098215\/\">Fresolimumab treatment decreases biomarkers and improves clinical symptoms in systemic sclerosis patients.\u00a0<\/a>J Clin Invest.\u00a02015 Jul 1;125(7):2795-807.\u00a0doi: 10.1172\/JCI77958.\u00a0Epub 2015 Jun 22.\u00a0PubMed PMID: 26098215; PubMed Central PMCID: PMC4563675.<\/p>\n<p style=\"font-weight: 400\">Chakravarty EF, Martyanov V, Fiorentino D, Wood TA, Haddon DJ, Jarrell JA, Utz PJ, Genovese MC, Whitfield ML, Chung L.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26071192\/\">Gene expression changes reflect clinical response in a placebo-controlled randomized trial of abatacept in patients with diffuse cutaneous systemic sclerosis.\u00a0<\/a>Arthritis Res Ther.\u00a02015 Jun 13;17(1):159.\u00a0doi: 10.1186\/s13075-015-0669-3.\u00a0PubMed PMID: 26071192; PubMed Central PMCID: PMC4487200.<\/p>\n<p style=\"font-weight: 400\">Marangoni RG, Korman BD, Wei J, Wood TA, Graham LV, Whitfield ML, Scherer PE, Tourtellotte WG, Varga J.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25504959\/\">Myofibroblasts in murine cutaneous fibrosis originate from adiponectin-positive intradermal progenitors.\u00a0<\/a>Arthritis Rheumatol.\u00a02015 Apr;67(4):1062-73.\u00a0doi: 10.1002\/art.38990.\u00a0PubMed PMID: 25504959; PubMed Central PMCID: PMC4472310.<\/p>\n<p style=\"font-weight: 400\">Long KB, Li Z, Burgwin CM, Choe SG, Martyanov V, Sassi-Gaha S, Earl JP, Eutsey RA, Ahmed A, Ehrlich GD, Artlett CM, Whitfield ML, Blankenhorn EP.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25330296\/\">The Tsk2\/+ mouse fibrotic phenotype is due to a gain-of-function mutation in the PIIINP segment of the Col3a1 gene.\u00a0<\/a>J Invest Dermatol.\u00a02015 Mar;135(3):718-27.\u00a0doi: 10.1038\/jid.2014.455.\u00a0Epub 2014 Oct 20.\u00a0PubMed PMID: 25330296; PubMed Central PMCID: PMC4324084.<\/p>\n<p style=\"font-weight: 400\">Johnson ME, Mahoney JM, Taroni J, Sargent JL, Marmarelis E, Wu MR, Varga J, Hinchcliff ME, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25607805\/\">Experimentally-derived fibroblast gene signatures identify molecular pathways associated with distinct subsets of systemic sclerosis patients in three independent cohorts.\u00a0<\/a>PLoS One.\u00a02015;10(1):e0114017.\u00a0doi: 10.1371\/journal.pone.0114017.\u00a0eCollection 2015.\u00a0PubMed PMID: 25607805; PubMed Central PMCID: PMC4301872.<\/p>\n<p style=\"font-weight: 400\">Mahoney JM, Taroni J, Martyanov V, Wood TA, Greene CS, Pioli PA, Hinchcliff ME, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25569146\/\">Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms.\u00a0<\/a>PLoS Comput Biol.\u00a02015 Jan;11(1):e1004005.\u00a0doi: 10.1371\/journal.pcbi.1004005.\u00a0eCollection 2015 Jan.\u00a0PubMed PMID: 25569146; PubMed Central PMCID: PMC4288710.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML.\u00a0Systems biology in systemic sclerosis.\u00a0In:\u00a0Varga J, editor.\u00a0Scleroderma: From Pathogenesis to Comprehensive Management\u00a0London: Springer;\u00a02015.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML, Hinchcliff M.\u00a0Disease classification using molecular signatures.\u00a0In:\u00a0Varga J, editor.\u00a0Scleroderma: From Pathogenesis to Comprehensive Management\u00a0London: Springer;\u00a02015.\u00a0Chapter 8.<\/p>\n<p style=\"font-weight: 400\">Arron ST, Dimon MT, Li Z, Johnson ME, Wood TA, Feeney L, Angeles JG, Lafyatis R, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24608988\/\">High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis.\u00a0<\/a>J Invest Dermatol.\u00a02014 Aug;134(8):2138-2145.\u00a0doi: 10.1038\/jid.2014.127.