Morningside Graduate School of Biomedical Sciences
Endowed Chair in Biochemistry and Molecular Biotechnology II
For more information about the Postdoctoral position in Dr. Rando’s lab please use the link provided. Post doc position
Rotation projects are available to study chromatin structure and function. Project 1. Measure histone dynamics in yeast. Histone dynamics play major roles in chromatin metabolism and in the inheritance of chromatin states. To measure histone replacement rates in yeast, we have created yeast strains carrying inducible epitope-tagged histones H3 and H2A. Using microarrays, we will measure histone replacement rates in a variety of mutant yeast to ascertain the role of various chromatin remodeling factors in histone exchange reactions. Project 2. Characterize mechanisms for epigenetic inheritance in yeast. We have identified a variety of genes whose expression state in yeast is epigenetically heritable. We will screen the yeast genome for genes that affect the inheritance of these expression patterns. Project 3. Measure histone dynamics in embryonic stem cells. Embryonic stem cells are pluripotent cells that can give rise to every type of cell in the adult animal. The role of chromatin structure in maintaining this pluripotent state is poorly understood, but it appears that stem cell chromatin is exceptionally labile relative to that in differentiated cells. We will create stem cell lines with inducible tagged histones to measure histone replacement rates across the mouse genome.
The project aims to develop computational algorithms and software programs for analyzing high-throughput sequence data such as ChIP-Seq RNA-Seq small RNA sequencing data. PhD required. A strong background in computational biology especially experience with analyzing high-throughput sequencing data is highly desirable. Excellent communication and writing skills and the ability to work with experimental and computational collaborators are essential. To apply please forward CV cover letter and three references to: Zhiping.Weng@umassmed.edu
Please contact Dr. Weng for information on rotations that are available in her lab.
Please contact Dr. Imbalzano to discuss the possibility of a postdoctoral training.See lab research interests and publications for recent topics of research. http://www.umassmed.edu/imbalzanolab/ http://www.umassmed.edu/imbalzanolab/publications/
Please contact Dr. Imbalzano to discuss the possibility of a rotation project. Rotation projects are generally based on current work and tailored to the interests of the student. See lab research interests and publications for recent topics. http://www.umassmed.edu/imbalzanolab/ http://www.umassmed.edu/imbalzanolab/publications/
Joseph J. Byrne Chair in Biomedical Research
? Rotation Projects Multiple rotation projects are available in several areas related to long-range gene regulation and higher order chromosome organization. Projects include thorough analyses of the biochemical mechanisms of long-range gene regulation of specific disease-related genes, as well as large-scale analyses of chromosome organization using high-throughput genomics technologies (5C and Hi-C). The lab employs a wide range of experimental approaches, including cell culture, protein biochemistry, microscopy, genomics as well computational approaches such as bioinformatics and modeling. Specific rotation projects are determined dependent on the interest of the student.
Alexandru Ioan Cuza University, Computer Science
Biochemistry and Molecular Biotechnology
The newly established Moore lab is looking for highly motivated post-doctoral fellows to be founding members of our team. We study gene regulation and its role in human disease by interpreting large scale multi-omic datasets using machine learning approaches. Ideal candidates will have extensive experience in multi-omic data processing and analysis (RNA-seq, ATAC-seq, ChIP-seq, etc.) and are interested in learning about the fundamental mechanisms governing gene regulation (regulating transcription, splicing, translation, etc.). Candidates from related fields, such as computer science or biomedical engineering, with machine learning experience are also highly encouraged to apply. To Apply: Interested candidates should email a cover letter, CV, and 3 references to: Jill Moore at Jill.Moore@umassmed.edu
Interested in rotating in the lab? Please contact Dr. Moore for more information.
Kelly Elisabeth Garrahan APRN, MSN, FNP-C
Systems Computational and Quantitative Biology
Biophysical Chemical and Computational Biology
Glasscock CJ, Pecoraro R, McHugh R, Doyle LA, Chen W, Boivin O, Lonnquist B, Na E, Politanska Y, Haddox HK, Cox D, Norn C, Coventry B, Goreshnik I, Vafeados D, Lee GR, Gordan R, Stoddard BL, DiMaio F, Baker D
bioRxiv : the preprint server for biology
Glasscock CJ, Pecoraro R, McHugh R, Doyle LA, Chen W, Boivin O, Lonnquist B, Na E, Politanska Y, Haddox HK, Cox D, Norn C, Coventry B, Goreshnik I, Vafeados D, Lee GR, Gordan R, Stoddard BL, DiMaio F, Baker D. Computational design of sequence-specific DNA-binding proteins. bioRxiv. 2023 Sep 21.
