Gordan, Raluca
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education and training: Alexandru Ioan Cuza University, Computer Science
education and training: Duke University, Computer Science
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Rando, Oliver
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Endowed Chair Honorary Title: Endowed Chair in Biochemistry and Molecular Biotechnology II
Post Docs: For more information about the Postdoctoral position in Dr. Rando’s lab please use the link provided. Post doc position
Rotation Projects: 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.
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Weng, Zhiping
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Post Docs: 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
Rotation Projects: Please contact Dr. Weng for information on rotations that are available in her lab.
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Imbalzano, Anthony
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Post Docs: 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/
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Peterson, Craig
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Dekker, Job
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Endowed Chair Honorary Title: Joseph J. Byrne Chair in Biomedical Research
Rotation Projects: ? 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.
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Rivest, Molly
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Alexandru Ioan Cuza University, Computer Science
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Moore, Jill
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Post Docs: 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
Rotation Projects: Interested in rotating in the lab? Please contact Dr. Moore for more information.
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Authorship 133303
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linked author: Gordan, Raluca
linked information resource: UV irradiation alters TFAM binding to mitochondrial DNA.

Authorship 133304
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author rank in publication: 11
linked author: Gordan, Raluca
linked information resource: Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions.

Authorship 133305
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author rank in publication: 1
linked author: Gordan, Raluca
linked information resource: Deciphering the impact of genomic variation on function.

Authorship 133306
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author rank in publication: 9
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linked information resource: DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum.

Authorship 133307
type: Authorship
author rank in publication: 6
linked author: Gordan, Raluca
linked information resource: High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma.

Authorship 133308
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins.

Authorship 133309
type: Authorship
author rank in publication: 17
linked author: Gordan, Raluca
linked information resource: Computational design of sequence-specific DNA-binding proteins.

Authorship 133310
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author rank in publication: 11
linked author: Gordan, Raluca
linked information resource: Short tandem repeats bind transcription factors to tune eukaryotic gene expression.

Authorship 133311
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linked author: Gordan, Raluca
linked information resource: UV irradiation remodels the specificity landscape of transcription factors.

Authorship 133312
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linked information resource: Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer.

Authorship 133313
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author rank in publication: 13
linked author: Gordan, Raluca
linked information resource: MESH1 knockdown triggers proliferation arrest through TAZ repression.

Authorship 133314
type: Authorship
author rank in publication: 3
linked author: Gordan, Raluca
linked information resource: Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains.

Authorship 133315
type: Authorship
author rank in publication: 4
linked author: Gordan, Raluca
linked information resource: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions.

Authorship 133316
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author rank in publication: 4
linked author: Gordan, Raluca
linked information resource: Mutational processes in cancer preferentially affect binding of particular transcription factors.

Authorship 133317
type: Authorship
author rank in publication: 15
linked author: Gordan, Raluca
linked information resource: DNA mismatches reveal conformational penalties in protein-DNA recognition.

Authorship 133318
type: Authorship
author rank in publication: 4
linked author: Gordan, Raluca
linked information resource: DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling.

Authorship 133319
type: Authorship
author rank in publication: 8
linked author: Gordan, Raluca
linked information resource: Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine.

Authorship 133320
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants.

Authorship 133321
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase.

Authorship 133322
type: Authorship
author rank in publication: 18
linked author: Gordan, Raluca
linked information resource: Genetic variation determines VEGF-A plasma levels in cancer patients.

Authorship 133323
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: The vitamin D receptor gene as a determinant of survival in pancreatic cancer patients: Genomic analysis and experimental validation.

Authorship 133324
type: Authorship
author rank in publication: 10
linked author: Gordan, Raluca
linked information resource: Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In?Vivo Binding.

Authorship 133325
type: Authorship
author rank in publication: 10
linked author: Gordan, Raluca
linked information resource: Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.

Authorship 133326
type: Authorship
author rank in publication: 12
linked author: Gordan, Raluca
linked information resource: Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood.

Authorship 133327
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.

Authorship 133328
type: Authorship
author rank in publication: 53
linked author: Gordan, Raluca
linked information resource: Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.

Authorship 133329
type: Authorship
author rank in publication: 7
linked author: Gordan, Raluca
linked information resource: Expression level is a key determinant of E2F1-mediated cell fate.

Authorship 133330
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author rank in publication: 3
linked author: Gordan, Raluca
linked information resource: Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

Authorship 133331
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linked author: Gordan, Raluca
linked information resource: Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources.

