World's Best Scientists 2026 revealed!

D-Index & Metrics

Computer Science

D-Index
39
Citations
25162
World Ranking
9459
National Ranking
4001

Research.com Recognitions

  • 2012 - Fellow of Alfred P. Sloan Foundation

Overview

Carl Kingsford is affiliated with Carnegie Mellon University in the United States. Their research spans the fields of Biochemistry, Genetics and Molecular Biology as well as Computer Science, with a focus on several associated subfields including Molecular Biology, Artificial Intelligence, Computational Theory and Mathematics, Genetics, and Plant Science.

The main topics of their work include:

  • Genomics and Phylogenetic Studies
  • Algorithms and Data Compression
  • Genomics and Chromatin Dynamics
  • RNA and protein synthesis mechanisms
  • Molecular Biology Techniques and Applications
  • Advanced biosensing and bioanalysis techniques
  • Gene expression and cancer classification

Frequent publication venues for Kingsford's research are:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Journal of Computational Biology
  • Bioinformatics
  • Algorithms for Molecular Biology
  • Journal of Clinical Oncology

Recent papers authored or co-authored by Kingsford include:

  • "Alignment and mapping methodology influence transcript abundance estimation," 2020, Genome biology
  • "Improved design and analysis of practical minimizers," 2020, Bioinformatics
  • "Sequence-specific minimizers via polar sets," 2021, Bioinformatics
  • "Creating and Using Minimizer Sketches in Computational Genomics," 2023, Journal of Computational Biology
  • "Constructing small genome graphs via string compression," 2021, Bioinformatics

The scientist has collaborated frequently with colleagues including Guillaume Marçais, Hongyu Zheng, Yutong Qiu, Minh Hoang, and Rob Patro.

Kingsford has received recognition in the form of awards such as the Fellow of Alfred P. Sloan Foundation in 2012.

Best Publications

  • Salmon provides fast and bias-aware quantification of transcript expression

    Rob Patro;Geet Duggal;Michael I Love;Rafael A Irizarry

  • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

    Guillaume Marçais;Carl Kingsford

  • Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

    Robert Patro;Stephen M. Mount;Carl Kingsford

  • What are decision trees

    Carl Kingsford;Steven L Salzberg

  • Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms

    Rob Patro;Stephen M. Mount;Carl Kingsford

  • Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

    Carleton L Kingsford;Kunmi Ayanbule;Steven L Salzberg

  • The power of protein interaction networks for associating genes with diseases

    Saket Navlakha;Carl Kingsford

  • Identification of alternative topological domains in chromatin

    Darya Filippova;Robert Patro;Geet Duggal;Carl Kingsford

  • Global network alignment using multiscale spectral signatures

    Rob Patro;Carl Kingsford

  • Accurate assembly of transcripts through phase-preserving graph decomposition.

    Mingfu Shao;Carl Kingsford

  • The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

    Michael P. Snyder;Shin Lin

  • Alignment and mapping methodology influence transcript abundance estimation.

    Avi Srivastava;Laraib Malik;Hirak Sarkar;Mohsen Zakeri

  • Assembly complexity of prokaryotic genomes using short reads

    Carl Kingsford;Michael C Schatz;Mihai Pop

  • Fast search of thousands of short-read sequencing experiments

    Brad Solomon;Carl Kingsford

  • Network archaeology: uncovering ancient networks from present-day interactions.

    Saket Navlakha;Carl Kingsford

  • Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

    James Robert White;Saket Navlakha;Niranjan Nagarajan;Mohammadreza Ghodsi

  • A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies

    Bernard Chazelle;Carl Kingsford;Mona Singh

  • GiRaF: robust, computational identification of influenza reassortments via graph mining

    Niranjan Nagarajan;Carl Kingsford

  • Revealing biological modules via graph summarization.

    Saket Navlakha;Michael C. Schatz;Carl Kingsford

  • Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

    Heewook Lee;Carl Kingsford

  • Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability

    John H. Reif;Thomas H. LaBean;Michael Pirrung;Vipul S. Rana

Frequent Co-Authors

Niranjan Nagarajan
Niranjan Nagarajan Genome Institute of Singapore
Mihai Pop
Mihai Pop University of Maryland, College Park
Steven L. Salzberg
Steven L. Salzberg Johns Hopkins University
Ron Shamir
Ron Shamir Tel Aviv University
Maria-Florina Balcan
Maria-Florina Balcan Carnegie Mellon University
Tuomas Sandholm
Tuomas Sandholm Carnegie Mellon University
Sridhar Hannenhalli
Sridhar Hannenhalli National Institutes of Health
James R. White
James R. White Johns Hopkins University School of Medicine
Can Alkan
Can Alkan Bilkent University
Michael C. Schatz
Michael C. Schatz Johns Hopkins University

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