| Year |
Citation |
Score |
| 2021 |
Akimov SS, Jiang M, Kedaigle AJ, Arbez N, Marque LO, Eddings CR, Ranum PT, Whelan E, Tang A, Wang R, DeVine LR, Talbot CC, Cole RN, Ratovitski T, Davidson BL, ... Fraenkel E, et al. Immortalized striatal precursor neurons from Huntington's disease patient-derived iPS cells as a platform for target identification and screening for experimental therapeutics. Human Molecular Genetics. PMID 34296279 DOI: 10.1093/hmg/ddab200 |
0.73 |
|
| 2020 |
Smith-Geater C, Hernandez SJ, Lim RG, Adam M, Wu J, Stocksdale JT, Wassie BT, Gold MP, Wang KQ, Miramontes R, Kopan L, Orellana I, Joy S, Kemp PJ, Allen ND, ... Fraenkel E, et al. Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation. Stem Cell Reports. PMID 32109367 DOI: 10.1016/J.Stemcr.2020.01.015 |
0.313 |
|
| 2020 |
Patel-Murray NL, Adam M, Huynh N, Wassie BT, Milani P, Fraenkel E. A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules. Scientific Reports. 10: 954. PMID 31969612 DOI: 10.1038/S41598-020-57691-7 |
0.33 |
|
| 2020 |
Chapman OS, Ehrenberger T, Archer TC, Gold MP, Mundt F, Adam M, Mah CK, Krug K, Chandran S, Dixon JR, Pomeroy SL, Fraenkel E, Mesirov JP, Chavez L. Abstract 447: Integrated omics modeling of transcriptional regulation in medulloblastoma subtypes Cancer Research. 80: 447-447. DOI: 10.1158/1538-7445.Am2020-447 |
0.393 |
|
| 2019 |
Yildirim F, Ng CW, Kappes V, Ehrenberger T, Rigby SK, Stivanello V, Gipson TA, Soltis AR, Vanhoutte P, Caboche J, Housman DE, Fraenkel E. Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington's disease. Proceedings of the National Academy of Sciences of the United States of America. PMID 31744868 DOI: 10.1073/Pnas.1908113116 |
0.395 |
|
| 2019 |
Kedaigle AJ, Reidling JC, Lim RG, Adam M, Wu J, Wassie B, Stocksdale JT, Casale MS, Fraenkel E, Thompson LM. Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice. Human Molecular Genetics. PMID 31696228 DOI: 10.1093/Hmg/Ddz264 |
0.727 |
|
| 2019 |
Woo AJ, Patry CA, Ghamari A, Pregernig G, Yuan D, Zheng K, Piers T, Hibbs M, Li J, Fidalgo M, Wang JY, Lee JH, Leedman PJ, Wang J, Fraenkel E, et al. Zfp281 (ZBP-99) plays a functionally redundant role with Zfp148 (ZBP-89) during erythroid development. Blood Advances. 3: 2499-2511. PMID 31455666 DOI: 10.1182/Bloodadvances.2018030551 |
0.355 |
|
| 2019 |
Kedaigle AJ, Fraenkel E, Atwal RS, Wu M, Gusella JF, MacDonald ME, Kaye JA, Finkbeiner S, Mattis VB, Tom CM, Svendsen C, King AR, Chen Y, Stocksdale JT, Lim RG, et al. Bioenergetic deficits in Huntington's disease iPSC-derived neural cells and rescue with glycolytic metabolites. Human Molecular Genetics. PMID 30768179 DOI: 10.1093/Hmg/Ddy430 |
0.727 |
|
| 2018 |
Köksal AS, Beck K, Cronin DR, McKenna A, Camp ND, Srivastava S, MacGilvray ME, Bodík R, Wolf-Yadlin A, Fraenkel E, Fisher J, Gitter A. Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data. Cell Reports. 24: 3607-3618. PMID 30257219 DOI: 10.1016/J.Celrep.2018.08.085 |
0.344 |
|
| 2018 |
