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Jonathan Schug, Ph.D. - Publications

Affiliations: 
2005 University of Pennsylvania, Philadelphia, PA, United States 
Area:
Intelligent Systems: Robotics
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59 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 Avrahami D, Wang YJ, Schug J, Feleke E, Gao L, Liu C, Consortium HPAP, Naji A, Glaser B, Kaestner KH. Single cell transcriptomics of human islet ontogeny defines the molecular basis of β cell dedifferentiation in T2D. Molecular Metabolism. 101057. PMID 32739450 DOI: 10.1016/J.Molmet.2020.101057  0.315
2020 Wu H, Reizel T, Wang YJ, Lapiro JL, Kren BT, Schug J, Rao S, Morgan A, Herman A, Shekels LL, Rassette MS, Lane AN, Cassel T, Fan TWM, Manivel JC, et al. A negative reciprocal regulatory axis between cyclin D1 and HNF4α modulates cell cycle progression and metabolism in the liver. Proceedings of the National Academy of Sciences of the United States of America. PMID 32631996 DOI: 10.1073/Pnas.2002898117  0.302
2019 Sarantopoulou D, Tang SY, Ricciotti E, Lahens NF, Lekkas D, Schug J, Guo XS, Paschos GK, FitzGerald GA, Pack AI, Grant GR. Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input. Scientific Reports. 9: 13477. PMID 31530843 DOI: 10.1038/S41598-019-49889-1  0.309
2017 Galivo F, Benedetti E, Wang Y, Pelz C, Schug J, Kaestner KH, Grompe M. Reprogramming human gallbladder cells into insulin-producing β-like cells. Plos One. 12: e0181812. PMID 28813430 DOI: 10.1371/Journal.Pone.0181812  0.362
2017 Lahens NF, Ricciotti E, Smirnova O, Toorens E, Kim EJ, Baruzzo G, Hayer KE, Ganguly T, Schug J, Grant GR. A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. Bmc Genomics. 18: 602. PMID 28797240 DOI: 10.1186/S12864-017-4011-0  0.334
2016 Wang YJ, Golson ML, Schug J, Traum D, Liu C, Vivek K, Dorrell C, Naji A, Powers AC, Chang KM, Grompe M, Kaestner KH. Single-Cell Mass Cytometry Analysis of the Human Endocrine Pancreas. Cell Metabolism. 24: 616-626. PMID 27732837 DOI: 10.1016/J.Cmet.2016.09.007  0.309
2016 Dorrell C, Schug J, Canaday PS, Russ HA, Tarlow BD, Grompe MT, Horton T, Hebrok M, Streeter PR, Kaestner KH, Grompe M. Human islets contain four distinct subtypes of β cells. Nature Communications. 7: 11756. PMID 27399229 DOI: 10.1038/Ncomms11756  0.33
2016 Wang YJ, Schug J, Won KJ, Liu C, Naji A, Avrahami D, Golson ML, Kaestner KH. Single cell transcriptomics of the human endocrine pancreas. Diabetes. PMID 27364731 DOI: 10.2337/Db16-0405  0.338
2016 Nam KN, Mounier A, Fitz NF, Wolfe C, Schug J, Lefterov I, Koldamova R. RXR controlled regulatory networks identified in mouse brain counteract deleterious effects of Aβ oligomers. Scientific Reports. 6: 24048. PMID 27051978 DOI: 10.1038/Srep24048  0.327
2016 Ackermann AM, Wang Z, Schug J, Naji A, Kaestner KH. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Molecular Metabolism. 5: 233-44. PMID 26977395 DOI: 10.1016/J.Molmet.2016.01.002  0.352
2016 Sheaffer KL, Schug J. ChIP-Seq: Library Preparation and Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1402: 101-17. PMID 26721486 DOI: 10.1007/978-1-4939-3378-5_9  0.327
