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Genetics

D-Index
118
Citations
86339
World Ranking
398
National Ranking
204

Overview

John Quackenbush is affiliated with Harvard University in the United States. Their research primarily spans the broad field of Biochemistry, Genetics, and Molecular Biology, with a particular focus on Molecular Biology. Additional areas of study include Pulmonary and Respiratory Medicine, Genetics, Cancer Research, and Statistical and Nonlinear Physics.

The scientist's work addresses several main topics, especially Bioinformatics and Genomic Networks, Gene expression and cancer classification, and Gene Regulatory Network Analysis. Other topics covered include Genomics and Chromatin Dynamics, Genetic Associations and Epidemiology, RNA modifications and cancer, and Genomics and Phylogenetic Studies.

John Quackenbush has contributed numerous papers to the scientific community. Notable recent publications include:

  • Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues, 2020, published in Cell Reports
  • Transparency and reproducibility in artificial intelligence, 2020, published in Nature
  • Molecular networks in Network Medicine: Development and applications, 2020, published in WIREs Systems Biology and Medicine
  • Genome-Wide Sex and Gender Differences in Cancer, 2020, published in Frontiers in Oncology
  • GRAND: a database of gene regulatory network models across human conditions, 2021, published in Nucleic Acids Research

The scientist collaborates frequently and has several established coauthors, including Marouen Ben Guebila, Camila M. Lopes-Ramos, Kimberly Glass, Dawn L. DeMeo, and Enakshi Saha.

John Quackenbush's research outputs have appeared in a variety of publication venues. The most frequent venues include bioRxiv (Cold Spring Harbor Laboratory), Cancer Research, arXiv (Cornell University), Zenodo (CERN European Organization for Nuclear Research), and Genome Research.

Best Publications

  • Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

    Joel S. Parker;Michael Mullins;Maggie C.U. Cheang;Samuel Leung

  • TM4: a free, open-source system for microarray data management and analysis.

    A.I. Saeed;V. Sharov;J. White;J. Li

  • Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

    Alvis Brazma;Pascal Hingamp;John Quackenbush;Gavin Sherlock

  • The complete genome sequence of the gastric pathogen Helicobacter pylori

    Jean-F. Tomb;Owen White;Anthony R. Kerlavage;Rebecca A. Clayton

  • The Transcriptional Landscape of the Mammalian Genome

    P. Carninci;T. Kasukawa;S. Katayama;J. Gough

  • Microarray data normalization and transformation

    John Quackenbush

  • Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi

    Claire M. Fraser;Sherwood Casjens;Wai Mun Huang;Granger G. Sutton

  • COMPUTATIONAL ANALYSIS OF MICROARRAY DATA

    John Quackenbush

  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

    Y. Okazaki;M. Furuno;T. Kasukawa;J. Adachi

  • Genesis: cluster analysis of microarray data

    Alexander Sturn;John Quackenbush;Zlatko Trajanoski

  • TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets

    Geo Pertea;Xiaoqiu Huang;Feng Liang;Valentin Antonescu

  • TM4 microarray software suite

    Alexander I. Saeed;Nirmal K. Bhagabati;John C. Braisted;Wei Liang

  • The molecular portraits of breast tumors are conserved across microarray platforms

    Zhiyuan Hu;Cheng Fan;Daniel S Oh;JS Marron

  • The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

    Hans-Peter Klenk;Rebecca A. Clayton;Jean-Francois Tomb;Owen White

  • Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors

    Jason I Herschkowitz;Karl Simin;Victor J Weigman;Igor Mikaelian

  • A Concise Guide to cDNA Microarray Analysis

    P. Hegde;R. Qi;K. Abernathy

  • A gene map of the human genome

    G. D. Schuler;M. S. Boguski;E. A. Stewart;L. D. Stein

  • Multiple-laboratory comparison of microarray platforms

    Rafael A Irizarry;Daniel Warren;Forrest Spencer;Irene F Kim

  • Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

    Jane M. Carlton;Samuel V. Angiuoli;Bernard B. Suh;Taco W. Kooij

  • Department of Pathology, Thom as Jeffe rson University, Identific ation of conserved gene expression features between murine mammary carcinoma models and human breast tumors.

    Jason I Herschkowitz;Karl Simin;Victor J Weigman;Igor Mikaelian

Frequent Co-Authors

Benjamin Haibe-Kains
Benjamin Haibe-Kains Princess Margaret Cancer Centre
David A. Schwartz
David A. Schwartz University of Colorado Denver
Dawn L. DeMeo
Dawn L. DeMeo Brigham and Women's Hospital
Naftali Kaminski
Naftali Kaminski Yale University
Hugo J.W.L. Aerts
Hugo J.W.L. Aerts Brigham and Women's Hospital
Aedín C. Culhane
Aedín C. Culhane University of Limerick
Avrum Spira
Avrum Spira Boston University
Frank C. Sciurba
Frank C. Sciurba University of Pittsburgh
Ivana V. Yang
Ivana V. Yang University of Colorado Denver
Edwin K. Silverman
Edwin K. Silverman Brigham and Women's Hospital

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