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David (Mark) Eckley

居住地: United States of America


学歴: Ph.D. in Cell Biology (Johns Hopkins School of Medicine; USA)



コミュニケーションスタイル

ESL(英語が母国語でない)研究者との交流経験がある。平易な英語をゆっくり話す。


  1. 対応可能な相談内容
論文の書き方、ジャーナルの選び方、引用数の増やし方、リジェクトされた際の対応方法、研究倫理について、研究テーマの選び方、カンファレンスでの人脈作り、参考文献の管理方法、ポスドクの就職面接について、査読のプロセスについて、など
  1. 講師略歴(日本語)
Cellをはじめ、20を超える査読付き学術雑誌に単著、共著による論文掲載実績がある。主な専門分野は生物細胞学、コンピューター解析、データ・画像処理。現在、アメリカ国立衛生研究所の傘下であるアメリカ国立老化研究所の研究員を務めている。プロジェクトマネジメント、スタッフ教育の経験があり、論文の被引用回数は2,700回を超える。 上記に加えて、以下の研究相談にも対応可能。
  • CRISPRにもとづく遺伝子変化
  • 幹細胞培養
  • タンパク質精製
  • 共焦点光学顕微鏡検査法
  • ウィルス形質導入
  • 三次元イメージングシステムDeltavisionの実用的なヒント
  1. 詳細な講師プロフィール(英語)
David (Mark) has authored/co-authored over 20 peer-reviewed publications (including a co-authored paper in Cell), primarily in the fields of cell biology, computational analysis and data/image processing. He is currently working as a research contractor for the National Institute of Aging, a division of the U.S. National Institutes of Health and he has received recognition for his achievements and service. David is experienced in the area of project management and staff training and has received over 2,700 citations. Ph.D. trained biologist with 13 of years of experience planning cell biology experiments and implementing computational analysis and data/image processing. Successfully led teams, worked on multiple projects simultaneously and collaborated with internal and external investigators. Proficient using microscopes, liquid handlers, and all computer platforms. Prepared summaries of results, submitted manuscripts for review and published findings. In addition to the above, David would also offer research consultation in the following areas:
  • CRISPR-based genetic alterations
  • Stem cell culture
  • Protein purification
  • Confocal and light microscopy
  • Viral transduction
  • Practical tips on the Deltavision 3D reconstruction system.
Education
  • Ph.D. Cell Biology, The Johns Hopkins School of Medicine, BCMB department
  • M.A. Immunology, University of California, Santa Barbara, Neuroscience Research Institute
  • B.A. Chemistry, University of Colorado, Boulder, Chemistry department
Skills and Expertise
  • Computational Analysis:
  • Command line implementation of Fiji, WND-CHARM for image feature calculation
  • Microarray Data Normalization, Z score calculation for group to group comparisons, PCA
  • OpenCV image calculation package (Keras, Theano for deep learning)
  • NGS data using Biopython
  • Molecular biology:
  • Recombinant DNA, gene cloning and expression.
  • CRISPR gene knockout and knockin to produce intentional genetic alterations (IGA)
  • DNA sequencing, PCR and qPCR for IGA validation.
  • RNA seq, microarray hybridizations.
  • ELISA, Western blot, in-gel proteolysis.
  • Cell Biology:
  • Ex vivo culture of immortalized and primary Stem Cells.
  • Optimized cytokine mixture for stroma-free B-cell cultures.
  • Flow cytometry (Beckman-Coulter CytoFlex, Becton-Dickinson Canto II).
  • Virus generation: lentivirus and retrovirus, viral transduction to produce cell lines.
  • Microscopy:
  • Confocal and light microscopy, 3D reconstruction and structured illumination.
  • Microtubule gliding and vesicle motility assays
  • Microinjection of cultured cells and germline to produce IGA (nematodes).
  • Protein biochemistry:
  • Native and recombinant protein purification
  • FPLC, ion exchange chromatography
  • Sucrose gradient and size exclusion chromatography
Professional Experience
  • National Institute on Aging, Intramural Research Program (NIA-IRP)
