Research

My publications are listed below, or you can visit my Google Scholar profile.

Submitted

  • “Interference generates type I and type II errors in isobaric multiplexed quantitative proteomics.”  Amanda L Edwards, Matthew D Edwards, David K Gifford, Wilhelm Haas (2016).

Preprints

  • “Accurate eQTL prioritization with an ensemble-based framework.”  Haoyang Zeng, Matthew D Edwards, Yuchun Guo, David K Gifford (2016). [link] [code]

Articles

  • “Convolutional neural network architectures for predicting DNA-protein binding.”  Haoyang Zeng, Matthew D Edwards, Ge Liu, David K Gifford.  Bioinformatics (2016). [link] [code]
  • “High-throughput mapping of regulatory DNA.”  Nisha Rajagopal, Sharanya Srinivasan, Kameron Kooshesh, Yuchun Guo, Matthew D Edwards, Budhaditya Banerjee, Tahin Syed, Bart JM Emons, David K Gifford, and Richard I Sherwood.  Nature Biotechnology (2016). [link] [press]
  • “Interactions between chromosomal and nonchromosomal elements reveal missing heritability.”  Matthew D Edwards, Anna Symbor-Nagrabska, Lindsey Dollard, David K Gifford, and Gerald R Fink.  Proceedings of the National Academy of Sciences (2014). [link] [press]
  • “An integrated model of multiple-condition ChIP-seq data reveals predeterminants of Cdx2 binding.”  Shaun Mahony*, Matthew D Edwards*, Esteban O Mazzoni, Richard I Sherwood, Akshay Kakumanu, Carolyn A Morrison, Hynek Wichterle, and David K Gifford.  PLoS Computational Biology (2014). [link] [code]
  • “Universal count correction for high-throughput sequencing.”  Tatsunori B Hashimoto, Matthew D Edwards, and David K Gifford.  PLoS Computational Biology (2014). [link] [code]
  • “High-resolution genetic mapping with pooled sequencing.”  Matthew D Edwards and David K Gifford.  BMC Bioinformatics (2012). [link] [code]
  • “An integrated semiconductor device enabling non-optical genome sequencing.”  Jonathan M Rothberg, Wolfgang Hinz, Todd M Rearick, Jonathan Schultz, William Mileski, Mel Davey, John H Leamon, Kim Johnson, Mark J Milgrew, Matthew Edwards, Jeremy Hoon, Jan F Simons, David Marran, Jason W Myers, John F Davidson, Annika Branting, John R Nobile, Bernard P Puc, David Light, Travis A Clark, Martin Huber, Jeffrey T Branciforte, Isaac B Stoner, Simon E Cawley, Michael Lyons, Yutao Fu, Nils Homer, Marina Sedova, Xin Miao, Brian Reed, Jeffrey Sabina, Erika Feierstein, Michelle Schorn, Mohammad Alanjary, Eileen Dimalanta, Devin Dressman, Rachel Kasinskas, Tanya Sokolsky, Jacqueline A Fidanza, Eugeni Namsaraev, Kevin J McKernan, Alan Williams, G Thomas Roth, James Bustillo.  Nature (2011). [link] [press]

* Equal contribution.

Theses

  • “Information-sharing models for computational genetics.” MIT PhD thesis (2016). [link]
  • “Computational methods for high-throughput pooled genetic experiments.”  MIT SM thesis (2011).  [link]
  • “Data-driven extensions to Gibbs sampling for motif discovery.” Duke BS thesis (2008).  [link]

Other writing (projects and notes)

  • “Approximation algorithms for genomic structural variant detection.” Course project for Advanced Algorithms (6.854) (2009).  [link]
  • “Identification and characterization of regulatory evolution in yeast.” Course project for Advanced Computational Biology (6.878) (2009).  [link]
  • “SeqDB: a relational system for high-throughput biology.” With Adrian Dalca, project for Database Systems (6.830) (2010).  [link]