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Joshua M. Francis, Ph.D. - Publications

Affiliations: 
2006 University of Virginia, Charlottesville, VA 
Area:
Molecular Biology
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Liu Y, Guo B, Aguilera-Jimenez E, Chu VS, Zhou J, Wu Z, Francis JM, Yang X, Choi PS, Bailey SD, Zhang X. Chromatin Looping Shapes KLF5-dependent Transcriptional Programs in Human Epithelial Cancers. Cancer Research. PMID 33115806 DOI: 10.1158/0008-5472.CAN-20-1287  0.334
2019 Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, et al. Multi-Omics analysis identifies MGA as a negative regulator of the MYC pathway in lung adenocarcinoma. Molecular Cancer Research : McR. PMID 31862696 DOI: 10.1158/1541-7786.Mcr-19-0657  0.409
2019 Sharifnia T, Wawer MJ, Chen T, Huang QY, Weir BA, Sizemore A, Lawlor MA, Goodale A, Cowley GS, Vazquez F, Ott CJ, Francis JM, Sassi S, Cogswell P, Sheppard HE, et al. Small-molecule targeting of brachyury transcription factor addiction in chordoma. Nature Medicine. PMID 30664779 DOI: 10.1038/S41591-018-0312-3  0.423
2019 Palmer CD, Bulik B, Yang A, Hart M, Davis M, Francis J, Duke F, Zhou R, Busby J, Murphy T, Clark A, Young L, Zhong M, Caldwell K, Abhyankar J, et al. Abstract 4059: Identification of pre-existing neoantigen-specific T cells in patients receiving checkpoint inhibitor therapy using a deep learning antigen prediction model Cancer Research. 79: 4059-4059. DOI: 10.1158/1538-7445.Am2019-4059  0.31
2018 Bulik-Sullivan B, Busby J, Davis M, Young L, Murphy T, Clark A, Duke F, Busby M, Derti A, Skoberne M, Jooss K, Gustafson CE, Rienzo AD, Richards WG, Dao NT, ... ... Francis J, et al. Abstract 5722: Antigen identification for cancer immunotherapy by deep learning on tumor HLA peptides Cancer Research. 78: 5722-5722. DOI: 10.1158/1538-7445.Am2018-5722  0.315
2017 Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, ... ... Francis JM, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nature Communications. 8: 1324. PMID 29109393 DOI: 10.1038/S41467-017-00965-Y  0.33
2017 Zhang X, Choi PS, Francis JM, Gao GF, Campbell JD, Ramachandran A, Mitsuishi Y, Ha G, Shih J, Vazquez F, Tsherniak A, Taylor AM, Zhou J, Wu Z, Berger AC, et al. Somatic super-enhancer duplications and hotspot mutations lead to oncogenic activation of the KLF5 transcription factor. Cancer Discovery. PMID 28963353 DOI: 10.1158/2159-8290.Cd-17-0532  0.452
2017 Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, et al. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Research. PMID 28679620 DOI: 10.1101/Gr.217331.116  0.398
2017 Fan J, Wang L, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Chin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, et al. Abstract 27: Integrated analysis of targeted single-cell genetic and transcriptional heterogeneity suggests novel drivers of chronic lymphocytic leukemia Clinical Cancer Research. 23: 27-27. DOI: 10.1158/1557-3265.Hemmal17-27  0.397
2016 Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, Neftel C, Desai N, Nyman J, Izar B, Luo CC, ... Francis JM, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. PMID 27806376 DOI: 10.1038/Nature20123  0.343
2016 Lin W, Francis JM, Li H, Gao X, Pedamallu CS, Ernst P, Meyerson M. Kmt2a cooperates with menin to suppress tumorigenesis in mouse pancreatic islets. Cancer Biology & Therapy. 0. PMID 27801610 DOI: 10.1080/15384047.2016.1250986  0.354
2016 Kim N, Cho A, Watanabe H, Choi YL, Aziz M, Kassner M, Joung JG, Park AK, Francis JM, Bae JS, Ahn SM, Kim KM, Park JO, Park WY, Ahn MJ, et al. Integrated genomic approaches identify upregulation of SCRN1 as a novel mechanism associated with acquired resistance to erlotinib in PC9 cells harboring oncogenic EGFR mutation. Oncotarget. PMID 26883194 DOI: 10.18632/Oncotarget.7318  0.322
2016 Adalsteinsson VA, Ha G, Freeman S, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed S, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Cohen O, Oh C, Kim J, ... ... Francis J, et al. Abstract LB-136: High concordance of whole-exome sequencing of cell-free DNA and matched biopsies enables genomic discovery in metastatic cancer Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Lb-136  0.362