Computational design of sequence-specific DNA-binding proteins.
Sun T, Ding CC, Zhang Y, Zhang Y, Lin CC, Wu J, Setayeshpour Y, Coggins S, Shepard C, Macias E, Kim B, Zhou P, Gord?n R, Chi JT
Sun T, Ding CC, Zhang Y, Zhang Y, Lin CC, Wu J, Setayeshpour Y, Coggins S, Shepard C, Macias E, Kim B, Zhou P, Gord?n R, Chi JT. MESH1 knockdown triggers proliferation arrest through TAZ repression. Cell Death Dis. 2022 03 10; 13(3):221.
MESH1 knockdown triggers proliferation arrest through TAZ repression.
Barrera J, Song L, Gamache JE, Garrett ME, Safi A, Yun Y, Premasinghe I, Sprague D, Chipman D, Li J, Fradin H, Soldano K, Gord?n R, Ashley-Koch AE, Crawford GE, Chiba-Falek O
Barrera J, Song L, Gamache JE, Garrett ME, Safi A, Yun Y, Premasinghe I, Sprague D, Chipman D, Li J, Fradin H, Soldano K, Gord?n R, Ashley-Koch AE, Crawford GE, Chiba-Falek O. Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains. Mol Neurodegener. 2021 08 24; 16(1):58.
Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains.
Liu M, Boot A, Ng AWT, Gord?n R, Rozen SG
Liu M, Boot A, Ng AWT, Gord?n R, Rozen SG. Mutational processes in cancer preferentially affect binding of particular transcription factors. Sci Rep. 2021 02 08; 11(1):3339.
Mutational processes in cancer preferentially affect binding of particular transcription factors.
Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R
Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R. Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In?Vivo Binding. Cell Syst. 2018 Apr 25; 6(4):470-483.e8.
Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In?Vivo Binding.
Sparks EE, Drapek C, Gaudinier A, Li S, Ansariola M, Shen N, Hennacy JH, Zhang J, Turco G, Petricka JJ, Foret J, Hartemink AJ, Gord?n R, Megraw M, Brady SM, Benfey PN
Sparks EE, Drapek C, Gaudinier A, Li S, Ansariola M, Shen N, Hennacy JH, Zhang J, Turco G, Petricka JJ, Foret J, Hartemink AJ, Gord?n R, Megraw M, Brady SM, Benfey PN. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Dev Cell. 2016 12 05; 39(5):585-596.
Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.
Boyd JL, Skove SL, Rouanet JP, Pilaz LJ, Bepler T, Gord?n R, Wray GA, Silver DL
Boyd JL, Skove SL, Rouanet JP, Pilaz LJ, Bepler T, Gord?n R, Wray GA, Silver DL. Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Curr Biol. 2015 Mar 16; 25(6):772-779.
Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex.
Afek A, Schipper JL, Horton J, Gord?n R, Lukatsky DB
Proceedings of the National Academy of Sciences of the United States of America
Afek A, Schipper JL, Horton J, Gord?n R, Lukatsky DB. Protein-DNA binding in the absence of specific base-pair recognition. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):17140-5.
Protein-DNA binding in the absence of specific base-pair recognition.
Slattery M, Zhou T, Yang L, Dantas Machado AC, Gord?n R, Rohs R
Slattery M, Zhou T, Yang L, Dantas Machado AC, Gord?n R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci. 2014 Sep; 39(9):381-99.
Absence of a simple code: how transcription factors read the genome.
Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gord?n R, Rohs R
Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gord?n R, Rohs R. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. 2014 Jan; 42(Database issue):D148-55.
TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Gord?n R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML
Gord?n R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep. 2013 Apr 25; 3(4):1093-104.
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
Gord?n R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML
Gord?n R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol. 2011 Dec 21; 12(12):R125.
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.
Snyder LF, O'Brien EM, Zhao J, Liang J, Bruce BJ, Zhang Y, Zhu W, Cassier TH, Schnicker NJ, Zhou X, Gord?n R, He BZ
Snyder LF, O'Brien EM, Zhao J, Liang J, Bruce BJ, Zhang Y, Zhu W, Cassier TH, Schnicker NJ, Zhou X, Gord?n R, He BZ. Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions. bioRxiv. 2025 May 02.
Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions.
Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gord?n R, Llin?s M
Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gord?n R, Llin?s M. DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res. 2024 Sep 23; 52(17):10161-10179.
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum.
Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- )
Zhao J, Martin V, Gord?n R. Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer. Res Comput Mol Biol. 2022 May; 13278:36-51.
Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer.
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gord?n R
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gord?n R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature. 2020 11; 587(7833):291-296.
DNA mismatches reveal conformational penalties in protein-DNA recognition.
Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O, Shahar A, Zarivach R, Gordan R, Arbely E
Biochimica et biophysica acta. General subjects
Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O, Shahar A, Zarivach R, Gordan R, Arbely E. Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine. Biochim Biophys Acta Gen Subj. 2019 09; 1863(9):1343-1350.
Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine.
Afek A, Ilic S, Horton J, Lukatsky DB, Gordan R, Akabayov B
Afek A, Ilic S, Horton J, Lukatsky DB, Gordan R, Akabayov B. DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase. iScience. 2018 Apr 27; 2:141-147.
DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase.
Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, Gord?n R, Yao G, You L
Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, Gord?n R, Yao G, You L. Expression level is a key determinant of E2F1-mediated cell fate. Cell Death Differ. 2017 04; 24(4):626-637.
Expression level is a key determinant of E2F1-mediated cell fate.
Frank CL, Manandhar D, Gord?n R, Crawford GE
Frank CL, Manandhar D, Gord?n R, Crawford GE. HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells. Epigenetics Chromatin. 2016; 9:15.
HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.
King DE, Beard EE, Satusky MJ, Ryde I, George A, Johnson C, Dolan EL, Zhang Y, Zhu W, Wilkins H, Corden E, Murphy SK, Erie D, Gord?n R, Meyer JN
King DE, Beard EE, Satusky MJ, Ryde I, George A, Johnson C, Dolan EL, Zhang Y, Zhu W, Wilkins H, Corden E, Murphy SK, Erie D, Gord?n R, Meyer JN. UV irradiation alters TFAM binding to mitochondrial DNA. bioRxiv. 2025 Sep 15.
UV irradiation alters TFAM binding to mitochondrial DNA.
Deciphering the impact of genomic variation on function. Nature. 2024 Sep; 633(8028):47-57.
Deciphering the impact of genomic variation on function.
Ilic S, Cohen S, Afek A, Gordan R, Lukatsky DB, Akabayov B
Journal of visualized experiments : JoVE
Ilic S, Cohen S, Afek A, Gordan R, Lukatsky DB, Akabayov B. DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling. J Vis Exp. 2019 10 08; (152).
DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling.
Martin V, Zhao J, Afek A, Mielko Z, Gord?n R
Martin V, Zhao J, Afek A, Mielko Z, Gord?n R. QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. Nucleic Acids Res. 2019 07 02; 47(W1):W127-W135.
QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants.
Innocenti F, Jiang C, Sibley AB, Etheridge AS, Hatch AJ, Denning S, Niedzwiecki D, Shterev ID, Lin J, Furukawa Y, Kubo M, Kindler HL, Auman JT, Venook AP, Hurwitz HI, McLeod HL, Ratain MJ, Gordan R, Nixon AB, Owzar K
Innocenti F, Jiang C, Sibley AB, Etheridge AS, Hatch AJ, Denning S, Niedzwiecki D, Shterev ID, Lin J, Furukawa Y, Kubo M, Kindler HL, Auman JT, Venook AP, Hurwitz HI, McLeod HL, Ratain MJ, Gordan R, Nixon AB, Owzar K. Genetic variation determines VEGF-A plasma levels in cancer patients. Sci Rep. 2018 11 05; 8(1):16332.
Genetic variation determines VEGF-A plasma levels in cancer patients.
Zhao J, Li D, Seo J, Allen AS, Gord?n R. Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. Res Comput Mol Biol. 2017 May; 10229:336-352.
Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.