2015 Avrahami D, Li C, Zhang J, Schug J, Avrahami R, Rao S, Stadler MB, Burger L, Schübeler D, Glaser B, Kaestner KH. Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function. Cell Metabolism. PMID 26321660 DOI: 10.1016/J.Cmet.2015.07.025  0.34
2015 Mounier A, Georgiev D, Nam KN, Fitz NF, Castranio EL, Wolfe CM, Cronican AA, Schug J, Lefterov I, Koldamova R. Bexarotene-activated retinoid X receptors regulate neuronal differentiation and dendritic complexity. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 35: 11862-11876. PMID 26311769 DOI: 10.1523/Jneurosci.1001-15.2015  0.303
2015 Lefterov I, Schug J, Mounier A, Nam KN, Fitz NF, Koldamova R. RNA-sequencing reveals transcriptional up-regulation of Trem2 in response to bexarotene treatment. Neurobiology of Disease. 82: 132-40. PMID 26071899 DOI: 10.1016/J.Nbd.2015.05.019  0.366
2015 Elliott EN, Sheaffer KL, Schug J, Stappenbeck TS, Kaestner KH. Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium. Development (Cambridge, England). 142: 2163-72. PMID 26023099 DOI: 10.1242/Dev.117341  0.303
2015 Galivo F, Benedetti E, Wang Y, Lee J, Schug J, Kim S, Kaestner K, Grompe M. 274. Expansion and Conversion of Patient-Derived Human Gallbladder Cells Into Insulin-Producing Pancreatic Endocrine-Like Type Cells Molecular Therapy. 23: S109-S110. DOI: 10.1016/S1525-0016(16)33883-7  0.334
2014 Johnson ME, Zhao J, Schug J, Deliard S, Xia Q, Guy VC, Sainz J, Kaestner KH, Wells AD, Grant SF. Two novel type 2 diabetes loci revealed through integration of TCF7L2 DNA occupancy and SNP association data. Bmj Open Diabetes Research & Care. 2: e000052. PMID 25469308 DOI: 10.1136/Bmjdrc-2014-000052  0.319
2014 Yashiro-Ohtani Y, Wang H, Zang C, Arnett KL, Bailis W, Ho Y, Knoechel B, Lanauze C, Louis L, Forsyth KS, Chen S, Chung Y, Schug J, Blobel GA, Liebhaber SA, et al. Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proceedings of the National Academy of Sciences of the United States of America. 111: E4946-53. PMID 25369933 DOI: 10.1073/Pnas.1407079111  0.326
2014 Dorrell C, Tarlow B, Wang Y, Canaday PS, Haft A, Schug J, Streeter PR, Finegold MJ, Shenje LT, Kaestner KH, Grompe M. The organoid-initiating cells in mouse pancreas and liver are phenotypically and functionally similar. Stem Cell Research. 13: 275-83. PMID 25151611 DOI: 10.1016/J.Scr.2014.07.006  0.332
2014 Golson ML, Maulis MF, Dunn JC, Poffenberger G, Schug J, Kaestner KH, Gannon MA. Activated FoxM1 attenuates streptozotocin-mediated β-cell death. Molecular Endocrinology (Baltimore, Md.). 28: 1435-47. PMID 25073103 DOI: 10.1210/Me.2014-1024  0.338
2014 Ediger BN, Du A, Liu J, Hunter CS, Walp ER, Schug J, Kaestner KH, Stein R, Stoffers DA, May CL. Islet-1 Is essential for pancreatic β-cell function. Diabetes. 63: 4206-17. PMID 25028525 DOI: 10.2337/Db14-0096  0.341
2014 Johnson ME, Schug J, Wells AD, Kaestner KH, Grant SF. Genome-wide analyses of ChIP-Seq derived FOXA2 DNA occupancy in liver points to genetic networks underpinning multiple complex traits. The Journal of Clinical Endocrinology and Metabolism. 99: E1580-5. PMID 24878043 DOI: 10.1210/Jc.2013-4503  0.363