\u00a0Epub 2014 Mar 7.\u00a0PubMed PMID: 24608988; PubMed Central PMCID: PMC4102619.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24431280\/\">Editorial: plasma and B cell gene signatures: quantitative targeting and monitoring of B cell-depleting therapies in autoimmune diseases in the genomic era.\u00a0<\/a>Arthritis Rheumatol.\u00a02014 Jan;66(1):10-4.\u00a0doi: 10.1002\/art.38192.\u00a0PubMed PMID: 24431280.<\/p>\n<p style=\"font-weight: 400\">Grant GD, Brooks L 3rd, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24109597\/\">Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors.\u00a0<\/a>Mol Biol Cell.\u00a02013 Dec;24(23):3634-50.\u00a0doi: 10.1091\/mbc.E13-05-0264.\u00a0Epub 2013 Oct 9.\u00a0PubMed PMID: 24109597; PubMed Central PMCID: PMC3842991.<\/p>\n<p style=\"font-weight: 400\">\n<p style=\"font-weight: 400\">Hinchcliff M, Huang CC, Wood TA, Matthew Mahoney J, Martyanov V, Bhattacharyya S, Tamaki Z, Lee J, Carns M, Podlusky S, Sirajuddin A, Shah SJ, Chang RW, Lafyatis R, Varga J, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/23677167\/\">Molecular signatures in skin associated with clinical improvement during mycophenolate treatment in systemic sclerosis.\u00a0<\/a>J Invest Dermatol.\u00a02013 Aug;133(8):1979-89.\u00a0doi: 10.1038\/jid.2013.130.\u00a0Epub 2013 Mar 14.\u00a0PubMed PMID: 23677167; PubMed Central PMCID: PMC3714324.<\/p>\n<p style=\"font-weight: 400\">Cheng C, Ung M, Grant GD, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/23874175\/\">Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs.\u00a0<\/a>PLoS Comput Biol.\u00a02013;9(7):e1003132.\u00a0doi: 10.1371\/journal.pcbi.1003132.\u00a0Epub 2013 Jul 11.\u00a0PubMed PMID: 23874175; PubMed Central PMCID: PMC3708869.<\/p>\n<p style=\"font-weight: 400\">Lenna S, Farina AG, Martyanov V, Christmann RB, Wood TA, Farber HW, Scorza R, Whitfield ML, Lafyatis R, Trojanowska M.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/23400395\/\">Increased expression of endoplasmic reticulum stress and unfolded protein response genes in peripheral blood mononuclear cells from patients with limited cutaneous systemic sclerosis and pulmonary arterial hypertension.\u00a0<\/a>Arthritis Rheum.\u00a02013 May;65(5):1357-66.\u00a0doi: 10.1002\/art.37891.\u00a0PubMed PMID: 23400395; PubMed Central PMCID: PMC3636187.<\/p>\n<p style=\"font-weight: 400\">Grant GD, Gamsby J, Martyanov V, Brooks L 3rd, George LK, Mahoney JM, Loros JJ, Dunlap JC, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22740631\/\">Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control.\u00a0<\/a>Mol Biol Cell.\u00a02012 Aug;23(16):3079-93.\u00a0doi: 10.1091\/mbc.E11-02-0170.\u00a0Epub 2012 Jun 27.\u00a0PubMed PMID: 22740631; PubMed Central PMCID: PMC3418304.<\/p>\n<p style=\"font-weight: 400\">Wei J, Fang F, Lam AP, Sargent JL, Hamburg E, Hinchcliff ME, Gottardi CJ, Atit R, Whitfield ML, Varga J.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22328118\/\">Wnt\/\u03b2-catenin signaling is hyperactivated in systemic sclerosis and induces Smad-dependent fibrotic responses in mesenchymal cells.\u00a0<\/a>Arthritis Rheum.\u00a02012 Aug;64(8):2734-45.\u00a0doi: 10.1002\/art.34424.\u00a0PubMed PMID: 22328118; PubMed Central PMCID: PMC3553791.<\/p>\n<p style=\"font-weight: 400\">Lakota K, Wei J, Carns M, Hinchcliff M, Lee J, Whitfield ML, Sodin-Semrl S, Varga J.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22548780\/\">Levels of adiponectin, a marker for PPAR-gamma activity, correlate with skin fibrosis in systemic sclerosis: potential utility as biomarker?.\u00a0<\/a>Arthritis Res Ther.