My publications are listed below, or you can visit my Google Scholar profile.
- “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).
- “Accurate eQTL prioritization with an ensemble-based framework.” Haoyang Zeng, Matthew D Edwards, Yuchun Guo, David K Gifford (2016). [link] [code]
- “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.
- “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]