Works by Zack, Donald J.

Results: 81

Analysis of regulatory network topology reveals functionally distinct classes of microRNAs.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 20, p. 6494, doi. 10.1093/nar/gkn712

By:

Yu, Xueping;
Lin, Jimmy;
Zack, Donald J.;
Mendell, Joshua T.;
Qian, Jiang

Publication type:

Article

Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 17, p. 4925, doi. 10.1093/nar/gkl595

By:

Yu, Xueping;
Lin, Jimmy;
Zack, Donald J.;
Qian, Jiang

Publication type:

Article

Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 3, p. 917

By:

Yu, Xueping;
Lin, Jimmy;
Masuda, Tomohiro;
Esumi, Noriko;
Zack, Donald J.;
Qian, Jiang

Publication type:

Article

Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 12, p. 3953, doi. 10.1093/nar/gki719

By:

Qian, Jiang;
Esumi, Noriko;
Chen, Yangjian;
Wang, Qingliang;
Chowers, Itay;
Zack, Donald J.

Publication type:

Article

Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 11, p. 3479, doi. 10.1093/nar/gki658

By:

Qian, Jiang;
Esumi, Noriko;
Chen, Yangjian;
Wang, Qingliang;
Chowers, Itay;
Zack, Donald J.

Publication type:

Article

Intercellular communication atlas reveals Oprm1 as a neuroprotective factor for retinal ganglion cells.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-46428-z

By:

Qian, Cheng;
Xin, Ying;
Qi, Cheng;
Wang, Hui;
Dong, Bryan C.;
Zack, Donald J.;
Blackshaw, Seth;
Hattar, Samer;
Zhou, Feng-Quan;
Qian, Jiang

Publication type:

Article

Complement component 3 from astrocytes mediates retinal ganglion cell loss during neuroinflammation.

Published in:

Acta Neuropathologica, 2021, v. 142, n. 5, p. 899, doi. 10.1007/s00401-021-02366-4

By:

Gharagozloo, Marjan;
Smith, Matthew D.;
Jin, Jing;
Garton, Thomas;
Taylor, Michelle;
Chao, Alyssa;
Meyers, Keya;
Kornberg, Michael D.;
Zack, Donald J.;
Ohayon, Joan;
Calabresi, Brent A.;
Reich, Daniel S.;
Eberhart, Charles G.;
Pardo, Carlos A.;
Kemper, Claudia;
Whartenby, Katharine A.;
Calabresi, Peter A.

Publication type:

Article

Reporter gene expression in cones in transgenic mice carrying bovine rhodopsin promoter/lacZ transgenes.

Published in:

Visual Neuroscience, 1994, v. 11, n. 6, p. 1227, doi. 10.1017/S0952523800007021

By:

Gouras, Peter;
Kjeldbye, Hild;
Zack, Donald J.

Publication type:

Article

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03856-y

By:

Jie Wang;
Zibetti, Cristina;
Peng Shang;
Sripathi, Srinivasa R.;
Pingwu Zhang;
Cano, Marisol;
Thanh Hoang;
Shuli Xia;
Hongkai Ji;
Merbs, Shannath L.;
Zack, Donald J.;
Handa, James T.;
Sinha, Debasish;
Blackshaw, Seth;
Jiang Qian

Publication type:

Article

Increased Expression of Brain-Derived Neurotrophic Factor Preserves Retinal Function and Slows Cell Death from Rhodopsin Mutation or Oxidative Damage.

Published in:

Journal of Neuroscience, 2003, v. 23, n. 10, p. 4164, doi. 10.1523/JNEUROSCI.23-10-04164.2003

By:

Okoye, Godwin;
Zimmer, Joelle;
Sung, Jennifer;
Gehlbach, Peter;
Deering, Tye;
Nambu, Hiroyuki;
Hackett, Sean;
Melia, Michele;
Esumi, Noriko;
Zack, Donald J.;
Campochiaro, Peter A.

Publication type:

Article

Different effects of angiopoietin-2 in different vascular beds: new vessels are most sensitive.

Published in:

FASEB Journal, 2005, v. 19, n. 8, p. 963, doi. 10.1096/fj.04-2209fje

By:

Oshima, Yuji;
Oshima, Sachiko;
Nambu, Hiroyuki;
Kachi, Shu;
Takahashi, Kyoichi;
Umeda, Naoyasu;
Shen, JiKui;
Dong, Aling;
Apte, Rajendra S.;
Duh, Elia;
Hackett, Sean F.;
Okoye, Godwin;
Ishibashi, Kazuki;
Handa, James;
Melia, Michele;
Wiegand, Stanley;
Yancopoulos, George;
Zack, Donald J.;
Campochiaro, Peter A.