\u00a02012 May 1;14(3):R102.\u00a0doi: 10.1186\/ar3827.\u00a0PubMed PMID: 22548780; PubMed Central PMCID: PMC3446479.<\/p>\n<p style=\"font-weight: 400\">Pendergrass SA, Lemaire R, Francis IP, Mahoney JM, Lafyatis R, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22318389\/\">Intrinsic gene expression subsets of diffuse cutaneous systemic sclerosis are stable in serial skin biopsies.\u00a0<\/a>J Invest Dermatol.\u00a02012 May;132(5):1363-73.\u00a0doi: 10.1038\/jid.2011.472.\u00a0Epub 2012 Feb 9.\u00a0PubMed PMID: 22318389; PubMed Central PMCID: PMC3326181.<\/p>\n<p style=\"font-weight: 400\">Greenblatt MB, Sargent JL, Farina G, Tsang K, Lafyatis R, Glimcher LH, Whitfield ML, Aliprantis AO.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22245215\/\">Interspecies comparison of human and murine scleroderma reveals IL-13 and CCL2 as disease subset-specific targets.\u00a0<\/a>Am J Pathol.\u00a02012 Mar;180(3):1080-1094.\u00a0doi: 10.1016\/j.ajpath.2011.11.024.\u00a0Epub 2012 Jan 11.\u00a0PubMed PMID: 22245215; PubMed Central PMCID: PMC3349888.<\/p>\n<p style=\"font-weight: 400\">Allen JA, Peterson A, Sufit R, Hinchcliff ME, Mahoney JM, Wood TA, Miller FW, Whitfield ML, Varga J.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21702023\/\">Post-epidemic eosinophilia-myalgia syndrome associated with L-tryptophan.\u00a0<\/a>Arthritis Rheum.\u00a02011 Nov;63(11):3633-9.\u00a0doi: 10.1002\/art.30514.\u00a0PubMed PMID: 21702023; PubMed Central PMCID: PMC3848710.<\/p>\n<p style=\"font-weight: 400\">Bhattacharyya S, Sargent JL, Du P, Lin S, Tourtellotte WG, Takehara K, Whitfield ML, Varga J.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21931594\/\">Egr-1 induces a profibrotic injury\/repair gene program associated with systemic sclerosis.\u00a0<\/a>PLoS One.\u00a02011;6(9):e23082.\u00a0doi: 10.1371\/journal.pone.0023082.\u00a0Epub 2011 Sep 13.\u00a0PubMed PMID: 21931594; PubMed Central PMCID: PMC3172216.<\/p>\n<p style=\"font-weight: 400\">Sargent JL, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21790289\/\">Capturing the heterogeneity in systemic sclerosis with genome-wide expression profiling.\u00a0<\/a>Expert Rev Clin Immunol.\u00a02011 Jul;7(4):463-73.\u00a0doi: 10.1586\/eci.11.41.\u00a0Review.\u00a0PubMed PMID: 21790289; PubMed Central PMCID: PMC3178333.<\/p>\n<p style=\"font-weight: 400\">Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, Wang Y, Kong B, Langer\u00f8d A, B\u00f8rresen-Dale AL, Kim SK, van de Vijver M, Sukumar S, Whitfield ML, Kellis M, Xiong Y, Wong DJ, Chang HY.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21642992\/\">Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters.\u00a0<\/a>Nat Genet.\u00a02011 Jun 5;43(7):621-9.\u00a0doi: 10.1038\/ng.848.\u00a0PubMed PMID: 21642992; PubMed Central PMCID: PMC3652667.<\/p>\n<p style=\"font-weight: 400\">Christmann RB, Hayes E, Pendergrass S, Padilla C, Farina G, Affandi AJ, Whitfield ML, Farber HW, Lafyatis R.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21425123\/\">Interferon and alternative activation of monocyte\/macrophages in systemic sclerosis-associated pulmonary arterial hypertension.\u00a0<\/a>Arthritis Rheum.\u00a02011 Jun;63(6):1718-28.\u00a0doi: 10.1002\/art.30318.\u00a0PubMed PMID: 21425123; PubMed Central PMCID: PMC4030759.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML, Lafyatis R.\u00a0Disease classification using molecular signatures.\u00a0In:\u00a0Varga J, editor.\u00a0Scleroderma: From Pathogenesis to Comprehensive Management\u00a0London: Springer;\u00a02011.\u00a0Chapter 8.<\/p>\n<p style=\"font-weight: 400\">Katsumoto TR, Whitfield ML, Connolly MK.