On Learning Bounded-Width Branching Programs. - Funda Ergün; Ravi Kumar 001; Ronitt Rubinfeld (COLT, 1995)

Testing multivariate linear functions: overcoming the generator bottleneck. - Funda Ergün (STOC, 1995)

Approximate Checking of Polynomials and Functional Equations (extended abstract). - Funda Ergün; Ravi Kumar 001; Ronitt Rubinfeld (FOCS, 1996)

Learning Distributions from Random Walks. - Funda Ergün; Ravi Kumar 001; Ronitt Rubinfeld (COLT, 1997)

Checking Properties of Polynomials (Extended Abstract). - Bruno Codenotti; Funda Ergün; Peter Gemmell; Ravi Kumar 001 (ICALP, 1997)

A Note on the Limits of Collusion-Resistant Watermarks. - Funda Ergün; Joe Kilian; Ravi Kumar 001 (EUROCRYPT, 1999)

Fast Approximate PCPs. - Funda Ergün; Ravi Kumar 001; Ronitt Rubinfeld (STOC, 1999)

QoS Routing with Performance-Dependent Costs. - Funda Ergün; Rakesh K. Sinha; Lisa Zhang (INFOCOM, 2000)

Spot-Checkers. - Funda Ergün; Sampath Kannan; Ravi Kumar 001; Ronitt Rubinfeld; Mahesh Viswanathan 001 (J. Comput. Syst. Sci., 2000)

Self-Testing without the Generator Bottleneck. - Funda Ergün; Ravi Kumar 001; D. Sivakumar 001 (SIAM J. Comput., 2000)

Biased Skip Lists for Highly Skewed Access Patterns. - Funda Ergün; Süleyman Cenk Sahinalp; Jonathan Sharp; Rakesh K. Sinha (ALENEX, 2001)

A Dynamic Lookup Scheme for Bursty Access Patterns. - Funda Ergün; Suvo Mittra; Süleyman Cenk Sahinalp; Jonathan Sharp; Rakesh K. Sinha (INFOCOM, 2001)

Biased dictionaries with fast insert/deletes. - Funda Ergün; Süleyman Cenk Sahinalp; Jonathan Sharp; Rakesh K. Sinha (STOC, 2001)

Checking Approximate Computations of Polynomials and Functional Equations. - Funda Ergün; Ravi Kumar 001; Ronitt Rubinfeld (SIAM J. Comput., 2001)

Statistical Identification of Uniformly Mutated Segments within Repeats. - Süleyman Cenk Sahinalp; Evan E. Eichler; Paul W. Goldberg; Petra Berenbrink; Tom Friedetzky; Funda Ergün (CPM, 2002)

An improved FPTAS for Restricted Shortest Path. - Funda Ergün; Rakesh K. Sinha; Lisa Zhang (Inf. Process. Lett., 2002)

Comparing Sequences with Segment Rearrangements. - Funda Ergün; S. Muthukrishnan 001; Süleyman Cenk Sahinalp (FSTTCS, 2003)

Sublinear-time approximation of Euclidean minimum spanning tree. - Artur Czumaj; Funda Ergün; Lance Fortnow; Avner Magen; Ilan Newman; Ronitt Rubinfeld; Christian Sohler (SODA, 2003)

A sublinear algorithm for weakly approximating edit distance. - Tugkan Batu; Funda Ergün; Joe Kilian; Avner Magen; Sofya Raskhodnikova; Ronitt Rubinfeld; Rahul Sami (STOC, 2003)

Sublinear Methods for Detecting Periodic Trends in Data Streams. - Funda Ergün; S. Muthukrishnan 001; Süleyman Cenk Sahinalp (LATIN, 2004)

Fast approximate probabilistically checkable proofs. - Funda Ergün; Ravi Kumar 001; Ronitt Rubinfeld (Inf. Comput., 2004)

Identifying Uniformly Mutated Segments within Repeats. - Süleyman Cenk Sahinalp; Evan E. Eichler; Paul W. Goldberg; Petra Berenbrink; Tom Friedetzky; Funda Ergün (J. Bioinform. Comput. Biol., 2004)