Archer TC, Ehrenberger T, Mundt F, Gold MP, Krug K, Mah CK, Mahoney EL, Daniel CJ, LeNail A, Ramamoorthy D, Mertins P, Mani DR, Zhang H, Gillette MA, Clauser K, ... ... Fraenkel E, et al. Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 34: 396-410.e8. PMID 30205044 DOI: 10.1016/J.Ccell.2018.08.004 |
0.328 |
|
| 2018 |
Kedaigle A, Fraenkel E. Turning omics data into therapeutic insights. Current Opinion in Pharmacology. 42: 95-101. PMID 30149217 DOI: 10.1016/J.Coph.2018.08.006 |
0.724 |
|
| 2018 |
Wang L, Xia J, Li J, Hagemann TL, Jones JR, Fraenkel E, Weitz DA, Zhang SC, Messing A, Feany MB. Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease. Nature Communications. 9: 1899. PMID 29765022 DOI: 10.1038/S41467-018-04269-7 |
0.349 |
|
| 2018 |
Kedaigle AJ, Fraenkel E. Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data. Methods in Molecular Biology (Clifton, N.J.). 1711: 13-26. PMID 29344883 DOI: 10.1007/978-1-4939-7493-1_2 |
0.737 |
|
| 2018 |
Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, ... ... Fraenkel E, et al. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems. 6: 13-24. PMID 29199020 DOI: 10.1016/J.Cels.2017.11.001 |
0.381 |
|
| 2017 |
Soltis AR, Kennedy NJ, Xin X, Zhou F, Ficarro SB, Yap YS, Matthews BJ, Lauffenburger DA, White FM, Marto JA, Davis RJ, Fraenkel E. Hepatic Dysfunction Caused by Consumption of a High-Fat Diet. Cell Reports. 21: 3317-3328. PMID 29241556 DOI: 10.1016/J.Celrep.2017.11.059 |
0.306 |
|
| 2017 |
Ursu O, Gosline SJC, Beeharry N, Fink L, Bhattacharjee V, Huang SC, Zhou Y, Yen T, Fraenkel E. Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. Plos One. 12: e0185650. PMID 29023490 DOI: 10.1371/Journal.Pone.0185650 |
0.62 |
|
| 2017 |
Wilson JL, Kefalogianni E, Stopfer L, Harrison C, Sabbisetti VS, Fraenkel E, Lauffenburger DA, Herrlich A. Functional Genomics Approach Identifies Novel Signaling Regulators of TGFα Ectodomain Shedding. Molecular Cancer Research : McR. PMID 29018056 DOI: 10.1158/1541-7786.Mcr-17-0140 |
0.338 |
|
| 2017 |
Pirhaji L, Milani P, Dalin S, Wassie BT, Dunn DE, Fenster RJ, Avila-Pacheco J, Greengard P, Clish CB, Heiman M, Lo DC, Fraenkel E. Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements. Nature Communications. 8: 623. PMID 28931805 DOI: 10.1038/S41467-017-00353-6 |
0.4 |
|
| 2017 |
Akhmedov M, Kedaigle A, Chong RE, Montemanni R, Bertoni F, Fraenkel E, Kwee I. PCSF: An R-package for network-based interpretation of high-throughput data. Plos Computational Biology. 13: e1005694. PMID 28759592 DOI: 10.1371/Journal.Pcbi.1005694 |
0.747 |
|
| 2017 |
Northcott PA, Buchhalter I, Morrissy AS, Hovestadt V, Weischenfeldt J, Ehrenberger T, Gröbner S, Segura-Wang M, Zichner T, Rudneva VA, Warnatz HJ, Sidiropoulos N, Phillips AH, Schumacher S, Kleinheinz K, ... ... Fraenkel E, et al. The whole-genome landscape of medulloblastoma subtypes. Nature. 547: 311-317. PMID 28726821 DOI: 10.1038/Nature22973 |
0.343 |
|
| 2017 |
Lim RG, Quan C, Reyes-Ortiz AM, Lutz SE, Kedaigle AJ, Gipson TA, Wu J, Vatine GD, Stocksdale J, Casale MS, Svendsen CN, Fraenkel E, Housman DE, Agalliu D, Thompson LM. Huntington's Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits. Cell Reports. 19: 1365-1377. PMID 28514657 DOI: 10.1016/J.Celrep.2017.04.021 |