2014 Sheaffer KL, Kim R, Aoki R, Elliott EN, Schug J, Burger L, Schübeler D, Kaestner KH. DNA methylation is required for the control of stem cell differentiation in the small intestine Genes and Development. 28: 652-664. PMID 24637118 DOI: 10.1101/Gad.230318.113  0.335
2014 Kameswaran V, Bramswig NC, McKenna LB, Penn M, Schug J, Hand NJ, Chen Y, Choi I, Vourekas A, Won KJ, Liu C, Vivek K, Naji A, Friedman JR, Kaestner KH. Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets. Cell Metabolism. 19: 135-45. PMID 24374217 DOI: 10.1016/J.Cmet.2013.11.016  0.326
2014 Koldamova R, Schug J, Lefterova M, Cronican AA, Fitz NF, Davenport FA, Carter A, Castranio EL, Lefterov I. Genome-wide approaches reveal EGR1-controlled regulatory networks associated with neurodegeneration. Neurobiology of Disease. 63: 107-14. PMID 24269917 DOI: 10.1016/J.Nbd.2013.11.005  0.355
2013 Hickey RD, Galivo F, Schug J, Brehm MA, Haft A, Wang Y, Benedetti E, Gu G, Magnuson MA, Shultz LD, Lagasse E, Greiner DL, Kaestner KH, Grompe M. Generation of islet-like cells from mouse gall bladder by direct ex vivo reprogramming. Stem Cell Research. 11: 503-15. PMID 23562832 DOI: 10.1016/J.Scr.2013.02.005  0.372
2013 Bramswig NC, Everett LJ, Schug J, Dorrell C, Liu C, Luo Y, Streeter PR, Naji A, Grompe M, Kaestner KH. Epigenomic plasticity enables human pancreatic α to β cell reprogramming. The Journal of Clinical Investigation. 123: 1275-84. PMID 23434589 DOI: 10.1172/Jci66514  0.355
2013 Xie R, Everett LJ, Lim HW, Patel NA, Schug J, Kroon E, Kelly OG, Wang A, D'Amour KA, Robins AJ, Won KJ, Kaestner KH, Sander M. Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells. Cell Stem Cell. 12: 224-37. PMID 23318056 DOI: 10.1016/J.Stem.2012.11.023  0.375
2013 Tsai Y, Shastri N, Smith KD, Schug J, Casellas R, Brown EJ. Abstract 1777: Genome-wide identification of replication-associated breakpoints. Cancer Research. 73: 1777-1777. DOI: 10.1158/1538-7445.Am2013-1777  0.314
2012 Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell. 151: 1608-16. PMID 23260146 DOI: 10.1016/J.Cell.2012.11.018  0.341
2012 Bochkis IM, Schug J, Ye DZ, Kurinna S, Stratton SA, Barton MC, Kaestner KH. Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. Plos Genetics. 8: e1002770. PMID 22737085 DOI: 10.1371/Journal.Pgen.1002770  0.371
2012 Khoo C, Yang J, Weinrott SA, Kaestner KH, Naji A, Schug J, Stoffers DA. Research resource: the pdx1 cistrome of pancreatic islets. Molecular Endocrinology (Baltimore, Md.). 26: 521-33. PMID 22322596 DOI: 10.1210/Me.2011-1231  0.375
2011 Dorrell C, Schug J, Lin CF, Canaday PS, Fox AJ, Smirnova O, Bonnah R, Streeter PR, Stoeckert CJ, Kaestner KH, Grompe M. Transcriptomes of the major human pancreatic cell types Diabetologia. 54: 2832-2844. PMID 21882062 DOI: 10.1007/S00125-011-2283-5  0.337
2011 Wang H, Zou J, Zhao B, Johannsen E, Ashworth T, Wong H, Pear WS, Schug J, Blacklow SC, Arnett KL, Bernstein BE, Kieff E, Aster JC. Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proceedings of the National Academy of Sciences of the United States of America. 108: 14908-13. PMID 21737748 DOI: 10.1073/Pnas.1109023108  0.329