Authorship 133332
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linked author: Gordan, Raluca
linked information resource: Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.

Authorship 133333
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author rank in publication: 3
linked author: Gordan, Raluca
linked information resource: HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.

Authorship 133334
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: Survey of variation in human transcription factors reveals prevalent DNA binding changes.

Authorship 133335
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author rank in publication: 4
linked author: Gordan, Raluca
linked information resource: Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.

Authorship 133336
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author rank in publication: 8
linked author: Gordan, Raluca
linked information resource: Quantitative modeling of transcription factor binding specificities using DNA shape.

Authorship 133337
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author rank in publication: 6
linked author: Gordan, Raluca
linked information resource: Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex.

Authorship 133338
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author rank in publication: 4
linked author: Gordan, Raluca
linked information resource: Protein-DNA binding in the absence of specific base-pair recognition.

Authorship 133339
type: Authorship
author rank in publication: 1
linked author: Gordan, Raluca
linked information resource: Sequence specificity incompletely defines the genome-wide occupancy of Myc.

Authorship 133340
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: Absence of a simple code: how transcription factors read the genome.

Authorship 133341
type: Authorship
author rank in publication: 3
linked author: Gordan, Raluca
linked information resource: COUGER--co-factors associated with uniquely-bound genomic regions.

Authorship 133342
type: Authorship
author rank in publication: 2
linked author: Gordan, Raluca
linked information resource: Protein-DNA binding: complexities and multi-protein codes.

Authorship 133343
type: Authorship
author rank in publication: 6
linked author: Gordan, Raluca
linked information resource: TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

Authorship 133344
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: Stability selection for regression-based models of transcription factor-DNA binding specificity.

Authorship 133345
type: Authorship
author rank in publication: 1
linked author: Gordan, Raluca
linked information resource: Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.

Authorship 133346
type: Authorship
author rank in publication: 1
linked author: Gordan, Raluca
linked information resource: Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.

Authorship 133347
type: Authorship
author rank in publication: 1
linked author: Gordan, Raluca
linked information resource: Identification of cell cycle-regulated, putative hyphal genes in Candida albicans.

Authorship 133348
type: Authorship
author rank in publication: 5
linked author: Gordan, Raluca
linked information resource: Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.

Authorship 133351
type: Authorship
author rank in publication: 6
linked author: Gordan, Raluca
linked information resource: The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency.