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21090968\/\">The pathogenesis of systemic sclerosis.\u00a0<\/a>Annu Rev Pathol.\u00a02011;6:509-37.\u00a0doi: 10.1146\/annurev-pathol-011110-130312.\u00a0Review.\u00a0PubMed PMID: 21090968.<\/p>\n<p style=\"font-weight: 400\">Wei J, Ghosh AK, Sargent JL, Komura K, Wu M, Huang QQ, Jain M, Whitfield ML, Feghali-Bostwick C, Varga J.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21072170\/\">PPAR\u03b3 downregulation by TGF\u00df in fibroblast and impaired expression and function in systemic sclerosis: a novel mechanism for progressive fibrogenesis.\u00a0<\/a>PLoS One.\u00a02010 Nov 2;5(11):e13778.\u00a0doi: 10.1371\/journal.pone.0013778.\u00a0PubMed PMID: 21072170; PubMed Central PMCID: PMC2970611.<\/p>\n<p style=\"font-weight: 400\">Pendergrass SA, Hayes E, Farina G, Lemaire R, Farber HW, Whitfield ML, Lafyatis R.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/20808962\/\">Limited systemic sclerosis patients with pulmonary arterial hypertension show biomarkers of inflammation and vascular injury.\u00a0<\/a>PLoS One.\u00a02010 Aug 17;5(8):e12106.\u00a0doi: 10.1371\/journal.pone.0012106.\u00a0PubMed PMID: 20808962; PubMed Central PMCID: PMC2923145.<\/p>\n<p style=\"font-weight: 400\">Lemaire R, Farina G, Bayle J, Dimarzio M, Pendergrass SA, Milano A, Perbal B, Whitfield ML, Lafyatis R.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/20182440\/\">Antagonistic effect of the matricellular signaling protein CCN3 on TGF-beta- and Wnt-mediated fibrillinogenesis in systemic sclerosis and Marfan syndrome.\u00a0<\/a>J Invest Dermatol.\u00a02010 Jun;130(6):1514-23.\u00a0doi: 10.1038\/jid.2010.15.\u00a0Epub 2010 Feb 25.\u00a0PubMed PMID: 20182440; PubMed Central PMCID: PMC3071475.<\/p>\n<p style=\"font-weight: 400\">Sargent JL, Milano A, Bhattacharyya S, Varga J, Connolly MK, Chang HY, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19812599\/\">A TGFbeta-responsive gene signature is associated with a subset of diffuse scleroderma with increased disease severity.\u00a0<\/a>J Invest Dermatol.\u00a02010 Mar;130(3):694-705.\u00a0doi: 10.1038\/jid.2009.318.\u00a0Epub 2009 Oct 8.\u00a0PubMed PMID: 19812599; PubMed Central PMCID: PMC3867816.<\/p>\n<p style=\"font-weight: 400\">Milks MW, Cripps JG, Lin H, Wang J, Robinson RT, Sargent JL, Whitfield ML, Gorham JD.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19490417\/\">The role of Ifng in alterations in liver gene expression in a mouse model of fulminant autoimmune hepatitis.\u00a0<\/a>Liver Int.\u00a02009 Oct;29(9):1307-15.\u00a0doi: 10.1111\/j.1478-3231.2009.02028.x.\u00a0Epub 2009 Apr 16.\u00a0PubMed PMID: 19490417; PubMed Central PMCID: PMC3038248.<\/p>\n<p style=\"font-weight: 400\">Chandriani S, Frengen E, Cowling VH, Pendergrass SA, Perou CM, Whitfield ML, Cole MD.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19690609\/\">A core MYC gene expression signature is prominent in basal-like breast cancer but only partially overlaps the core serum response.\u00a0<\/a>PLoS One.\u00a02009 Aug 19;4(8):e6693.\u00a0doi: 10.1371\/journal.pone.0006693.\u00a0PubMed PMID: 19690609; PubMed Central PMCID: PMC2723908.<\/p>\n<p style=\"font-weight: 400\">MOLECULAR SIGNATURES FOR DIAGNOSING SCLERODERMA.\u00a0United States US 2011\/0190156 A1.\u00a02009 July.<\/p>\n<p style=\"font-weight: 400\">Varga J, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19482698\/\">Transforming growth factor-beta in systemic sclerosis (scleroderma).\u00a0<\/a>Front Biosci (Schol Ed).\u00a02009 Jun 1;1(1):226-35.\u00a0doi: 10.2741\/s22.\u00a0Review.