Publication type:

Article

Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1271-4

By:

Jun Wan;
Oliver, Verity F.;
Guohua Wang;
Heng Zhu;
Zack, Donald J.;
Merbs, Shannath L.;
Jiang Qian

Publication type:

Article

Prolonged blockade of VEGF receptors does not damage retinal photoreceptors or ganglion cells.

Published in:

Journal of Cellular Physiology, 2010, v. 224, n. 1, p. 262, doi. 10.1002/jcp.22129

By:

MIKI, AKIKO;
MIKI, KATSUAKI;
UENO, SHINJI;
WERSINGER, DELPHINE M. BONNET;
BERLINICKE, CYNTHIA;
SHAW, GILLIAN C.;
SHINICHI USUI;
YUXIA WANG;
ZACK, DONALD J.;
CAMPOCHIARO, PETER A.

Publication type:

Article

Prolonged blockade of VEGF family members does not cause identifiable damage to retinal neurons or vessels.

Published in:

Journal of Cellular Physiology, 2008, v. 217, n. 1, p. 13, doi. 10.1002/jcp.21445

By:

Ueno, Shinji;
Pease, Mary Ellen;
Bonnet Wersinger, Delphine M.;
Masuda, Tomohiro;
Vinores, Stanley A.;
Licht, Tamar;
Zack, Donald J.;
Quigley, Harry;
Keshet, Eli;
Campochiaro, Peter A.

Publication type:

Article

Increased expression of VEGF in retinal pigmented epithelial cells is not sufficient to cause choroidal neovascularization.

Published in:

Journal of Cellular Physiology, 2004, v. 201, n. 3, p. 393, doi. 10.1002/jcp.20110

By:

Yuji Oshima;
Sachiko Oshima;
Hiroyuki Nambu;
Shu Kachi;
Sean F. Hackett;
Michele Melia;
Michael Kaleko;
Sheila Connelly;
Noriko Esumi;
Donald J. Zack;
Peter A. Campochiaro

Publication type:

Article

Pigment epithelium-derived factor inhibits retinal and choroidal neovascularization.

Published in:

Journal of Cellular Physiology, 2001, v. 188, n. 2, p. 253, doi. 10.1002/jcp.1114

By:

Mori, Keisuke;
Duh, Elia;
Gehlbach, Peter;
Ando, Akira;
Takahashi, Kyoichi;
Pearlman, Joel;
Mori, Keiko;
Yang, Hoseong S.;
Zack, Donald J.;
Ettyreddy, Damodar;
Brough, Douglas E.;
Wei, Lisa L.;
Campochiaro, Peter A.

Publication type:

Article

Cell injury unmasks a latent proangiogenic phenotype in mice with increased expression of FGF2 in the retina.

Published in:

Journal of Cellular Physiology, 2000, v. 185, n. 1, p. 135, doi. 10.1002/1097-4652(200010)185:1<135::AID-JCP13>3.0.CO;2-Y

By:

Yamada, Haruhiko;
Yamada, Eri;
Kwak, Nohoon;
Ando, Akira;
Suzuki, Akiko;
Esumi, Noriko;
Zack, Donald J.;
Campochiaro, Peter A.

Publication type:

Article

A Novel Approach to Increase Glial Cell Populations in Brain Microphysiological Systems.

Published in:

Advanced Biology, 2024, v. 8, n. 8, p. 1, doi. 10.1002/adbi.202300198

By:

Morales Pantoja, Itzy E.;
Ding, Lixuan;
Leite, Paulo E. C.;
Marques, Suelen A.;
Romero, July Carolina;
Alam El Din, Dowlette‐Mary;
Zack, Donald J.;
Chamling, Xitiz;
Smirnova, Lena

Publication type:

Article

Off Target, but Sequence-Specific, shRNA-Associated Trans-Activation of Promoter Reporters in Transient Transfection Assays.

Published in:

PLoS ONE, 2016, v. 11, n. 12, p. 1, doi. 10.1371/journal.pone.0167867

By:

Masuda, Tomohiro;
Wan, Jun;
Yerrabelli, Anitha;
Berlinicke, Cindy;
Kallman, Alyssa;
Qian, Jiang;
Zack, Donald J.

Publication type:

Article

Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells.