0.72 |
|
| 2017 |
Soltis AR, Motola S, Vernia S, Ng CW, Kennedy NJ, Dalin S, Matthews BJ, Davis RJ, Fraenkel E. Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis. Scientific Reports. 7: 174. PMID 28282965 DOI: 10.1038/S41598-017-00267-9 |
0.314 |
|
| 2017 |
Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, ... ... Fraenkel E, et al. Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. Cell Systems. PMID 28131822 DOI: 10.1016/J.Cels.2016.12.011 |
0.419 |
|
| 2016 |
Pirhaji L, Milani P, Leidl M, Curran T, Avila-Pacheco J, Clish CB, White FM, Saghatelian A, Fraenkel E. Revealing disease-associated pathways by network integration of untargeted metabolomics. Nature Methods. PMID 27479327 DOI: 10.1038/Nmeth.3940 |
0.405 |
|
| 2016 |
Tuncbag N, Milani P, Pokorny JL, Johnson H, Sio TT, Dalin S, Iyekegbe DO, White FM, Sarkaria JN, Fraenkel E. Network Modeling Identifies Patient-specific Pathways in Glioblastoma. Scientific Reports. 6: 28668. PMID 27354287 DOI: 10.1038/Srep28668 |
0.346 |
|
| 2016 |
Wilson JL, Dalin S, Gosline S, Hemann M, Fraenkel E, Lauffenburger DA. Pathway-based network modeling finds hidden genes in shRNA screen for regulators of acute lymphoblastic leukemia. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 27315426 DOI: 10.1039/C6Ib00040A |
0.416 |
|
| 2016 |
Milani P, Escalante-Chong R, Shelley BC, Patel-Murray NL, Xin X, Adam M, Mandefro B, Sareen D, Svendsen CN, Fraenkel E. Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells. Scientific Reports. 6: 25474. PMID 27146274 DOI: 10.1038/Srep25474 |
0.313 |
|
| 2016 |
Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E. Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. Plos Computational Biology. 12: e1004879. PMID 27096930 DOI: 10.1371/Journal.Pcbi.1004879 |
0.756 |
|
| 2016 |
Hanaford AR, Archer TC, Price A, Kahlert UD, Maciaczyk J, Nikkhah G, Kim JW, Ehrenberger T, Clemons PA, Dančík V, Seashore-Ludlow B, Viswanathan V, Stewart ML, Rees M, Shamji AF, ... ... Fraenkel E, et al. DiSCoVERing innovative therapies for rare tumors: combining genetically accurate disease models with in silico analysis to identify novel therapeutic targets. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 27012813 DOI: 10.1158/1078-0432.Ccr-15-3011 |
0.35 |
|
| 2016 |
Wong AS, Choi GC, Cui CH, Pregernig G, Milani P, Adam M, Perli SD, Kazer SW, Gaillard A, Hermann M, Shalek AK, Fraenkel E, Lu TK. Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. Proceedings of the National Academy of Sciences of the United States of America. PMID 26864203 DOI: 10.1073/Pnas.1517883113 |
0.362 |
|
| 2016 |
Ghamari A, Pregerning G, Fraenkel E, Cantor AB. GATA Factor Switching during Erythroid Differentiation Is Facilitated By FBW7 Mediated Clearance of GATA2 Blood. 128: 1479-1479. DOI: 10.1182/Blood.V128.22.1479.1479 |
0.35 |
|
| 2016 |