\u00a0PubMed PMID: 19482698.<\/p>\n<p style=\"font-weight: 400\">Chung L, Fiorentino DF, Benbarak MJ, Adler AS, Mariano MM, Paniagua RT, Milano A, Connolly MK, Ratiner BD, Wiskocil RL, Whitfield ML, Chang HY, Robinson WH.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19180499\/\">Molecular framework for response to imatinib mesylate in systemic sclerosis.\u00a0<\/a>Arthritis Rheum.\u00a02009 Feb;60(2):584-91.\u00a0doi: 10.1002\/art.24221.\u00a0PubMed PMID: 19180499; PubMed Central PMCID: PMC2638060.<\/p>\n<p style=\"font-weight: 400\">Beyrouthy MJ, Alexander KE, Baldwin A, Whitfield ML, Bass HW, McGee D, Hurt MM.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19079774\/\">Identification of G1-regulated genes in normally cycling human cells.\u00a0<\/a>PLoS One.\u00a02008;3(12):e3943.\u00a0doi: 10.1371\/journal.pone.0003943.\u00a0Epub 2008 Dec 15.\u00a0PubMed PMID: 19079774; PubMed Central PMCID: PMC2600614.<\/p>\n<p style=\"font-weight: 400\">Milano A, Pendergrass SA, Sargent JL, George LK, McCalmont TH, Connolly MK, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18648520\/\">Molecular subsets in the gene expression signatures of scleroderma skin.\u00a0<\/a>PLoS One.\u00a02008 Jul 16;3(7):e2696.\u00a0doi: 10.1371\/journal.pone.0002696.\u00a0PubMed PMID: 18648520; PubMed Central PMCID: PMC2481301.<\/p>\n<p style=\"font-weight: 400\">Sargent JL, Milano A, Connolly MK, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18638428\/\">Scleroderma gene expression and pathway signatures.\u00a0<\/a>Curr Rheumatol Rep.\u00a02008 Jul;10(3):205-11.\u00a0doi: 10.1007\/s11926-008-0034-5.\u00a0Review.\u00a0PubMed PMID: 18638428.<\/p>\n<p style=\"font-weight: 400\">Emmons J, Townley-Tilson WH, Deleault KM, Skinner SJ, Gross RH, Whitfield ML, Brooks SA.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18367721\/\">Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation.\u00a0<\/a>RNA.\u00a02008 May;14(5):888-902.\u00a0doi: 10.1261\/rna.748408.\u00a0Epub 2008 Mar 26.\u00a0PubMed PMID: 18367721; PubMed Central PMCID: PMC2327351.<\/p>\n<p style=\"font-weight: 400\">Andrew AS, Jewell DA, Mason RA, Whitfield ML, Moore JH, Karagas MR.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18414638\/\">Drinking-water arsenic exposure modulates gene expression in human lymphocytes from a U.S. population.\u00a0<\/a>Environ Health Perspect.\u00a02008 Apr;116(4):524-31.\u00a0doi: 10.1289\/ehp.10861.\u00a0PubMed PMID: 18414638; PubMed Central PMCID: PMC2290973.<\/p>\n<p style=\"font-weight: 400\">Pendergrass SA, Whitfield ML, Gardner H.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/17917536\/\">Understanding systemic sclerosis through gene expression profiling.\u00a0<\/a>Curr Opin Rheumatol.\u00a02007 Nov;19(6):561-7.\u00a0doi: 10.1097\/BOR.0b013e3282f00375.\u00a0Review.\u00a0PubMed PMID: 17917536.<\/p>\n<p style=\"font-weight: 400\">Townley-Tilson WH, Pendergrass SA, Marzluff WF, Whitfield ML.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16931877\/\">Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein.\u00a0<\/a>RNA.\u00a02006 Oct;12(10):1853-67.\u00a0doi: 10.1261\/rna.76006.\u00a0Epub 2006 Aug 24.\u00a0PubMed PMID: 16931877; PubMed Central PMCID: PMC1581977.<\/p>\n<p style=\"font-weight: 400\">Cowling VH, Chandriani S, Whitfield ML, Cole MD.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16705173\/\">A conserved Myc protein domain, MBIV, regulates DNA binding, apoptosis, transformation, and G2 arrest.\u00a0<\/a>Mol Cell Biol.\u00a02006 Jun;26(11):4226-39.\u00a0doi: 10.1128\/MCB.01959-05.\u00a0PubMed PMID: 16705173; PubMed Central PMCID: PMC1489101.