Published in:

PLoS ONE, 2016, v. 11, n. 3, p. 1, doi. 10.1371/journal.pone.0150758

By:

Kole, Christo;
Berdugo, Naomi;
Da Silva, Corinne;
Aït-Ali, Najate;
Millet-Puel, Géraldine;
Pagan, Delphine;
Blond, Frédéric;
Poidevin, Laetitia;
Ripp, Raymond;
Fontaine, Valérie;
Wincker, Patrick;
Zack, Donald J.;
Sahel, José-Alain;
Poch, Olivier;
Léveillard, Thierry

Publication type:

Article

The Transcription Factor GTF2IRD1 Regulates the Topology and Function of Photoreceptors by Modulating Photoreceptor Gene Expression across the Retina.

Published in:

Journal of Neuroscience, 2014, v. 34, n. 46, p. 15356, doi. 10.1523/JNEUROSCI.2089-14.2014

By:

Masuda, Tomohiro;
Zhang, Xiaodong;
Berlinicke, Cindy;
Wan, Jun;
Yerrabelli, Anitha;
Conner, Elizabeth A.;
Kjellstrom, Sten;
Bush, Ronald;
Thorgeirsson, Snorri S.;
Swaroop, Anand;
Chen, Shiming;
Zack, Donald J.

Publication type:

Article

A 5-bp deletion in ELOVL4 is associated with two related forms of autosomal dominant macular dystrophy.

Published in:

Nature Genetics, 2001, v. 27, n. 1, p. 89, doi. 10.1038/83817

By:

Zhang, Kang;
Kniazeva, Marina;
Han, Min;
Li, Wen;
Yu, Zhengya;
Yang, Zhenglin;
Li, Yang;
Metzker, Michael L.;
Allikmets, Rando;
Zack, Donald J.;
Kakuk, Laura E.;
Lagali, Pamela S.;
Wong, Paul W.;
MacDonald, Ian M.;
Sieving, Paul A.;
Figueroa, David J.;
Austin, Christopher P.;
Gould, Robert J.;
Ayyagari, Radha

Publication type:

Article

A mutation in NRL is associated with autosomal dominant retinitis pigmentosa.

Published in:

Nature Genetics, 1999, v. 21, n. 4, p. 355, doi. 10.1038/7678

By:

Bessant, David A.R.;
Payne, Annette M.;
Mitton, Kenneth P.;
Wang, Qing-Liang;
Swain, Prabodha K.;
Plant, Catherine;
Bird, Alan C.;
Zack, Donald J.;
Swaroop, Anand;
Bhattacharya, Shomi S.

Publication type:

Article

Neutral sphingomyelinase inhibition promotes local and network degeneration in vitro and in vivo.

Published in:

Cell Communication & Signaling, 2023, v. 21, n. 1, p. 1, doi. 10.1186/s12964-023-01291-1

By:

Risner, Michael L.;
Ribeiro, Marcio;
McGrady, Nolan R.;
Kagitapalli, Bhanu S.;
Chamling, Xitiz;
Zack, Donald J.;
Calkins, David J.

Publication type:

Article

A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples.

Published in:

Epigenetics & Chromatin, 2013, v. 6, n. 1, p. 1, doi. 10.1186/1756-8935-6-17

By:

Oliver, Verity F.;
Wan, Jun;
Agarwal, Saurabh;
Zack, Donald J.;
Jiang Qian;
Merbs, Shannath L.

Publication type:

Article

MITF-M, a 'melanocyte-specific' isoform, is expressed in the adult retinal pigment epithelium.

Published in:

Pigment Cell & Melanoma Research, 2012, v. 25, n. 5, p. 641, doi. 10.1111/j.1755-148X.2012.01033.x

By:

Maruotti, Julien;
Thein, Thuzar;
Zack, Donald J.;
Esumi, Noriko

Publication type:

Article

Highly efficient scarless knock-in of reporter genes into human and mouse pluripotent stem cells via transient antibiotic selection.

Published in:

PLoS ONE, 2018, v. 13, n. 11, p. 1, doi. 10.1371/journal.pone.0201683

By:

Sluch, Valentin M.;
Chamling, Xitiz;
Wenger, Claire;
Duan, Yukan;
Rice, Dennis S.;
Zack, Donald J.

Publication type:

Article

Ibuprofen reduces inflammation, necroptosis and protects photoreceptors from light-induced retinal degeneration.

Published in:

Journal of Neuroinflammation, 2025, v. 22, n. 1, p. 1, doi. 10.1186/s12974-024-03329-8

By:

Zhang, Ping-Wu;
Wan, Zi-He;
Li, Weifeng;
Vats, Abhishek;
Mehta, Kunal;
Fan, Laura;
Zhou, Lingli;
Li, Sean;
Li, Gloria;
Keuthan, Casey J.;
Berlinicke, Cynthia;
Qian, Cheng;
Esumi, Noriko;
Duh, Elia J;
Zack, Donald J.