2011 Dorrell C, Erker L, Schug J, Kopp JL, Canaday PS, Fox AJ, Smirnova O, Duncan AW, Finegold MJ, Sander M, Kaestner KH, Grompe M. Prospective isolation of a bipotential clonogenic liver progenitor cell in adult mice. Genes & Development. 25: 1193-203. PMID 21632826 DOI: 10.1101/Gad.2029411  0.318
2011 Shin S, Walton G, Aoki R, Brondell K, Schug J, Fox A, Smirnova O, Dorrell C, Erker L, Chu AS, Wells RG, Grompe M, Greenbaum LE, Kaestner KH. Foxl1-Cre-marked adult hepatic progenitors have clonogenic and bilineage differentiation potential. Genes & Development. 25: 1185-92. PMID 21632825 DOI: 10.1101/Gad.2027811  0.328
2011 Li Z, Schug J, Tuteja G, White P, Kaestner KH. The nucleosome map of the mammalian liver. Nature Structural & Molecular Biology. 18: 742-6. PMID 21623366 DOI: 10.1038/Nsmb.2060  0.336
2011 Gao Y, Schug J, McKenna LB, Le Lay J, Kaestner KH, Greenbaum LE. Tissue-specific regulation of mouse microRNA genes in endoderm-derived tissues. Nucleic Acids Research. 39: 454-63. PMID 20843784 DOI: 10.1093/Nar/Gkq782  0.339
2010 Zhao J, Schug J, Li M, Kaestner KH, Grant SFA. Disease-associated loci are significantly over-represented among genes bound by transcription factor 7-like 2 (TCF7L2) in vivo Diabetologia. 53: 2340-2346. PMID 20640398 DOI: 10.1007/S00125-010-1852-3  0.372
2010 Gao N, Le Lay J, Qin W, Doliba N, Schug J, Fox AJ, Smirnova O, Matschinsky FM, Kaestner KH. Foxa1 and Foxa2 maintain the metabolic and secretory features of the mature beta-cell. Molecular Endocrinology (Baltimore, Md.). 24: 1594-604. PMID 20534694 DOI: 10.1210/Me.2009-0513  0.315
2010 Steger DJ, Grant GR, Schupp M, Tomaru T, Lefterova MI, Schug J, Manduchi E, Stoeckert CJ, Lazar MA. Propagation of adipogenic signals through an epigenomic transition state. Genes & Development. 24: 1035-44. PMID 20478996 DOI: 10.1101/Gad.1907110  0.336
2010 Bhandare R, Schug J, Le Lay J, Fox A, Smirnova O, Liu C, Naji A, Kaestner KH. Genome-wide analysis of histone modifications in human pancreatic islets. Genome Research. 20: 428-33. PMID 20181961 DOI: 10.1101/Gr.102038.109  0.343
2009 Rieck S, White P, Schug J, Fox AJ, Smirnova O, Gao N, Gupta RK, Wang ZV, Scherer PE, Keller MP, Attie AD, Kaestner KH. The transcriptional response of the islet to pregnancy in mice. Molecular Endocrinology (Baltimore, Md.). 23: 1702-12. PMID 19574445 DOI: 10.1210/Me.2009-0144  0.343
2009 Tuteja G, White P, Schug J, Kaestner KH. Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Research. 37: e113. PMID 19553195 DOI: 10.1093/Nar/Gkp536  0.318
2009 Bochkis IM, Schug J, Rubins NE, Chopra AR, O'Malley BW, Kaestner KH. Foxa2-dependent hepatic gene regulatory networks depend on physiological state. Physiological Genomics. 38: 186-95. PMID 19417011 DOI: 10.1152/Physiolgenomics.90376.2008  0.311
2009 Schupp M, Cristancho AG, Lefterova MI, Hanniman EA, Briggs ER, Steger DJ, Qatanani M, Curtin JC, Schug J, Ochsner SA, McKenna NJ, Lazar MA. Re-expression of GATA2 cooperates with peroxisome proliferator-activated receptor-gamma depletion to revert the adipocyte phenotype. The Journal of Biological Chemistry. 284: 9458-64. PMID 19136559 DOI: 10.1074/Jbc.M809498200  0.349