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML, George LK, Grant GD, Perou CM.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16491069\/\">Common markers of proliferation.\u00a0<\/a>Nat Rev Cancer.\u00a02006 Feb;6(2):99-106.\u00a0doi: 10.1038\/nrc1802.\u00a0Review.\u00a0PubMed PMID: 16491069.<\/p>\n<p style=\"font-weight: 400\">Jones SB, DePrimo SE, Whitfield ML, Brooks JD.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15767336\/\">Resveratrol-induced gene expression profiles in human prostate cancer cells.\u00a0<\/a>Cancer Epidemiol Biomarkers Prev.\u00a02005 Mar;14(3):596-604.\u00a0doi: 10.1158\/1055-9965.EPI-04-0398.\u00a0PubMed PMID: 15767336; PubMed Central PMCID: PMC3889115.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML, Kaygun H, Erkmann JA, Townley-Tilson WH, Dominski Z, Marzluff WF.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15358832\/\">SLBP is associated with histone mRNA on polyribosomes as a component of the histone mRNP.\u00a0<\/a>Nucleic Acids Res.\u00a02004;32(16):4833-42.\u00a0doi: 10.1093\/nar\/gkh798.\u00a0Print 2004.\u00a0PubMed PMID: 15358832; PubMed Central PMCID: PMC519100.<\/p>\n<p style=\"font-weight: 400\">Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15004229\/\">Diverse and specific gene expression responses to stresses in cultured human cells.\u00a0<\/a>Mol Biol Cell.\u00a02004 May;15(5):2361-74.\u00a0doi: 10.1091\/mbc.e03-11-0799.\u00a0Epub 2004 Mar 5.\u00a0PubMed PMID: 15004229; PubMed Central PMCID: PMC404029.<\/p>\n<p style=\"font-weight: 400\">Novoradovskaya N, Whitfield ML, Basehore LS, Novoradovsky A, Pesich R, Usary J, Karaca M, Wong WK, Aprelikova O, Fero M, Perou CM, Botstein D, Braman J.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15113400\/\">Universal Reference RNA as a standard for microarray experiments.\u00a0<\/a>BMC Genomics.\u00a02004 Mar 9;5(1):20.\u00a0doi: 10.1186\/1471-2164-5-20.\u00a0PubMed PMID: 15113400; PubMed Central PMCID: PMC394318.<\/p>\n<p style=\"font-weight: 400\">Zhao H, Whitfield ML, Xu T, Botstein D, Brooks JD.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/14617803\/\">Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells.\u00a0<\/a>Mol Biol Cell.\u00a02004 Feb;15(2):506-19.\u00a0doi: 10.1091\/mbc.e03-07-0501.\u00a0Epub 2003 Nov 14.\u00a0PubMed PMID: 14617803; PubMed Central PMCID: PMC329225.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/14530402\/\">Systemic and cell type-specific gene expression patterns in scleroderma skin.\u00a0<\/a>Proc Natl Acad Sci U S A.\u00a02003 Oct 14;100(21):12319-24.\u00a0doi: 10.1073\/pnas.1635114100.\u00a0Epub 2003 Oct 6.\u00a0PubMed PMID: 14530402; PubMed Central PMCID: PMC218756.<\/p>\n<p style=\"font-weight: 400\">Allard P, Champigny MJ, Skoggard S, Erkmann JA, Whitfield ML, Marzluff WF, Clarke HJ.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/12415002\/\">Stem-loop binding protein accumulates during oocyte maturation and is not cell-cycle-regulated in the early mouse embryo.\u00a0<\/a>J Cell Sci.\u00a02002 Dec 1;115(Pt 23):4577-86.\u00a0doi: 10.1242\/jcs.00132.\u00a0PubMed PMID: 12415002; PubMed Central PMCID: PMC5115915.<\/p>\n<p style=\"font-weight: 400\">Zhao H, Hastie T, Whitfield ML, B\u00f8rresen-Dale AL, Jeffrey SS.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/12445333\/\">Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis.\u00a0<\/a>BMC Genomics.\u00a02002 Oct 30;3(1):31.\u00a0doi: 10.1186\/1471-2164-3-31.\u00a0Epub 2002 Oct 30.\u00a0PubMed PMID: 12445333; PubMed Central PMCID: PMC137577.