Journal and Conference Publications


  1. Integrating Hi-C links with assembly graphs for chromosome-scale assembly
    (With Arang Rhie, Brian P. Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam Phillippy and Sergey Koren): Under Review, available on bioRxiv
    2. [Paper]

  2. A Succinct Four Russians Speedup for Edit Distance Computation and One-against-many Banded Alignment
    (With Brian Brubach): Accepted at Combinatorial Pattern Matching (CPM) 2018 Conference
    3. [Paper]

  3. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
    (with Nathan D. Olson, Todd J. Treangen, Christopher M. Hill, Victoria Cepeda-Espinoza, Sergey Koren and Mihai Pop): Briefings in Bioinformatics
    4. [Paper]

  4. Better Greedy Sequence Clustering with Fast Banded Alignment
    (with Brian Brubach, Aravind Srinivasan and Mihai Pop): Proc. Algorithms in Bioinformatics, WABI-2017
    5. [Paper]

  5. Scaffolding of long read assemblies using long range contact information
    (with Mihai Pop, Sergey Koren, Derek Bickhart and Chen Shan Chin):BMC Genomics
    6. [Link]

  6. Better Identification of Repeats in Metagenomic Scaffolding
    (with Mihai Pop): Proc. Algorithms in Bioinformatics, WABI-2016
    7. [Paper]

  7. Metagenomic Assembly: Overview, Challenges and Applications
    (with Victoria Cepeda-Espinoza and Mihai Pop): Yale Journal of Biology and Medicine
    8. [Link]

  8. A Framework to Model Human Behavior at Large Scale during Natural Disasters
    (with Vanessa Frais-Martinez): 17th IEEE conference on Mobile Data Management 2016
    9. [Paper]

  9. Identifying Inter-Genomic Repeats Using Fast, Approximate Methods for Betweenness Centrality
    (with Chris M. Hill and Mihai Pop): Poster Presentation at ACM-BCB/WABI 2015
    10. [Poster]

Talks


  1. Better Greedy Sequence Clustering with Fast Banded Alignment
    Workshop for Algorithms in Bioinformatics 2017, Boston, USA
    [Slides]

  2. Chromosome Scale De Novo assembly of Mammalian Genomes Using Chromatin Interaction Data
    Invited Talk, Pacbio Bioinformatics Workshop 2017, Baltimore, USA

  3. Chromosome Scale De Novo assembly of Mammalian Genomes Using Chromatin Interaction Data
    Great Lake Bioinformatics Conferene, 2017, Chicago, USA
    [Slides]

  4. Better Identification of Repeats in Metagenomic Scaffolding
    Workshop of Algorithms in Bioinformatics 2016, Aarhus, Denmark
    [Slides]

  5. A Framework to Model Human Behavior at Large Scale during Natural Disasters
    17th IEEE conference on Mobile Data Management, Porto, Portugal
    [Slides]

Code


  1. SALSA: Simple AssembLy ScAffolder
    A scaffolder which uses Hi-C data to scaffold long read assemblies to chromosomes
    [code]