2016 Kim N, Cho A, Watanabe H, Choi Y, Aziz M, Kassner M, Joung J, Park AK, Francis J, Bae JS, Ahn S, Kim K, Park J, Park W, Ahn M, et al. Abstract 2931: Integrated genomic approaches identify upregulation of SCRN1 as a novel mechanism associated with acquired resistance to erlotinib in non small cell lung cancer cells with oncogenic EGFR mutation Cancer Research. 76: 2931-2931. DOI: 10.1158/1538-7445.Am2016-2931  0.337
2015 Zhang X, Choi PS, Francis JM, Imielinski M, Watanabe H, Cherniack AD, Meyerson M. Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers. Nature Genetics. PMID 26656844 DOI: 10.1038/Ng.3470  0.417
2015 Karpathakis A, Dibra H, Pipinikas C, Feber A, Morris T, Francis JM, Oukrif D, Mandair D, Pericleous M, Mohmaduvesh M, Serra S, Ogunbiyi O, Novelli M, Luong T, Asa SL, et al. Prognostic impact of novel molecular subtypes of small intestinal neuroendocrine tumour. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 26169971 DOI: 10.1158/1078-0432.Ccr-15-0373  0.331
2015 Zhang CZ, Spektor A, Cornils H, Francis JM, Jackson EK, Liu S, Meyerson M, Pellman D. Chromothripsis from DNA damage in micronuclei. Nature. 522: 179-84. PMID 26017310 DOI: 10.1038/Nature14493  0.339
2015 Abedalthagafi MS, Bi WL, Merrill PH, Gibson WJ, Rose MF, Du Z, Francis JM, Du R, Dunn IF, Ligon AH, Beroukhim R, Santagata S. ARID1A and TERT promoter mutations in dedifferentiated meningioma. Cancer Genetics. 208: 345-50. PMID 25963524 DOI: 10.1016/J.Cancergen.2015.03.005  0.321
2015 van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell. 161: 933-45. PMID 25957691 DOI: 10.1016/J.Cell.2015.03.053  0.344
2015 Zhang CZ, Adalsteinsson VA, Francis J, Cornils H, Jung J, Maire C, Ligon KL, Meyerson M, Love JC. Calibrating genomic and allelic coverage bias in single-cell sequencing. Nature Communications. 6: 6822. PMID 25879913 DOI: 10.1038/Ncomms7822  0.325
2015 Park AK, Francis JM, Park WY, Park JO, Cho J. Constitutive asymmetric dimerization drives oncogenic activation of epidermal growth factor receptor carboxyl-terminal deletion mutants. Oncotarget. 6: 8839-50. PMID 25826094 DOI: 10.18632/Oncotarget.3559  0.324
2015 Lin W, Watanabe H, Peng S, Francis JM, Kaplan N, Pedamallu CS, Ramachandran A, Agoston A, Bass AJ, Meyerson M. Dynamic epigenetic regulation by menin during pancreatic islet tumor formation. Molecular Cancer Research : McR. 13: 689-98. PMID 25537453 DOI: 10.1158/1541-7786.Mcr-14-0457  0.488
2015 Zhang X, Francis J, Lin C, Rahl P, Bradner J, Young R. Abstract A38: The role of MGA loss-of-function mutations in lung adenocarcinomas Molecular Cancer Research. 13. DOI: 10.1158/1557-3125.Myc15-A38  0.358
2014 Shankar GM, Taylor-Weiner A, Lelic N, Jones RT, Kim JC, Francis JM, Abedalthagafi M, Borges LF, Coumans JV, Curry WT, Nahed BV, Shin JH, Paek SH, Park SH, Stewart C, et al. Sporadic hemangioblastomas are characterized by cryptic VHL inactivation. Acta Neuropathologica Communications. 2: 167. PMID 25589003 DOI: 10.1186/S40478-014-0167-X  0.344
2014 Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, et al. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nature Biotechnology. 32: 479-84. PMID 24752078 DOI: 10.1038/Nbt.2892  0.337
2014 Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis JM, Pedamallu CS, DeLuca DS, Brooks AN, Wang S, Que J, Rustgi AK, Wong KK, et al. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas. The Journal of Clinical Investigation. 124: 1636-45. PMID 24590290 DOI: 10.1172/Jci71545  0.42
2014 Karpathakis A, Dibra H, Morris T, Oukrife D, Pipinikas CP, Pearce K, Francis J, Pericleous M, Mandair D, Feber A, Toumpanakis C, Luong TV, Meyerson M, Caplin ME, Beck S, et al. Genome-wide DNA methylation profiling of gastrointestinal neuroendocrine tumors to identify hypermethylation of mTOR, Wnt, and Notch pathways in GI NET pathogenesis. Journal of Clinical Oncology. 32: 212-212. DOI: 10.1200/Jco.2014.32.3_Suppl.212  0.305
2014 Adalsteinsson VA, Lohr JG, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis J, Zhang C, Shalek AK, Satija R, Trombetta JT, Lu D, Tallapragada N, Tahirova NT, Kim S, et al. Abstract 993: Whole exome sequencing of CTCs as a window into metastatic cancer Cancer Research. 74: 993-993. DOI: 10.1158/1538-7445.Am2014-993  0.337
2014 Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis JM, Pedamallu CS, Deluca DS, Brooks AN, Que J, Rustgi AK, Wong K, Ligon KL, et al. Abstract 1391: SOX2-p63 interaction and genomic co-localization in squamous cell carcinomas Cancer Research. 74: 1391-1391. DOI: 10.1158/1538-7445.Am2014-1391  0.38