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/12058064\/\">Identification of genes periodically expressed in the human cell cycle and their expression in tumors.\u00a0<\/a>Mol Biol Cell.\u00a02002 Jun;13(6):1977-2000.\u00a0doi: 10.1091\/mbc.02-02-0030.\u00a0PubMed PMID: 12058064; PubMed Central PMCID: PMC117619.<\/p>\n<p style=\"font-weight: 400\">Richardson RT, Batova IN, Widgren EE, Zheng LX, Whitfield M, Marzluff WF, O'Rand MG.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10893414\/\">Characterization of the histone H1-binding protein, NASP, as a cell cycle-regulated somatic protein.\u00a0<\/a>J Biol Chem.\u00a02000 Sep 29;275(39):30378-86.\u00a0doi: 10.1074\/jbc.M003781200.\u00a0PubMed PMID: 10893414.<\/p>\n<p style=\"font-weight: 400\">Whitfield ML, Zheng LX, Baldwin A, Ohta T, Hurt MM, Marzluff WF.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10825184\/\">Stem-loop binding protein, the protein that binds the 3' end of histone mRNA, is cell cycle regulated by both translational and posttranslational mechanisms.\u00a0<\/a>Mol Cell Biol.\u00a02000 Jun;20(12):4188-98.\u00a0doi: 10.1128\/MCB.20.12.4188-4198.2000.\u00a0PubMed PMID: 10825184; PubMed Central PMCID: PMC85788.<\/p>\n<p style=\"font-weight: 400\">Marzluff WF, Whitfield ML, Dominski Z, Wang ZF.\u00a0Identification of the Protein That Interacts with the 3' End of Histone mRNA..\u00a0In:\u00a0Richter JD, editor.\u00a0mRNA Formation and Function\u00a0New York: Academic Press;\u00a01997.\u00a0p.163-193.<\/p>\n<p style=\"font-weight: 400\">Wang ZF, Whitfield ML, Ingledue TC 3rd, Dominski Z, Marzluff WF.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/8957003\/\">The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing.\u00a0<\/a>Genes Dev.\u00a01996 Dec 1;10(23):3028-40.\u00a0doi: 10.1101\/gad.10.23.3028.\u00a0PubMed PMID: 8957003.<\/p>\n<p style=\"font-weight: 400\">Dominski Z, Sumerel J, Hanson RJ, Whitfield ML, Marzluff WF.\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/8643381\/\">The polyribosomal protein bound to the 3' end of histone mRNA can function in histone pre-mRNA processing.\u00a0<\/a>Nucleic Acids Symp Ser.\u00a01995;(33):234-6.\u00a0PubMed PMID: 8643381.<\/p>\n<p style=\"font-weight: 400\">Grant GD, Parker JJ, Whitfield ML.\u00a0Identification of FOXM1 targets in a genome-wide analysis of periodic gene expression.\u00a0American Society for Cell Biology;\u00a02007; c00.<\/p>\n<p style=\"font-weight: 400\">Chung L, Fiorentino DF, Benbarak MJ, Adler AS, Mariano MM, Panigua RT, Milano A, Connolly MK, Ratiner BD, Wiskocil RL, Whitfield ML, Chang HY, Robinson WH.\u00a0Molecular Framework for Response to Imatinib in Systemic Sclerosis.\u00a0American College of Rheumatology Annual Meeting;\u00a02008; c00.<\/p>\n<p style=\"font-weight: 400\">Sargent JL, Milano A, Bhattacharyya S, Varga J, Chang HY, Connolly MK, Whitfield ML.\u00a0A transforming growth factor-b (TGFb)-responsive gene signature predicts more severe skin disease and occurrence of interstitial lung disease (ILD) in diffuse cutaneous systemic sclerosis (dcSSc).\u00a0American College of Rheumatology Annual Meeting;\u00a02007; c00.<\/p>\n<p style=\"font-weight: 400\">George LK, Whitfield ML.\u00a0Identification of a novel cell cycle-regulated gene involved in maintaining spindle bipolarity.\u00a0American Society for Cell Biology;\u00a02007; c00.<\/p>\n<p style=\"font-weight: 400\">Sargent JL, Aliprantis AO, Lemaire R, Lafyatis R, Glimcher L, Whitfield ML.\u00a0Microarray Analysis of Murine cGVHD as an Animal Model for Human Systemic Sclerosis.\u00a010th International Workshop on Scleroderma Research;\u00a02008; c00.