Publication type:

Article

Zinc-finger domains of the transcriptional repressor KLF15 bind multiple sites in rhodopsin and IRBP promoters including the CRS-1 and G-rich repressor elements.

Published in:

BMC Molecular Biology, 2005, v. 6, p. 15, doi. 10.1186/1471-2199-6-15

By:

Otteson, Deborah C.;
Hong Lai;
Yuhui Liu;
Zack, Donald J.

Publication type:

Article

Serum molecular signature for proliferative diabetic retinopathy in Saudi patients with type 2 diabetes.

Published in:

Molecular Vision, 2016, v. 22, p. 1

By:

Jianbo Pan;
Sheng Liu;
Farkas, Michael;
Consugar, Mark;
Zack, Donald J.;
Kozak, Igor;
Arevalo, J. Fernando;
Pierce, Eric;
Jiang Qian;
Al Kahtani, Eman

Publication type:

Article

Transcriptional Regulatory Network Prediction.

Published in:

Biotechnology & Genetic Engineering Reviews, 2005, v. 22, p. 45

By:

Lin, Jimmy;
Zack, Donald J.;
Jiang Qian

Publication type:

Article

Automated segmentation of mouse OCT volumes (ASiMOV): Validation & clinical study of a light damage model.

Published in:

PLoS ONE, 2017, v. 12, n. 8, p. 1, doi. 10.1371/journal.pone.0181059

By:

Antony, Bhavna Josephine;
Kim, Byung-Jin;
Lang, Andrew;
Carass, Aaron;
Prince, Jerry L.;
Zack, Donald J.

Publication type:

Article

De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei).

Published in:

PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0179061

By:

Liu, Melissa M.;
Farkas, Michael;
Spinnhirny, Perrine;
Pevet, Paul;
Pierce, Eric;
Hicks, David;
Zack, Donald J.

Publication type:

Article

Functional Dissection of the Promoter of the Interphotoreceptor Retinoid-Binding Protein Gene: The Cone-Rod-Homeobox Element Is Essential for Photoreceptor-Specific Expression In Vivo1.

Published in:

Journal of Biochemistry, 1999, v. 125, n. 6, p. 1189, doi. 10.1093/oxfordjournals.jbchem.a022403

By:

Fei, Yijian;
Matragoon, Suraporn;
Smith, Sylvia B.;
Overbeek, Paul A.;
Chen, Shiming;
Zack, Donald J.;
Liou, Gregory I.

Publication type:

Article

PanoView: An iterative clustering method for single-cell RNA sequencing data.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 8, p. 1, doi. 10.1371/journal.pcbi.1007040

By:

Hu, Ming-Wen;
Kim, Dong Won;
Liu, Sheng;
Zack, Donald J.;
Blackshaw, Seth;
Qian, Jiang

Publication type:

Article

Computational analysis of tissue-specific gene networks: application to murine retinal functional studies.

Published in:

Bioinformatics, 2010, v. 26, n. 18, p. 2289, doi. 10.1093/bioinformatics/btq408

By:

Jianfei Hu;
Jun Wan;
Hackler Jr., Laszlo;
Zack, Donald J.;
Jiang Qian

Publication type:

Article

Relating periodicity of nucleosome organization and gene regulation.

Published in:

Bioinformatics, 2009, v. 25, n. 14, p. 1782, doi. 10.1093/bioinformatics/btp323

By:

Jun Wan;
Jimmy Lin;
Donald J. Zack;
Jiang Qian

Publication type:

Article

Expression and permeation properties of the K<sup>+</sup> channel Kir7.1 in the retinal pigment epithelium.

Published in:

Journal of Physiology, 2001, v. 531, n. 2, p. 329, doi. 10.1111/j.1469-7793.2001.0329i.x

By:

Shimura, Masahiko;
Yuan, Yukun;
Chang, Jinghua T.;
Zhang, Suiyuan;
Campochiaro, Peter A.;
Zack, Donald J.;
Hughes, Bret A.

Publication type:

Article

Protein Phosphatase 1 binds strongly to the retinoblastoma protein butnot to p107 or p130 in vitro and in vivo.

Published in:

Current Eye Research, 2002, v. 24, n. 5, p. 392, doi. 10.1076/ceyr.24.5.392.8524

By:

Dunaief, Joshua L.;
King, Ayala;
Esumi, Noriko;
Eagen, Matthew;
Dentchev, Tzvete;
Sung, Ching-Hwa;
Chen, Shiming;
Zack, Donald J.