Computational design of sequence-specific DNA-binding proteins.
PubMed Identifier: 37790440
author list: 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
published in: bioRxiv : the preprint server for biology
information resource reference: 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.
journal title abbreviation: bioRxiv
publication date: 2023-09-21T00:00:00
year: 2023
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type: Document
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MESH1 knockdown triggers proliferation arrest through TAZ repression.
PubMed Identifier: 35273140
author list: 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
published in: Cell death & disease
information resource reference: 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.
journal title abbreviation: Cell Death Dis
publication date: 2022-03-10T00:00:00
year: 2022
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Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains.
PubMed Identifier: 34429139
author list: 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
published in: Molecular neurodegeneration
information resource reference: 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.
journal title abbreviation: Mol Neurodegener
publication date: 2021-08-24T00:00:00
year: 2021
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Mutational processes in cancer preferentially affect binding of particular transcription factors.
PubMed Identifier: 33558557
author list: Liu M, Boot A, Ng AWT, Gord?n R, Rozen SG
published in: Scientific reports
information resource reference: 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.
journal title abbreviation: Sci Rep
publication date: 2021-02-08T00:00:00
year: 2021
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Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In?Vivo Binding.
PubMed Identifier: 29605182
author list: Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R
published in: Cell systems
information resource reference: 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.
journal title abbreviation: Cell Syst
publication date: 2018-03-28T00:00:00
year: 2018
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Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.
PubMed Identifier: 27923776
author list: 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
published in: Developmental cell
information resource reference: 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.
journal title abbreviation: Dev Cell
publication date: 2016-10-27T00:00:00
year: 2016
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Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex.
PubMed Identifier: 25702574
author list: Boyd JL, Skove SL, Rouanet JP, Pilaz LJ, Bepler T, Gord?n R, Wray GA, Silver DL
published in: Current biology : CB
information resource reference: 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.
journal title abbreviation: Curr Biol
publication date: 2015-02-19T00:00:00
year: 2015
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Protein-DNA binding in the absence of specific base-pair recognition.
PubMed Identifier: 25313048
author list: Afek A, Schipper JL, Horton J, Gord?n R, Lukatsky DB
published in: Proceedings of the National Academy of Sciences of the United States of America
information resource reference: 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.
journal title abbreviation: Proc Natl Acad Sci U S A
publication date: 2014-10-13T00:00:00
year: 2014
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type: Document
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Absence of a simple code: how transcription factors read the genome.
PubMed Identifier: 25129887
author list: Slattery M, Zhou T, Yang L, Dantas Machado AC, Gord?n R, Rohs R
published in: Trends in biochemical sciences
information resource reference: 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.
journal title abbreviation: Trends Biochem Sci
publication date: 2014-08-14T00:00:00
year: 2014
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TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
PubMed Identifier: 24214955
author list: Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gord?n R, Rohs R
published in: Nucleic acids research
information resource reference: 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.
journal title abbreviation: Nucleic Acids Res
publication date: 2013-11-07T00:00:00
year: 2013
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Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
PubMed Identifier: 23562153
author list: Gord?n R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML
published in: Cell reports
information resource reference: 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.
journal title abbreviation: Cell Rep
publication date: 2013-04-04T00:00:00
year: 2013
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Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.
PubMed Identifier: 22189060
author list: Gord?n R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML
published in: Genome biology
information resource reference: 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.
journal title abbreviation: Genome Biol
publication date: 2011-12-21T00:00:00
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Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions.
PubMed Identifier: 39253425
author list: 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
published in: bioRxiv : the preprint server for biology
information resource reference: 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.
journal title abbreviation: bioRxiv
publication date: 2025-05-02T00:00:00
year: 2025
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DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum.
PubMed Identifier: 38966997
author list: Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gord?n R, Llin?s M
published in: Nucleic acids research
information resource reference: 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.
journal title abbreviation: Nucleic Acids Res
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Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer.
PubMed Identifier: 36507923
author list: Zhao J, Martin V, Gord?n R
published in: Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- )
information resource reference: 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.
journal title abbreviation: Res Comput Mol Biol
publication date: 2022-04-29T00:00:00
year: 2022
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DNA mismatches reveal conformational penalties in protein-DNA recognition.
PubMed Identifier: 33087930
author list: 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
published in: Nature
information resource reference: 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.
journal title abbreviation: Nature
publication date: 2020-10-21T00:00:00
year: 2020
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Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine.
PubMed Identifier: 31170499
author list: Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O, Shahar A, Zarivach R, Gordan R, Arbely E
published in: Biochimica et biophysica acta. General subjects
information resource reference: 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.
journal title abbreviation: Biochim Biophys Acta Gen Subj
publication date: 2019-06-03T00:00:00
year: 2019
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DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase.
PubMed Identifier: 30428370
author list: Afek A, Ilic S, Horton J, Lukatsky DB, Gordan R, Akabayov B
published in: iScience
information resource reference: 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.
journal title abbreviation: iScience
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Expression level is a key determinant of E2F1-mediated cell fate.
PubMed Identifier: 28211871
author list: Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, Gord?n R, Yao G, You L
published in: Cell death and differentiation
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journal title abbreviation: Cell Death Differ
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HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.
PubMed Identifier: 27087856
author list: Frank CL, Manandhar D, Gord?n R, Crawford GE
published in: Epigenetics & chromatin
information resource reference: 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.
journal title abbreviation: Epigenetics Chromatin
publication date: 2016-04-16T00:00:00
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UV irradiation alters TFAM binding to mitochondrial DNA.
PubMed Identifier: 39484377
author list: 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
published in: bioRxiv : the preprint server for biology
information resource reference: 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.
journal title abbreviation: bioRxiv
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Deciphering the impact of genomic variation on function.
PubMed Identifier: 39232149
published in: Nature
information resource reference: Deciphering the impact of genomic variation on function. Nature. 2024 Sep; 633(8028):47-57.
journal title abbreviation: Nature
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DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling.
PubMed Identifier: 31657797
author list: Ilic S, Cohen S, Afek A, Gordan R, Lukatsky DB, Akabayov B
published in: Journal of visualized experiments : JoVE
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QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants.
PubMed Identifier: 31114870
author list: Martin V, Zhao J, Afek A, Mielko Z, Gord?n R
published in: Nucleic acids research
information resource reference: 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.
journal title abbreviation: Nucleic Acids Res
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Genetic variation determines VEGF-A plasma levels in cancer patients.
PubMed Identifier: 30397360
author list: 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
published in: Scientific reports
information resource reference: 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.
journal title abbreviation: Sci Rep
publication date: 2018-11-05T00:00:00
year: 2018
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Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.
PubMed Identifier: 28691125
author list: Zhao J, Li D, Seo J, Allen AS, Gord?n R
published in: Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- )
information resource reference: 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.
journal title abbreviation: Res Comput Mol Biol
publication date: 2017-04-12T00:00:00
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Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.
PubMed Identifier: 28667006
author list: 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
published in: Cancer discovery
information resource reference: 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.
journal title abbreviation: Cancer Discov
publication date: 2017-06-30T00:00:00
year: 2017
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Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources.
PubMed Identifier: 27803259
author list: Schipper JL, Gord?n RM
published in: Cold Spring Harbor protocols
information resource reference: 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).
journal title abbreviation: Cold Spring Harb Protoc
publication date: 2016-11-01T00:00:00
year: 2016
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Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.
PubMed Identifier: 27162172
author list: Medina EM, Turner JJ, Gord?n R, Skotheim JM, Buchler NE
published in: eLife
information resource reference: 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.
journal title abbreviation: Elife
publication date: 2016-05-10T00:00:00
year: 2016
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Sequence specificity incompletely defines the genome-wide occupancy of Myc.
PubMed Identifier: 25287278
author list: Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gord?n R, Price DH
published in: Genome biology
information resource reference: 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.
journal title abbreviation: Genome Biol
publication date: 2014-01-01T00:00:00
year: 2014
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COUGER--co-factors associated with uniquely-bound genomic regions.
PubMed Identifier: 24861628
author list: Munteanu A, Ohler U, Gord?n R
published in: Nucleic acids research
information resource reference: 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.
journal title abbreviation: Nucleic Acids Res
publication date: 2014-05-26T00:00:00
year: 2014
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type: Document
type: Information Resource