<\/p>\n<p style=\"font-weight: 400\">Ghosh A, Wu M, Melichian D, Sargent JL, Milano A, Connolly MK, Whitfield ML, Varga J.\u00a0Novel Function of PPAR-g: Endogenous Anti-fibrotic that Ameliorates Murine Scleroderma and May be Defective in Systemic Sclerosis (SSc).\u00a0American College of Rheumatology Annual Meeting;\u00a02007; c00.<\/p>\n<p style=\"font-weight: 400\">Pendergrass SA, Lemaire R, Lafyatis RA, Whitfield ML.\u00a0Reproducible And Stable Gene Expression Subsets In Serial Skin Biopsies Taken From Patients Treated In An Open-label Trial Of Rituximab.\u00a0American College of Rheumatology Annual Meeting;\u00a02008; c00.<\/p>\n<p style=\"font-weight: 400\">Wei J, Leng E, Sargent JL, Whitfield ML, Lam A, Gottardi C, Varga J.\u00a0Profibrotic Wnt Signaling in Human Mesenchymal Cells: Implications for Scleroderma.\u00a0American College of Rheumatology Annual Meeting;\u00a02009; c00.<\/p>\n<p style=\"font-weight: 400\">Milano A, Pendergrass SA, Sargent JL, Dou X, Connolly MK, Whitfield ML.\u00a0Molecular subtypes of systemic sclerosis (SSc) from gene expression signatures.\u00a0American College of Rheumatology Annual Meeting;\u00a02007; c00.<\/p>\n<p style=\"font-weight: 400\">Sargent JL, Aliprantis AO, Greenblatt MB, Wu M, Farina GA, Lemaire R, Glimcher LH, Clark SH, Varga J, Lafyatis R, Whitfield ML.\u00a0Distinct Deregulated Pathways Underlie the Molecular Subsets of Scleroderma and Are Recapitulated in \u00a0Animal Models.\u00a0American College of Rheumatology Annual Meeting;\u00a02009; c00.<\/p>\n<p style=\"font-weight: 400\">\n<p style=\"font-weight: 400\">\n","protected":false},"excerpt":{"rendered":"<p><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/34533286\" target=\"_blank\" rel=\"noopener\">Clinical and Molecular Findings after Autologous Stem Cell Transplantation or Cyclophosphamide for Scleroderma: Handling Missing Longitudinal Data.<\/a><br \/>\nKeyes-Elstein L, Pinckney A, Goldmuntz E, Welch B, Franks JM, Martyanov V, Wood TA, Crofford L, Mayes M, McSweeney P, Nash R, Georges G, Csuka ME, Simms R, Furst D, Khanna D, St Clair EW, Whitfield ML, Sullivan KM<br \/>\nArthritis Care Res (Hoboken). 2021 Sep 17; doi: 10.1002\/acr.24785. Epub 2021 Sep 17.<br \/>\nPMID: 34533286<\/p>\n<p><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/34502134\" target=\"_blank\" rel=\"noopener\">SARS-CoV-2 Impairs Dendritic Cells and Regulates DC-SIGN Gene Expression in Tissues.<\/a><br \/>\nCai G, Du M, Bosse Y, Albrecht H, Qin F, Luo X, Androulakis XM, Cheng C, Nagarkatti M, Nagarkatti P, Christiani DC, Whitfield ML, Amos CI, Xiao F<br \/>\nInt J Mol Sci. 2021 Aug 26;22(17) pii: 9228. doi: 10.3390\/ijms22179228. Epub 2021 Aug 26.<br \/>\nPMID: 34502134<\/p>\n<p><a href=\"\/whitfield\/publications\/\">Read More<\/a><\/p>\n","protected":false},"author":36,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-17","page","type-page","status-publish","hentry","author-36"],"_links":{"self":[{"href":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/wp-json\/wp\/v2\/pages\/17","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/wp-json\/wp\/v2\/users\/36"}],"replies":[{"embeddable":true,"href":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/wp-json\/wp\/v2\/comments?post=17"}],"version-history":[{"count":3,"href":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/wp-json\/wp\/v2\/pages\/17\/revisions"}],"predecessor-version":[{"id":115,"href":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/wp-json\/wp\/v2\/pages\/17\/revisions\/115"}],"wp:attachment":[{"href":"https:\/\/geiselmed.dartmouth.edu\/whitfield\/wp-json\/wp\/v2\/media?parent=17"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}