Hanaford AR, Archer TC, Price A, Kahlert U, Maciaczyk J, Guido N, Kim W, Ehrenberger T, Clemons P, Dancik V, Seashore-Ludlow B, Viswanathan V, Stewart M, Rees M, Shamji A, ... ... Fraenkel E, et al. Abstract 2476: DiSCoVERing innovative therapies for rare tumors: Combining genetically accurate disease models with advanced in silico analysis to identify novel therapeutic targets Cancer Research. 76: 2476-2476. DOI: 10.1158/1538-7445.Am2016-2476 |
0.31 |
|
| 2016 |
Hanaford A, Archer T, Price A, Kahlert U, Maciaczyk J, Nikkhah G, Kim JW, Ehrenberger T, Clemons PA, Dančík V, Seashore-Ludlow B, Viswanathan V, Stewart ML, Rees MG, Shamji A, ... ... Fraenkel E, et al. MB-103DiSCoVERing INNOVATIVE THERAPIES: COMBINING GENETICALLY ACCURATE DISEASE MODELS OF MEDULLOBLASTOMA WITH ADVANCED IN SILICO ANALYSIS TO IDENTIFY NOVEL THERAPEUTIC TARGETS Neuro-Oncology. 18: iii120.3-iii120. DOI: 10.1093/Neuonc/Now076.98 |
0.319 |
|
| 2015 |
Gosline SJ, Gurtan AM, JnBaptiste CK, Bosson A, Milani P, Dalin S, Matthews BJ, Yap YS, Sharp PA, Fraenkel E. Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements. Cell Reports. PMID 26748710 DOI: 10.1016/J.Celrep.2015.12.031 |
0.328 |
|
| 2015 |
Gosline SJ, Oh C, Fraenkel E. SAMNetWeb: identifying condition-specific networks linking signaling and transcription. Bioinformatics (Oxford, England). 31: 1124-6. PMID 25414365 DOI: 10.1093/Bioinformatics/Btu748 |
0.367 |
|
| 2015 |
Gao R, Chen S, Kobayashi M, Yu H, Zhang Y, Wan Y, Young SK, Soltis A, Yu M, Vemula S, Fraenkel E, Cantor A, Antipin Y, Xu Y, Yoder MC, et al. Bmi1 promotes erythroid development through regulating ribosome biogenesis. Stem Cells (Dayton, Ohio). 33: 925-38. PMID 25385494 DOI: 10.1002/Stem.1896 |
0.348 |
|
| 2015 |
Gosline SJ, Gurtan AM, JnBaptiste CK, Bosson A, Milani P, Dalin S, Matthews B, Yap YS, Sharp PA, Fraenkel E. Abstract B2-45: Uncovering coordinated regulation of transcription factors by microRNAs using integrated network models Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B2-45 |
0.34 |
|
| 2015 |
Wilson JL, Fraenkel E, Lauffenburger DA, Herrlich A. Abstract B1-33: Network analyses identify hidden regulators of TGFa shedding Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-33 |
0.341 |
|
| 2014 |
Gosline S, Pregernig G, Oh C, Fraenkel E. Beyond Argonaute: understanding microRNA dysregulation in cancer and its effect on protein interaction and transcriptional regulatory networks F1000research. 5. DOI: 10.7490/F1000Research.1096455.1 |
0.351 |
|
| 2013 |
Vashishtha M, Ng CW, Yildirim F, Gipson TA, Kratter IH, Bodai L, Song W, Lau A, Labadorf A, Vogel-Ciernia A, Troncosco J, Ross CA, Bates GP, Krainc D, Sadri-Vakili G, ... ... Fraenkel E, et al. Targeting H3K4 trimethylation in Huntington disease. Proceedings of the National Academy of Sciences of the United States of America. 110: E3027-36. PMID 23872847 DOI: 10.1073/Pnas.1311323110 |
0.366 |
|
| 2013 |
Wilson JL, Hemann MT, Fraenkel E, Lauffenburger DA. Integrated network analyses for functional genomic studies in cancer. Seminars in Cancer Biology. 23: 213-8. PMID 23811269 DOI: 10.1016/J.Semcancer.2013.06.004 |
0.372 |
|
| 2013 |
Zhen AW, Nguyen NH, Gibert Y, Motola S, Buckett P, Wessling-Resnick M, Fraenkel E, Fraenkel PG. The small molecule, genistein, increases hepcidin expression in human hepatocytes. Hepatology (Baltimore, Md.). 58: 1315-25. PMID 23703590 DOI: 10.1002/Hep.26490 |