  • Research Contractor, Image Informatics & Computational Biology Unit, LGG
  • The Johns Hopkins School of Medicine
  • Postdoctoral Scientist, Institute of Genetic Medicine
  • Postdoctoral Fellow, Johns Hopkins University, Biology department
  • Graduate Student, The Johns Hopkins School of Medicine, BCMB program
Awards
  • Distinguished Achievement Award, Kelly Government Services (Feb 2015, Feb 2013, Oct 2008)
Certification
  • Pyimagesearch Gurus Computer Vision Course (November 2017).
Journal Publications
  • Eckley DM, Coletta CE, Orlov NV, Wilson MA, Bastian P, Lehrmann E, Zhang Y, Becker KG, Goldberg IG. Transcriptome States Reflect Imaging of Aging States. J Gerontol A Biol Sci Med Sci. 2017 Dec 5. doi: 10.1093/gerona/glx236.
  • Eckley, D Mark; Rahimi, Salim; Mantilla, Sandra; Orlov, Nikita V; Coletta, Christopher E; Wilson, Mark A; Iser, Wendy B; Delaney, John D; Zhang, Yongqing; Wood, William; Molecular characterization of the transition to mid-life in Caenorhabditis elegans Age (2013) v:35(3)pp.689-703
  • Orlov, Nikita V; Weeraratna, Ashani T; Hewitt, Stephen M; Coletta, Christopher E; Delaney, John D; Eckley, D. Mark; Shamir, Lior; Goldberg, Ilya G; Automatic detection of melanoma progression by histological analysis of secondary sites Cytometry Part A (2012) v:81(5)pp.364-373
  • Kazanis, Ilias; Lathia, Justin D; Vadakkan, Tegy J; Raborn, Eric; Wan, Ruiqian; Mughal, Mohamed R; Eckley, D Mark; Sasaki, Takako; Patton, Bruce; Mattson, Mark P; Quiescence and activation of stem and precursor cell populations in the subependymal zone of the mammalian brain are associated with distinct cellular and extracellular matrix signals Journal of Neuroscience (2010) v:30(29)pp.9771-9781
  • Shamir, Lior; Ling, Shari M; Scott Jr, William W; Bos, Angelo; Orlov, Nikita; Macura, Tomasz J; Eckley, D Mark; Ferrucci, Luigi; Goldberg, Ilya G; Knee X-ray image analysis method for automated detection of Osteoarthritis. IEEE Transactions on Biomedical Engineering (2009) v:56(2)pp.407-415
  • Orlov, Nikita; Shamir, Lior; Macura, Tomasz; Johnston, Josiah; Eckley, D Mark; Goldberg, Ilya G; WND-CHARM: Multi-purpose image classification using compound image transforms
  • Pattern recognition letters (2008) v:29(11)pp.1684-1693
  • Warren, Cheryl D; Eckley, D Mark; Lee, Marina S; Hanna, Joseph S; Hughes, Adam; Peyser, Brian; Jie, Chunfa; Irizarry, Rafael; Spencer, Forrest A; S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion Molecular biology of the cell (2004) v:15(4)pp.1724-1735
  • Eckley, D Mark; Schroer, Trina A; Interactions between the evolutionarily conserved, actin-related protein, Arp11, actin, and Arp1 Molecular biology of the cell (2003) v:14(7)pp.2645-2654
  • Salina, Davide; Bodoor, Khaldon; Eckley, D Mark; Schroer, Trina A; Rattner, JB; Burke, Brian; Cytoplasmic dynein as a facilitator of nuclear envelope breakdown Cell (2002) v:108(1)pp.97-107
  • Eckley, D Mark; Gill, Steven R; Melkonian, Karin A; Bingham, James B; Goodson, Holly V; Heuser, John E; Schroer, Trina A; Analysis of dynactin subcomplexes reveals a novel actin-related protein associated with the arp1 minifilament pointed end The Journal of cell biology (1999) v:147(2)pp.307-320
  • Eckley, D Mark; Ainsztein, Alexandra M; Mackay, Alastair M; Goldberg, Ilya G; Earnshaw, William C; Chromosomal proteins and cytokinesis: patterns of cleavage furrow formation and inner centromere protein positioning in mitotic heterokaryons and mid-anaphase cells. The Journal of cell biology (1997) v:136(6)pp.1169-1183.

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