Publication type:

Article

Evaluating the potential of poly(beta-amino ester) nanoparticles for reprogramming human fibroblasts to become induced pluripotent stem cells.

Published in:

International Journal of Nanomedicine, 2013, v. 8, p. 4641, doi. 10.2147/IJN.S53830

By:

Bhise, Nupura S.;
Wahlin, Karl J.;
Zack, Donald J.;
Green, Jordan J.

Publication type:

Article

Aquaporin 4 is not present in normal porcine and human lamina cribrosa.

Published in:

PLoS ONE, 2022, v. 17, n. 6, p. 1, doi. 10.1371/journal.pone.0268541

By:

Kimball, Elizabeth C.;
Quillen, Sarah;
Pease, Mary E.;
Keuthan, Casey;
Nagalingam, Aru;
Zack, Donald J.;
Johnson, Thomas V.;
Quigley, Harry A.

Publication type:

Article

Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Optic Nerve Crush and Experimental Glaucoma.

Published in:

International Journal of Molecular Sciences, 2023, v. 24, n. 18, p. 13719, doi. 10.3390/ijms241813719

By:

Keuthan, Casey J.;
Schaub, Julie A.;
Wei, Meihan;
Fang, Weixiang;
Quillen, Sarah;
Kimball, Elizabeth;
Johnson, Thomas V.;
Ji, Hongkai;
Zack, Donald J.;
Quigley, Harry A.

Publication type:

Article

TiGER: A database for tissue-specific gene expression and regulation.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-271

By:

Xiong Liu;
Xueping Yu;
Zack, Donald J.;
Heng Zhu;
Jiang Qian

Publication type:

Article

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 437, doi. 10.1186/1471-2105-8-437

By:

Xueping Yu;
Lin, Jimmy;
Zack, Donald J.;
Jiang Qian

Publication type:

Article

Three-Dimensional Retinal Organoids Facilitate the Investigation of Retinal Ganglion Cell Development, Organization and Neurite Outgrowth from Human Pluripotent Stem Cells.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-32871-8

By:

Fligor, Clarisse M.;
Langer, Kirstin B.;
Sridhar, Akshayalakshmi;
Ren, Yuan;
Shields, Priya K.;
Edler, Michael C.;
Ohlemacher, Sarah K.;
Sluch, Valentin M.;
Zack, Donald J.;
Zhang, Chi;
Suter, Daniel M.;
Meyer, Jason S.

Publication type:

Article

Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 18, p. 8503, doi. 10.1093/nar/gkt652

By:

Wan, Jun;
Oliver, Verity F.;
Zhu, Heng;
Zack, Donald J.;
Qian, Jiang;
Merbs, Shannath L.

Publication type:

Article

Dynamic usage of alternative splicing exons during mouse retina development.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 18, p. 7920, doi. 10.1093/nar/gkr545

By:

Wan, Jun;
Masuda, Tomohiro;
Hackler, Laszlo;
Torres, Kieron M.;
Merbs, Shannath L.;
Zack, Donald J.;
Qian, Jiang

Publication type:

Article

Expansion of the CRISPR-Cas9 genome targeting space through the use of H1 promoter-expressed guide RNAs.

Published in:

Nature Communications, 2014, v. 5, n. 8, p. 4516, doi. 10.1038/ncomms5516

By:

Ranganathan, Vinod;
Wahlin, Karl;
Maruotti, Julien;
Zack, Donald J.

Publication type:

Article

Differential DNA methylation identified in the blood and retina of AMD patients.

Published in:

Epigenetics, 2015, v. 10, n. 8, p. 698, doi. 10.1080/15592294.2015.1060388

By:

Oliver, Verity F;
Jaffe, Andrew E;
Song, Jin;
Wang, Guohua;
Zhang, Pingwu;
Branham, Kari E;
Swaroop, Anand;
Eberhart, Charles G;
Zack, Donald J;
Qian, Jiang;
Merbs, Shannath L

Publication type:

Article

Investigating cone photoreceptor development using patient-derived NRL null retinal organoids.

Published in:

Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-0808-5

By:

Kallman, Alyssa;
Capowski, Elizabeth E.;
Wang, Jie;
Kaushik, Aniruddha M.;
Jansen, Alex D.;
Edwards, Kimberly L.;
Chen, Liben;
Berlinicke, Cynthia A.;
Joseph Phillips, M.;
Pierce, Eric A.;
Qian, Jiang;
Wang, Tza-Huei;
Gamm, David M.;
Zack, Donald J.

Publication type:

Article