0.332 |
|
| 2013 |
Lodato MA, Ng CW, Wamstad JA, Cheng AW, Thai KK, Fraenkel E, Jaenisch R, Boyer LA. SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state. Plos Genetics. 9: e1003288. PMID 23437007 DOI: 10.1371/Journal.Pgen.1003288 |
0.385 |
|
| 2013 |
Huang SS, Clarke DC, Gosline SJ, Labadorf A, Chouinard CR, Gordon W, Lauffenburger DA, Fraenkel E. Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. Plos Computational Biology. 9: e1002887. PMID 23408876 DOI: 10.1371/Journal.Pcbi.1002887 |
0.459 |
|
| 2013 |
Tuncbag N, Braunstein A, Pagnani A, Huang SS, Chayes J, Borgs C, Zecchina R, Fraenkel E. Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 124-36. PMID 23383998 DOI: 10.1089/Cmb.2012.0092 |
0.361 |
|
| 2013 |
Ng CW, Yildirim F, Yap YS, Dalin S, Matthews BJ, Velez PJ, Labadorf A, Housman DE, Fraenkel E. Extensive changes in DNA methylation are associated with expression of mutant huntingtin. Proceedings of the National Academy of Sciences of the United States of America. 110: 2354-9. PMID 23341638 DOI: 10.1073/Pnas.1221292110 |
0.337 |
|
| 2012 |
Riva L, Koeva M, Yildirim F, Pirhaji L, Dinesh D, Mazor T, Duennwald ML, Fraenkel E. Poly-glutamine expanded huntingtin dramatically alters the genome wide binding of HSF1. Journal of Huntington's Disease. 1: 33-45. PMID 23293686 DOI: 10.3233/Jhd-2012-120020 |
0.33 |
|
| 2012 |
Gosline SJ, Spencer SJ, Ursu O, Fraenkel E. SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integrative Biology : Quantitative Biosciences From Nano to Macro. 4: 1415-27. PMID 23060147 DOI: 10.1039/C2Ib20072D |
0.432 |
|
| 2012 |
Mendillo ML, Santagata S, Koeva M, Bell GW, Hu R, Tamimi RM, Fraenkel E, Ince TA, Whitesell L, Lindquist S. HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers. Cell. 150: 549-62. PMID 22863008 DOI: 10.1016/J.Cell.2012.06.031 |
0.306 |
|
| 2012 |
Tuncbag N, McCallum S, Huang SS, Fraenkel E. SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. Nucleic Acids Research. 40: W505-9. PMID 22638579 DOI: 10.1093/Nar/Gks445 |
0.397 |
|
| 2012 |
Huang SS, Fraenkel E. Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods in Cell Biology. 110: 57-80. PMID 22482945 DOI: 10.1016/B978-0-12-388403-9.00003-5 |
0.423 |
|
| 2012 |
Yu M, Mazor T, Huang H, Huang HT, Kathrein KL, Woo AJ, Chouinard CR, Labadorf A, Akie TE, Moran TB, Xie H, Zacharek S, Taniuchi I, Roeder RG, Kim CF, ... ... Fraenkel E, et al. Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors. Molecular Cell. 45: 330-43. PMID 22325351 DOI: 10.1016/J.Molcel.2011.11.032 |
0.358 |
|
| 2012 |
Fraenkel E. Abstract SY19-01: Integrating proteomic, transcriptional, epigenomic, and interactome data reveals the signaling changes induced by oncogenic mutations Cancer Research. 72. DOI: 10.1158/1538-7445.Am2012-Sy19-01 |
0.363 |
|
| 2011 |
Carlson SM, Chouinard CR, Labadorf A, Lam CJ, Schmelzle K, Fraenkel E, White FM. Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3. Science Signaling. 4: rs11. PMID 22028470 DOI: 10.1126/Scisignal.2002010 |