2013 Francis JM, Kiezun A, Ramos AH, Serra S, Pedamallu CS, Qian ZR, Banck MS, Kanwar R, Kulkarni AA, Karpathakis A, Manzo V, Contractor T, Philips J, Nickerson E, Pho N, et al. Somatic mutation of CDKN1B in small intestine neuroendocrine tumors. Nature Genetics. 45: 1483-6. PMID 24185511 DOI: 10.1038/Ng.2821  0.302
2013 Watanabe H, Francis JM, Woo MS, Etemad B, Lin W, Fries DF, Peng S, Snyder EL, Tata PR, Izzo F, Schinzel AC, Cho J, Hammerman PS, Verhaak RG, Hahn WC, et al. Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target. Genes & Development. 27: 197-210. PMID 23322301 DOI: 10.1101/Gad.203208.112  0.428
2013 Watanabe H, Francis JM, Woo MS, Etemad B, Lin W, Fries DF, Peng S, Snyder EL, Tata PR, Schinzel AC, Cho J, Hammerman PS, Verhaak RG, Hahn WC, Rajagopal J, et al. Abstract 3127: Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target. Cancer Research. 73: 3127-3127. DOI: 10.1158/1538-7445.Am2013-3127  0.437
2012 Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, Cortes ML, Fernandez-Lopez JC, Peng S, Ardlie KG, Auclair D, ... ... Francis J, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 486: 405-9. PMID 22722202 DOI: 10.1038/Nature11154  0.325
2012 Banerji S, Cibulskis K, Rangel-Escareño C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, Cortes ML, Fernandez-Lopez JC, Peng S, Ardlie KG, Auclair D, ... ... Francis J, et al. Abstract PL07-01: Molecular profiling of breast cancer in Mexico: Identification of novel therapeutic targets through whole genome sequencing analysis. Cancer Epidemiology, Biomarkers & Prevention. 21. DOI: 10.1158/1055-9965.Disp12-Pl07-01  0.322
2011 Lin W, Cao J, Liu J, Beshiri ML, Fujiwara Y, Francis J, Cherniack AD, Geisen C, Blair LP, Zou MR, Shen X, Kawamori D, Liu Z, Grisanzio C, Watanabe H, et al. Loss of the retinoblastoma binding protein 2 (RBP2) histone demethylase suppresses tumorigenesis in mice lacking Rb1 or Men1. Proceedings of the National Academy of Sciences of the United States of America. 108: 13379-86. PMID 21788502 DOI: 10.1073/Pnas.1110104108  0.398
2011 Francis J, Lin W, Rozenblatt-Rosen O, Meyerson M. The menin tumor suppressor protein is phosphorylated in response to DNA damage Plos One. 6. PMID 21264250 DOI: 10.1371/Journal.Pone.0016119  0.381
2011 Lin W, Francis J, Watanabe H, Yan Q, Kaelin WG, Meyerson M. Abstract 62: Inhibition ofMen1-deficient tumor growth by inactivation of the Rbp2 histone demethylase Cancer Research. 71: 62-62. DOI: 10.1158/1538-7445.Am2011-62  0.327
2009 Rozenblatt-Rosen O, Nagaike T, Francis JM, Kaneko S, Glatt KA, Hughes CM, LaFramboise T, Manley JL, Meyerson M. The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors. Proceedings of the National Academy of Sciences of the United States of America. 106: 755-60. PMID 19136632 DOI: 10.1073/Pnas.0812023106  0.363
2006 Francis J, Babu DA, Deering TG, Chakrabarti SK, Garmey JC, Evans-Molina C, Taylor DG, Mirmira RG. Role of chromatin accessibility in the occupancy and transcription of the insulin gene by the pancreatic and duodenal homeobox factor 1. Molecular Endocrinology (Baltimore, Md.). 20: 3133-45. PMID 16901969 DOI: 10.1210/Me.2006-0126  0.541
2005 Francis J, Chakrabarti SK, Garmey JC, Mirmira RG. Pdx-1 links histone H3-Lys-4 methylation to RNA polymerase II elongation during activation of insulin transcription. The Journal of Biological Chemistry. 280: 36244-53. PMID 16141209 DOI: 10.1074/Jbc.M505741200  0.65
2005 Iype T, Francis J, Garmey JC, Schisler JC, Nesher R, Weir GC, Becker TC, Newgard CB, Griffen SC, Mirmira RG. Mechanism of insulin gene regulation by the pancreatic transcription factor Pdx-1: Application of pre-mRNA analysis and chromatin immunoprecipitation to assess formation of functional transcriptional complexes Journal of Biological Chemistry. 280: 16798-16807. PMID 15743769 DOI: 10.1074/Jbc.M414381200  0.649
2003 Chakrabarti SK, Francis J, Ziesmann SM, Garmey JC, Mirmira RG. Covalent histone modifications underlie the developmental regulation of insulin gene transcription in pancreatic beta cells. The Journal of Biological Chemistry. 278: 23617-23. PMID 12711597 DOI: 10.1074/Jbc.M303423200  0.646
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