2008 Schug J. Using TESS to predict transcription factor binding sites in DNA sequence. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 2.6. PMID 18428685 DOI: 10.1002/0471250953.Bi0206S21  0.313
2007 Mazzarelli JM, Brestelli J, Gorski RK, Liu J, Manduchi E, Pinney DF, Schug J, White P, Kaestner KH, Stoeckert CJ. EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Research. 35: D751-5. PMID 17071715 DOI: 10.1093/Nar/Gkl748  0.369
2007 Schug J, Mintz M, Stoeckert CJ. Data integration and pattern-finding in biological sequence with TESS's Annotation Grammar and Extraction Language (AnGEL) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4544: 188-203.  0.441
2005 Phuc Le P, Friedman JR, Schug J, Brestelli JE, Parker JB, Bochkis IM, Kaestner KH. Glucocorticoid receptor-dependent gene regulatory networks. Plos Genetics. 1: e16. PMID 16110340 DOI: 10.1371/Journal.Pgen.0010016  0.368
2005 Schug J, Schuller WP, Kappen C, Salbaum JM, Bucan M, Stoeckert CJ. Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biology. 6: R33. PMID 15833120 DOI: 10.1186/Gb-2005-6-4-R33  0.307
2004 Friedman JR, Larris B, Le PP, Peiris TH, Arsenlis A, Schug J, Tobias JW, Kaestner KH, Greenbaum LE. Orthogonal analysis of C/EBPbeta targets in vivo during liver proliferation. Proceedings of the National Academy of Sciences of the United States of America. 101: 12986-91. PMID 15317935 DOI: 10.1073/Pnas.0402875101  0.307
2004 Gunasekera AM, Patankar S, Schug J, Eisen G, Kissinger J, Roos D, Wirth DF. Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Molecular and Biochemical Parasitology. 136: 35-42. PMID 15138065 DOI: 10.1016/J.Molbiopara.2004.02.007  0.363
2003 Schug J. UNIT 2.6 Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence Current Protocols in Human Genetics. DOI: 10.1002/0471250953.Bi0206S00  0.326
2002 Bahl A, Brunk B, Coppel RL, Crabtree J, Diskin SJ, Fraunholz MJ, Grant GR, Gupta D, Huestis RL, Kissinger JC, Labo P, Li L, McWeeney SK, Milgram AJ, Roos DS, ... Schug J, et al. PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). Nucleic Acids Research. 30: 87-90. PMID 11752262 DOI: 10.1093/Nar/30.1.87  0.302
2002 Alur R, Belta C, Kumar V, Mintz M, Pappas GJ, Rubin H, Schug J. Modeling and analyzing biomolecular networks Computing in Science and Engineering. 4: 20. DOI: 10.1109/5992.976434  0.494
2001 Crabtree J, Wiltshire T, Brunk B, Zhao S, Schug J, Stoeckert CJ, Bucan M. High-resolution BAC-based map of the central portion of mouse chromosome 5 Genome Research. 11: 1746-1757. PMID 11591652 DOI: 10.1101/Gr.195101  0.302
2001 Alur R, Belta C, Ivančić F, Kumar V, Mintz M, Pappas GJ, Rubin H, Schug J. Hybrid modeling and simulation of biomolecular networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2034: 19-32.  0.475
1998 Bailey LC, Fischer S, Schug J, Crabtree J, Gibson M, Overton GC. GAIA: Framework annotation of genomic sequence Genome Research. 8: 234-250. PMID 9521927 DOI: 10.1101/Gr.8.3.234  0.301
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