Finding Frequent Patterns in a String in Sublinear Time. - Petra Berenbrink; Funda Ergün; Tom Friedetzky (ESA, 2005)

Unicast and Multicast QoS Routing with Multiple Constraints. - Dan Wang 002; Funda Ergün; Zhan Xu (QoS-IP, 2005)

Path Protection with Pre-identification for MPLS Networks. - Dan Wang 002; Funda Ergün (QSHINE, 2005)

A layered architecture for delay sensitive sensor networks. - Dan Wang 002; Yan Long; Funda Ergün (SECON, 2005)

Approximating the Weight of the Euclidean Minimum Spanning Tree in Sublinear Time. - Artur Czumaj; Funda Ergün; Lance Fortnow; Avner Magen; Ilan Newman; Ronitt Rubinfeld; Christian Sohler (SIAM J. Comput., 2005)

Oblivious string embeddings and edit distance approximations. - Tugkan Batu; Funda Ergün; Süleyman Cenk Sahinalp (SODA, 2006)

On distance to monotonicity and longest increasing subsequence of a data stream. - Funda Ergün; Hossein Jowhari (SODA, 2008)

Periodicity in Streams. - Funda Ergün; Hossein Jowhari; Mert Saglam (APPROX-RANDOM, 2010)

Periodicity testing with sublinear samples and space. - Funda Ergün; S. Muthukrishnan 001; Süleyman Cenk Sahinalp (ACM Trans. Algorithms, 2010)

Network design for tolerating multiple link failures using Fast Re-route (FRR). - Rakesh K. Sinha; Funda Ergün; Kostas N. Oikonomou; K. K. Ramakrishnan (DRCN, 2014)

Online load balancing for MapReduce with skewed data input. - Yanfang Le; Jiangchuan Liu; Funda Ergün; Dan Wang 002 (INFOCOM, 2014)

Palindrome Recognition In The Streaming Model. - Petra Berenbrink; Funda Ergün; Frederik Mallmann-Trenn; Erfan Sadeqi Azer (STACS, 2014)

On Datacenter-Network-Aware Load Balancing in MapReduce. - Yanfang Le; Feng Wang 001; Jiangchuan Liu; Funda Ergün (CLOUD, 2015)

On the monotonicity of a data stream. - Funda Ergün; Hossein Jowhari (Comb., 2015)

Streaming Periodicity with Mismatches. - Funda Ergün; Elena Grigorescu; Erfan Sadeqi Azer; Samson Zhou (APPROX-RANDOM, 2017)

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. - Erfan Sadeqi Azer; Farid Rashidi Mehrabadi; Salem Malikic; Xuan Cindy Li; Osnat Bartok; Kevin Litchfield; Ronen Levy; Yardena Samuels; Alejandro A. Schäffer; E. Michael Gertz; Chi-Ping Day; Eva Pérez-Guijarro; et al. (Bioinform., 2020)

Periodicity in Data Streams with Wildcards. - Funda Ergün; Elena Grigorescu; Erfan Sadeqi Azer; Samson Zhou (Theory Comput. Syst., 2020)

Fast intratumor heterogeneity inference from single-cell sequencing data. - Can Kizilkale; Farid Rashidi Mehrabadi; Erfan Sadeqi Azer; Eva Pérez-Guijarro; Kerrie Marie; Maxwell P. Lee; Chi-Ping Day; Glenn Merlino; Funda Ergün; Aydin Buluç; Süleyman Cenk Sahinalp; Salem Malikic (Nat. Comput. Sci., 2022)

A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data. - Farid Rashidi Mehrabadi; Erfan Sadeqi Azer; John D. Bridgers; Eva Pérez-Guijarro; Kerrie Marie; Howard H. Yang; Charli Gruen; Chih Hao Wu; Welles Robinson; Huaitian Liu; Can Kizilkale; Michael C. Kelly; et al. (RECOMB, 2025)

Improved Algorithms for Bi-Partition Function Computation. - John D. Bridgers; Jan Hoinka; S. Cenk Sahinalp; Salem Malikic; Teresa M. Przytycka; Funda Ergün (WABI, 2025)