0.337 |
|
| 2011 |
Lo KA, Bauchmann MK, Baumann AP, Donahue CJ, Thiede MA, Hayes LS, des Etages SA, Fraenkel E. Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes. Plos One. 6: e19778. PMID 21655096 DOI: 10.1371/Journal.Pone.0019778 |
0.372 |
|
| 2011 |
Lan A, Smoly IY, Rapaport G, Lindquist S, Fraenkel E, Yeger-Lotem E. ResponseNet: Revealing signaling and regulatory networks linking genetic and transcriptomic screening data Nucleic Acids Research. 39: W424-W429. PMID 21576238 DOI: 10.1093/Nar/Gkr359 |
0.412 |
|
| 2011 |
Mendillo M, Santagata S, Koeva M, Fraenkel E, Ince T, Whitesell L, Lindquist S. P3-01-09: Oncogenic Activation of HSF1 Enables the Malignant Progression of Breast Carcinoma. Cancer Research. 71. DOI: 10.1158/0008-5472.Sabcs11-P3-01-09 |
0.317 |
|
| 2010 |
Ling G, Sugathan A, Mazor T, Fraenkel E, Waxman DJ. Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Molecular and Cellular Biology. 30: 5531-44. PMID 20876297 DOI: 10.1128/Mcb.00601-10 |
0.311 |
|
| 2010 |
Macisaac KD, Fraenkel E. Sequence analysis of chromatin immunoprecipitation data for transcription factors. Methods in Molecular Biology (Clifton, N.J.). 674: 179-93. PMID 20827592 DOI: 10.1007/978-1-60761-854-6_11 |
0.365 |
|
| 2010 |
MacIsaac KD, Lo KA, Gordon W, Motola S, Mazor T, Fraenkel E. A quantitative model of transcriptional regulation reveals the influence of binding location on expression. Plos Computational Biology. 6: e1000773. PMID 20442865 DOI: 10.1371/Journal.Pcbi.1000773 |
0.363 |
|
| 2010 |
Hartwig S, Ho J, Pandey P, Macisaac K, Taglienti M, Xiang M, Alterovitz G, Ramoni M, Fraenkel E, Kreidberg JA. Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development. Development (Cambridge, England). 137: 1189-203. PMID 20215353 DOI: 10.1242/Dev.045732 |
0.382 |
|
| 2010 |
Yu M, Mazor T, Huang H, Huang E, Kathrein K, Woo A, Zon LI, Fraenkel E, Cantor AB. Role of Polycomb Repressive Complex 1 (PRC1) In Runx1 Mediated Gene Regulation Blood. 116: 3863-3863. DOI: 10.1182/Blood.V116.21.3863.3863 |
0.358 |
|
| 2009 |
Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Molecular Cell. 36: 682-95. PMID 19941827 DOI: 10.1016/J.Molcel.2009.11.002 |
0.35 |
|
| 2009 |
Huang SS, Fraenkel E. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Science Signaling. 2: ra40. PMID 19638617 DOI: 10.1126/Scisignal.2000350 |
0.431 |
|
| 2009 |
Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar AG, King OD, Auluck PK, Geddie ML, Valastyan JS, Karger DR, Lindquist S, Fraenkel E. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nature Genetics. 41: 316-23. PMID 19234470 DOI: 10.1038/Ng.337 |
0.373 |
|
| 2009 |
Huang SC, Fraenkel E. Abstract B72: A computational approach integrating proteomic, transcriptional, and interactome data for discovery of cellular signaling networks Cancer Research. 69. DOI: 10.1158/0008-5472.Fbcr09-B72 |
0.643 |
|
| 2007 |
Romer KA, Kayombya GR, Fraenkel E. WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. Nucleic Acids Research. 35: W217-20. PMID 17584794 DOI: 10.1093/Nar/Gkm376 |
0.335 |
|
| 2007 |
Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nature Genetics. 39: 730-2. PMID 17529977 DOI: 10.1038/Ng2047 |
0.325 |
|
| 2006 |
Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. High-resolution computational models of genome binding events. Nature Biotechnology. 24: 963-70. PMID 16900145 DOI: 10.1038/Nbt1233 |
0.384 |
|
| 2006 |
Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK, Fraenkel E, Bell GI, Young RA. Core transcriptional regulatory circuitry in human hepatocytes. Molecular Systems Biology. 2: 2006.0017. PMID 16738562 DOI: 10.1038/Msb4100059 |
0.363 |
|
| 2006 |
MacIsaac KD, Fraenkel E. Practical strategies for discovering regulatory DNA sequence motifs. Plos Computational Biology. 2: e36. PMID 16683017 DOI: 10.1371/Journal.Pcbi.0020036 |
0.376 |
|
| 2006 |
MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. Bmc Bioinformatics. 7: 113. PMID 16522208 DOI: 10.1186/1471-2105-7-113 |
0.35 |
|
| 2006 |
Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, Fraenkel E. A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics (Oxford, England). 22: 423-9. PMID 16332710 DOI: 10.1093/Bioinformatics/Bti815 |
0.387 |
|
| 2005 |
Gordon DB, Nekludova L, McCallum S, Fraenkel E. TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. Bioinformatics (Oxford, England). 21: 3164-5. PMID 15905282 DOI: 10.1093/Bioinformatics/Bti481 |
0.347 |
|
| 2004 |
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, ... ... Fraenkel E, et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 431: 99-104. PMID 15343339 DOI: 10.1038/Nature02800 |
0.34 |
|
| 2004 |
Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA. Control of pancreas and liver gene expression by HNF transcription factors. Science (New York, N.Y.). 303: 1378-81. PMID 14988562 DOI: 10.1126/Science.1089769 |
0.338 |
|
| 2003 |
Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Computational discovery of gene modules and regulatory networks. Nature Biotechnology. 21: 1337-42. PMID 14555958 DOI: 10.1038/Nbt890 |
0.404 |
|
| 2002 |
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, ... ... Fraenkel E, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (New York, N.Y.). 298: 799-804. PMID 12399584 DOI: 10.1126/Science.1075090 |
0.397 |
|
| 2001 |
Lin CH, Hare BJ, Wagner G, Harrison SC, Maniatis T, Fraenkel E. A small domain of CBP/p300 binds diverse proteins: solution structure and functional studies. Molecular Cell. 8: 581-90. PMID 11583620 DOI: 10.1016/S1097-2765(01)00333-1 |
0.498 |
|
| 1999 |
Zheng N, Fraenkel E, Pabo CO, Pavletich NP. Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes & Development. 13: 666-74. PMID 10090723 DOI: 10.1101/Gad.13.6.666 |
0.714 |
|
| 1998 |
Fraenkel E, Rould MA, Chambers KA, Pabo CO. Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures. Journal of Molecular Biology. 284: 351-61. PMID 9813123 DOI: 10.1006/Jmbi.1998.2147 |
0.608 |
|
| 1998 |
Fraenkel E, Pabo CO. Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. Nature Structural Biology. 5: 692-7. PMID 9699632 DOI: 10.1038/1382 |
0.604 |
|
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