Jusakul A, Cutcutache I, Yong CH, Lim JQ, Huang MN, Padmanabhan N, Nellore V, Kongpetch S, Ng AWT, Ng LM, Choo SP, Myint SS, Thanan R, Nagarajan S, Lim WK, Ng CCY, Boot A, Liu M, Ong CK, Rajasegaran V, Lie S, Lim AST, Lim TH, Tan J, Loh JL, McPherson JR, Khuntikeo N, Bhudhisawasdi V, Yongvanit P, Wongkham S, Totoki Y, Nakamura H, Arai Y, Yamasaki S, Chow PK, Chung AYF, Ooi LLPJ, Lim KH, Dima S, Duda DG, Popescu I, Broet P, Hsieh SY, Yu MC, Scarpa A, Lai J, Luo DX, Carvalho AL, Vettore AL, Rhee H, Park YN, Alexandrov LB, Gord?n R, Rozen SG, Shibata T, Pairojkul C, Teh BT, Tan P
Jusakul A, Cutcutache I, Yong CH, Lim JQ, Huang MN, Padmanabhan N, Nellore V, Kongpetch S, Ng AWT, Ng LM, Choo SP, Myint SS, Thanan R, Nagarajan S, Lim WK, Ng CCY, Boot A, Liu M, Ong CK, Rajasegaran V, Lie S, Lim AST, Lim TH, Tan J, Loh JL, McPherson JR, Khuntikeo N, Bhudhisawasdi V, Yongvanit P, Wongkham S, Totoki Y, Nakamura H, Arai Y, Yamasaki S, Chow PK, Chung AYF, Ooi LLPJ, Lim KH, Dima S, Duda DG, Popescu I, Broet P, Hsieh SY, Yu MC, Scarpa A, Lai J, Luo DX, Carvalho AL, Vettore AL, Rhee H, Park YN, Alexandrov LB, Gord?n R, Rozen SG, Shibata T, Pairojkul C, Teh BT, Tan P. Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma. Cancer Discov. 2017 10; 7(10):1116-1135.
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.
Schipper JL, Gord?n RM. Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources. Cold Spring Harb Protoc. 2016 11 01; 2016(11).
Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources.
Medina EM, Turner JJ, Gord?n R, Skotheim JM, Buchler NE
Medina EM, Turner JJ, Gord?n R, Skotheim JM, Buchler NE. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. Elife. 2016 05 10; 5.
Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.
Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gord?n R, Price DH
Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gord?n R, Price DH. Sequence specificity incompletely defines the genome-wide occupancy of Myc. Genome Biol. 2014; 15(10):482.
Sequence specificity incompletely defines the genome-wide occupancy of Myc.
Munteanu A, Ohler U, Gord?n R. COUGER--co-factors associated with uniquely-bound genomic regions. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W461-7.
COUGER--co-factors associated with uniquely-bound genomic regions.
Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gord?n R
Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gord?n R. Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinformatics. 2013 Jul 01; 29(13):i117-25.
Stability selection for regression-based models of transcription factor-DNA binding specificity.
Miller HB, Robinson TJ, Gord?n R, Hartemink AJ, Garcia-Blanco MA
Miller HB, Robinson TJ, Gord?n R, Hartemink AJ, Garcia-Blanco MA. Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. RNA. 2011 Apr; 17(4):665-74.
Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.
Duan M, Song S, Wasserman H, Lee PH, Liu KJ, Gord?n R, He Y, Mao P
Duan M, Song S, Wasserman H, Lee PH, Liu KJ, Gord?n R, He Y, Mao P. High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma. Proc Natl Acad Sci U S A. 2024 Jan 23; 121(4):e2310854121.
High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma.
Martin V, Zhuang F, Zhang Y, Pinheiro K, Gord?n R
Martin V, Zhuang F, Zhang Y, Pinheiro K, Gord?n R. High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins. Nucleic Acids Res. 2023 11 27; 51(21):11600-11612.
High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins.
Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gord?n R, Zeitlinger J, Kundaje A, Fordyce PM
Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gord?n R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science. 2023 09 22; 381(6664):eadd1250.
Short tandem repeats bind transcription factors to tune eukaryotic gene expression.
Mielko Z, Zhang Y, Sahay H, Liu Y, Schaich MA, Schnable B, Morrison AM, Burdinski D, Adar S, Pufall M, Van Houten B, Gord?n R, Afek A
Mielko Z, Zhang Y, Sahay H, Liu Y, Schaich MA, Schnable B, Morrison AM, Burdinski D, Adar S, Pufall M, Van Houten B, Gord?n R, Afek A. UV irradiation remodels the specificity landscape of transcription factors. Proc Natl Acad Sci U S A. 2023 03 14; 120(11):e2217422120.
UV irradiation remodels the specificity landscape of transcription factors.
