Samantha J. Riesenfeld: academic work

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Publications

^*These authors contributed equally to this work.
^† The order of the authors has no significance. Alphabetical order is typical in theoretical computer science.
^‡ In computer science, conference publications are often more influential than journal publications. Full papers are submitted to conferences for peer review. If accepted, they appear in printed or electronic proceedings and are presented in conference talks. Revised versions may be submitted to journals.

Smith RP^*, Riesenfeld SJ^*, Holloway AK, Murphy KK, Feliciano NM, Orecchia L, Li Q, Pollard KS, Ahituv A. Deciphering the vertebrate regulatory code using short synthetic enhancers in vivo. In prep.
Riesenfeld SJ, Pollard KS. MetaPASSAGE: A Metagenomic Pipeline for Automated Simulations and Analysis of Gene Families. In submission.
Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PHYLOTU: A high-throughput procedure quanitifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Computational Biology, 7(1): e1001061. doi:10.1371/journal.pcbi.1001061
Capra JA, Carbone L, Riesenfeld SJ, Wall JD (2010). Genomics through the lens of next-generation sequencing. Genome Biology, 11:306.
^†‡Daskalakis C, Karp RM, Mossel E, Riesenfeld S, Verbin E (2009). Sorting and selection in posets. SIAM J Comput, 40(3):597–622. Earlier version appears in Proc. Twentieth Annual ACM-SIAM Symp. Discrete Algorithms (SODA09), 2009, 392–401. [Blog post discussing this article.]
^†Chaudhuri K, Rao S, Riesenfeld S, Talwar K (2009). A push-relabel algorithm for approximating the minimum-degree MST problem and its generalization to matroids. Theoretical Computer Science, 410(44):4489–4503. (Invited submission.)
^†Chaudhuri K, Rao S, Riesenfeld S, Talwar K (2009). What would Edmonds do? Augmenting paths and witnesses for degree-bounded MSTs. Algorithmica, 55(1):157–189. (Invited submission.) ^‡Earlier version appears in Proc. 8th Intl. Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX), 2005; 3624/2005:26–39.
Riesenfeld, S (2008). Optimization and reconstruction over graphs. Ph.D. Thesis, Electrical Engineering and Computer Sciences Dept, U.C. Berkeley, CA. Technical Report No. UCB/EECS-2008-6.
^†‡Chaudhuri, K, Rao S, Riesenfeld S, Talwar K (2006). A push-relabel algorithm for approximating degree bounded MSTs. Proc. 33rd Intl. Colloq. on Automata, Languages, and Programming (ICALP), 4051/2006:191–201.
^†‡Bogdanov A, Maneva E, Riesenfeld S (2004). Power-aware base station positioning for sensor networks. Proc. INFOCOM Twenty-third Annual Joint Conf. of the IEEE Computer and Communications Societies; 1:575–585.

Invited Talks and Conference Presentations

Building phylogenies with metagenomic sequence reads. Conference presentation. Biology of Genomes Meeting, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 2010.
Sorting and ranking in partially ordered sets. Invited talk, Bay Area Theory Symposium (BATS), IBM Almaden Research Center, CA, 2006.
^‡A push-relabel algorithm for approximating degree-bounded minimum spanning trees. Conference presentation, ICALP, Venice, Italy, 2006.
Inferring reticulate evolution networks from consensus gene trees. Invited talk, Cyberinfrastructure for Phylogenetic Research (CIPRES) Annual All-Hands meeting, San Diego, CA, 2005. ^†Based on manuscript by Karp RM, Riesenfeld S, 2004.
^‡Sensor networks with base stations. Conference presentation, INFOCOM, Hong Kong, 2004.
A probabilistic look at the Schur and van der Waerden numbers. Conference presentation (with Jager A) at MAA/AMS Joint Winter Meetings, Baltimore, MD, 1998. ^†Based on manuscript by Godbole A, Jager A, Riesenfeld S, 1997.