Stability selection for regression-based models of transcription factor-DNA binding specificity.
PubMed Identifier: 23812975
author list: Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gord?n R
published in: Bioinformatics (Oxford, England)
information resource reference: 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.
journal title abbreviation: Bioinformatics
publication date: 2013-07-01T00:00:00
year: 2013
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type: Document
type: Information Resource

Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.
PubMed Identifier: 21282347
author list: Miller HB, Robinson TJ, Gord?n R, Hartemink AJ, Garcia-Blanco MA
published in: RNA (New York, N.Y.)
information resource reference: 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.
journal title abbreviation: RNA
publication date: 2011-01-31T00:00:00
year: 2011
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High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma.
PubMed Identifier: 38241433
author list: Duan M, Song S, Wasserman H, Lee PH, Liu KJ, Gord?n R, He Y, Mao P
published in: Proceedings of the National Academy of Sciences of the United States of America
information resource reference: 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.
journal title abbreviation: Proc Natl Acad Sci U S A
publication date: 2024-01-19T00:00:00
year: 2024
type: Academic Article
type: Article
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High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins.
PubMed Identifier: 37889068
author list: Martin V, Zhuang F, Zhang Y, Pinheiro K, Gord?n R
published in: Nucleic acids research
information resource reference: 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.
journal title abbreviation: Nucleic Acids Res
publication date: 2023-11-27T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
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Short tandem repeats bind transcription factors to tune eukaryotic gene expression.
PubMed Identifier: 37733848
author list: 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
published in: Science (New York, N.Y.)
information resource reference: 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.
journal title abbreviation: Science
publication date: 2023-09-22T00:00:00
year: 2023
type: Academic Article
type: Article
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UV irradiation remodels the specificity landscape of transcription factors.
PubMed Identifier: 36888663
author list: 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
published in: Proceedings of the National Academy of Sciences of the United States of America
information resource reference: 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.
journal title abbreviation: Proc Natl Acad Sci U S A
publication date: 2023-03-08T00:00:00
year: 2023
type: Academic Article
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Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions.
PubMed Identifier: 33975875
author list: Zhang Y, Ho TD, Buchler NE, Gord?n R
published in: Genome research
information resource reference: 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.
journal title abbreviation: Genome Res
publication date: 2021-05-11T00:00:00
year: 2021
type: Academic Article
type: Article
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The vitamin D receptor gene as a determinant of survival in pancreatic cancer patients: Genomic analysis and experimental validation.
PubMed Identifier: 30107003
author list: 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
published in: PloS one
information resource reference: 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.
journal title abbreviation: PLoS One
publication date: 2018-08-14T00:00:00
year: 2018
type: Academic Article
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Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.
PubMed Identifier: 28977539
author list: Manandhar D, Song L, Kabadi A, Kwon JB, Edsall LE, Ehrlich M, Tsumagari K, Gersbach CA, Crawford GE, Gord?n R
published in: Nucleic acids research
information resource reference: 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.
journal title abbreviation: Nucleic Acids Res
publication date: 2017-11-16T00:00:00
year: 2017
type: Academic Article
type: Article
type: Document
type: Information Resource

Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood.
PubMed Identifier: 28784765
author list: 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
published in: Proceedings of the National Academy of Sciences of the United States of America
information resource reference: 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.
journal title abbreviation: Proc Natl Acad Sci U S A
publication date: 2017-08-07T00:00:00
year: 2017
type: Academic Article
type: Article
type: Document
type: Information Resource

Survey of variation in human transcription factors reveals prevalent DNA binding changes.
PubMed Identifier: 27013732
author list: 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
published in: Science (New York, N.Y.)
information resource reference: 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.
journal title abbreviation: Science
publication date: 2016-03-24T00:00:00
year: 2016
type: Academic Article
type: Article
type: Document
type: Information Resource

Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.
PubMed Identifier: 26285121
author list: Afek A, Cohen H, Barber-Zucker S, Gord?n R, Lukatsky DB
published in: PLoS computational biology
information resource reference: 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.
journal title abbreviation: PLoS Comput Biol
publication date: 2015-08-18T00:00:00
year: 2015
type: Academic Article
type: Article
type: Document
type: Information Resource

Protein-DNA binding: complexities and multi-protein codes.
PubMed Identifier: 24243859
author list: Siggers T, Gord?n R
published in: Nucleic acids research
information resource reference: Siggers T, Gord?n R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res. 2014 Feb; 42(4):2099-111.
journal title abbreviation: Nucleic Acids Res
publication date: 2013-11-16T00:00:00
year: 2013
type: Academic Article
type: Article
type: Document
type: Information Resource

Identification of cell cycle-regulated, putative hyphal genes in Candida albicans.
PubMed Identifier: 22174285
author list: Gord?n R, Pyne S, Bulyk ML
published in: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
information resource reference: Gord?n R, Pyne S, Bulyk ML. Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pac Symp Biocomput. 2012; 299-310.
journal title abbreviation: Pac Symp Biocomput
publication date: 2012-01-01T00:00:00
year: 2012
type: Academic Article
type: Article
type: Document
type: Information Resource

The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency.
PubMed Identifier: 39970291
author list: Heilbrun EE, Tseitline D, Wasserman H, Kirshenbaum A, Cohen Y, Gordan R, Adar S
published in: Nucleic acids research
information resource reference: 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).
journal title abbreviation: Nucleic Acids Res
publication date: 2025-02-08T00:00:00
year: 2025
type: Academic Article
type: Article
type: Document
type: Information Resource

Quantitative modeling of transcription factor binding specificities using DNA shape.
PubMed Identifier: 25775564
author list: Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gord?n R, Rohs R
published in: Proceedings of the National Academy of Sciences of the United States of America
information resource reference: 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.
journal title abbreviation: Proc Natl Acad Sci U S A
publication date: 2015-03-09T00:00:00
year: 2015
type: Academic Article
type: Article
type: Document
type: Information Resource

https://profiles.umassmed.edu/profile/85559955
position in department: Biophysical Chemical and Computational Biology
position in division: https://profiles.umassmed.edu/profile/15590085
sort order: 4
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position in organization: Morningside Graduate School of Biomedical Sciences

https://profiles.umassmed.edu/profile/85559956
position in department: Systems Computational and Quantitative Biology
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position in organization: Morningside Graduate School of Biomedical Sciences

Professor
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position in department: Genomics and Computational Biology
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HR job title: Professor
position in organization: UMass Chan Medical School

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position in department: Genomics and Computational Biology
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position in organization: T.H. Chan School of Medicine

https://profiles.umassmed.edu/profile/85559967
position in department: Systems Biology
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position in organization: T.H. Chan School of Medicine

Authorship 135106
type: Authorship
author rank in publication: 14
linked author: Gordan, Raluca
linked information resource: DNA mutagenesis driven by transcription factor competition with mismatch repair.

DNA mutagenesis driven by transcription factor competition with mismatch repair.
PubMed Identifier: 40738104
author list: 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
published in: Cell
information resource reference: 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.
journal title abbreviation: Cell
publication date: 2025-07-29T00:00:00
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