Zhang Y, Ho TD, Buchler NE, Gord?n R. Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. Genome Res. 2021 Jul; 31(7):1216-1229.
Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions.
Innocenti F, Owzar K, Jiang C, Etheridge AS, Gord?n R, Sibley AB, Mulkey F, Niedzwiecki D, Glubb D, Neel N, Talamonti MS, Bentrem DJ, Seiser E, Yeh JJ, Van Loon K, McLeod H, Ratain MJ, Kindler HL, Venook AP, Nakamura Y, Kubo M, Petersen GM, Bamlet WR, McWilliams RR
Innocenti F, Owzar K, Jiang C, Etheridge AS, Gord?n R, Sibley AB, Mulkey F, Niedzwiecki D, Glubb D, Neel N, Talamonti MS, Bentrem DJ, Seiser E, Yeh JJ, Van Loon K, McLeod H, Ratain MJ, Kindler HL, Venook AP, Nakamura Y, Kubo M, Petersen GM, Bamlet WR, McWilliams RR. The vitamin D receptor gene as a determinant of survival in pancreatic cancer patients: Genomic analysis and experimental validation. PLoS One. 2018; 13(8):e0202272.
The vitamin D receptor gene as a determinant of survival in pancreatic cancer patients: Genomic analysis and experimental validation.
Manandhar D, Song L, Kabadi A, Kwon JB, Edsall LE, Ehrlich M, Tsumagari K, Gersbach CA, Crawford GE, Gord?n R
Manandhar D, Song L, Kabadi A, Kwon JB, Edsall LE, Ehrlich M, Tsumagari K, Gersbach CA, Crawford GE, Gord?n R. Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies. Nucleic Acids Res. 2017 Nov 16; 45(20):11684-11699.
Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.
Joh DY, Hucknall AM, Wei Q, Mason KA, Lund ML, Fontes CM, Hill RT, Blair R, Zimmers Z, Achar RK, Tseng D, Gordan R, Freemark M, Ozcan A, Chilkoti A
Joh DY, Hucknall AM, Wei Q, Mason KA, Lund ML, Fontes CM, Hill RT, Blair R, Zimmers Z, Achar RK, Tseng D, Gordan R, Freemark M, Ozcan A, Chilkoti A. Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood. Proc Natl Acad Sci U S A. 2017 08 22; 114(34):E7054-E7062.
Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood.
Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gord?n R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML
Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gord?n R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science. 2016 Mar 25; 351(6280):1450-1454.
Survey of variation in human transcription factors reveals prevalent DNA binding changes.
Afek A, Cohen H, Barber-Zucker S, Gord?n R, Lukatsky DB
Afek A, Cohen H, Barber-Zucker S, Gord?n R, Lukatsky DB. Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. PLoS Comput Biol. 2015 Aug; 11(8):e1004429.
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.
Siggers T, Gord?n R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res. 2014 Feb; 42(4):2099-111.
Protein-DNA binding: complexities and multi-protein codes.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Gord?n R, Pyne S, Bulyk ML. Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pac Symp Biocomput. 2012; 299-310.
Identification of cell cycle-regulated, putative hyphal genes in Candida albicans.
Heilbrun EE, Tseitline D, Wasserman H, Kirshenbaum A, Cohen Y, Gordan R, Adar S
Heilbrun EE, Tseitline D, Wasserman H, Kirshenbaum A, Cohen Y, Gordan R, Adar S. The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency. Nucleic Acids Res. 2025 Feb 08; 53(4).
The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency.
Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gord?n R, Rohs R
Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gord?n R, Rohs R. Quantitative modeling of transcription factor binding specificities using DNA shape. Proc Natl Acad Sci U S A. 2015 Apr 14; 112(15):4654-9.
Quantitative modeling of transcription factor binding specificities using DNA shape.
Zhu W, Zhang Y, Sahay H, Wasserman H, Afek A, Williams J, Shaltz S, Johnson C, Pinheiro K, MacAlpine DM, Weninger KR, Erie DA, Jinks-Robertson S, Gord?n R
Zhu W, Zhang Y, Sahay H, Wasserman H, Afek A, Williams J, Shaltz S, Johnson C, Pinheiro K, MacAlpine DM, Weninger KR, Erie DA, Jinks-Robertson S, Gord?n R. DNA mutagenesis driven by transcription factor competition with mismatch repair. Cell. 2025 Oct 02; 188(20):5735-5747.e15.
DNA mutagenesis driven by transcription factor competition with mismatch repair.