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D-Index & Metrics

Biology and Biochemistry

D-Index
53
Citations
17618
World Ranking
15919
National Ranking
552

Overview

Philip M. Kim is affiliated with the University of Toronto in Canada. Their research primarily spans the broad discipline of Biochemistry, Genetics and Molecular Biology, with a significant focus on Molecular Biology. Additional subfields include Radiology, Nuclear Medicine and Imaging, Computational Theory and Mathematics, Materials Chemistry, and Artificial Intelligence.

The scientist's research covers an array of interconnected topics, which include:

  • Protein Structure and Dynamics
  • RNA and protein synthesis mechanisms
  • Machine Learning in Bioinformatics
  • Monoclonal and Polyclonal Antibodies Research
  • Chemical Synthesis and Analysis
  • Computational Drug Discovery Methods
  • Genomics and Phylogenetic Studies

Philip M. Kim has contributed to publications in multiple venues, with frequent appearances in:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Bioinformatics
  • Nature Biotechnology
  • Nature Computational Science
  • Journal of Medicinal Chemistry

Significant recent papers authored or coauthored by the scientist include:

  • Fast and Flexible Protein Design Using Deep Graph Neural Networks, 2020, Cell Systems
  • Computational and artificial intelligence-based methods for antibody development, 2023, Trends in Pharmacological Sciences
  • A universal deep-learning model for zinc finger design enables transcription factor reprogramming, 2023, Nature Biotechnology
  • PepNN: a deep attention model for the identification of peptide binding sites, 2022, Communications Biology
  • Score-based generative modeling for de novo protein design, 2023, Nature Computational Science

The collaboration network of Philip M. Kim includes frequent coauthors:

  • Pedro A. Valiente
  • Osama Abdin
  • Satra Nim
  • Alexey Strokach
  • Carles Corbi-Verge

Best Publications

  • The genetic landscape of a cell.

    Michael Costanzo;Anastasia Baryshnikova;Jeremy Bellay;Yungil Kim

  • Classification of intrinsically disordered regions and proteins.

    Robin van der Lee;Robin van der Lee;Marija Buljan;Benjamin Lang;Robert J. Weatheritt

  • Paired-end mapping reveals extensive structural variation in the human genome.

    Jan O. Korbel;Alexander Eckehart Urban;Jason P. Affourtit;Brian Godwin

  • The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

    Nuno L. Barbosa-Morais;Nuno L. Barbosa-Morais;Manuel Irimia;Qun Pan;Hui Y. Xiong

  • The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.

    Haiyuan Yu;Philip M Kim;Emmett Sprecher;Valery Trifonov

  • Relating three-dimensional structures to protein networks provides evolutionary insights.

    Philip M. Kim;Long J. Lu;Yu Xia;Mark B. Gerstein

  • Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

    Jonathan D. Ellis;Miriam Barrios-Rodiles;Recep Çolak;Manuel Irimia

  • Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs

    Janine Mok;Philip M. Kim;Philip M. Kim;Hugo Y.K. Lam;Stacy Piccirillo

  • C2H2 zinc finger proteins greatly expand the human regulatory lexicon

    Hamed S Najafabadi;Sanie Mnaimneh;Frank W Schmitges;Michael Garton

  • Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data

    Philip M. Kim;Bruce Tidor

  • The role of disorder in interaction networks: a structural analysis

    Philip M Kim;Andrea Sboner;Yu Xia;Mark Gerstein

  • Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

    Hugo Y K Lam;Xinmeng Jasmine Mu;Adrian M Stütz;Andrea Tanzer

  • Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

    Raffi Tonikian;Xiaofeng Xin;Christopher P. Toret;David Gfeller

  • Fast and Flexible Protein Design Using Deep Graph Neural Networks

    Alexey Strokach;David Becerra;Carles Corbi-Verge;Albert Perez-Riba

  • Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

    Philip M. Kim;Hugo Y.K. Lam;Alexander E. Urban;Jan O. Korbel

  • Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.

    Philip M. Kim;Jan O. Korbel;Mark B. Gerstein

  • Bringing order to protein disorder through comparative genomics and genetic interactions

    Jeremy Bellay;Sangjo Han;Magali Michaut;Tae Hyung Kim

  • Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

    Ylva Ivarsson;Roland Arnold;Megan McLaughlin;Satra Nim

  • Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing

    Andreas Ernst;David Gfeller;Zhengyan Kan;Somasekar Seshagiri

  • Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli

    Mohan Babu;Roland Arnold;Cedoljub Bundalovic-Torma;Alla Gagarinova

Frequent Co-Authors

Mark Gerstein
Mark Gerstein Yale University
Sachdev S. Sidhu
Sachdev S. Sidhu University of Waterloo
Michael Snyder
Michael Snyder Stanford University
Kevin Y. Yip
Kevin Y. Yip Chinese University of Hong Kong
Gary D. Bader
Gary D. Bader University of Toronto
Charles Boone
Charles Boone University of Toronto
Jan O. Korbel
Jan O. Korbel European Molecular Biology Laboratory
Brenda J. Andrews
Brenda J. Andrews University of Toronto
Jason Moffat
Jason Moffat University of Toronto
Chad L. Myers
Chad L. Myers University of Minnesota

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