Funda Ergün

Indiana University Bloomington — United States

Computer Science · Physical Sciences

20h-index1.2kcitations53works0.52yr avg
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Research Topics

Algorithms and Data Compression(21), Complexity and Algorithms in Graphs(19), Machine Learning and Algorithms(16), Cryptography and Data Security(6), semigroups and automata theory(6)

Publications53 total

Shared memory consensus on a ring: Epigenetic Consensus
2025
A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data
Lecture notes in computer science·2025· 1 cited
Fast intratumor heterogeneity inference from single-cell sequencing data
Nature Computational Science·2022· 14 citedOpen Access
Abstract LB019: Trisicell: Scalable Tumor Phylogeny Reconstruction and Validation Reveals Developmental Origin and Therapeutic Impact of Intratumoral Heterogeneity
Cancer Research·2021
PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem
Bioinformatics·2020· 23 citedOpen Access
PhISCS-BnB: A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem
2020· 2 citedOpen Access
Periodicity in Data Streams with Wildcards
Theory of Computing Systems·2019· 2 cited
Periodicity in Data Streams with Wildcards
arXiv (Cornell University)·2018· 1 citedOpen Access
Periodicity in Data Streams with Wildcards
Lecture notes in computer science·2018· 4 cited
Streaming Periodicity with Mismatches
arXiv (Cornell University)·2017· 4 citedOpen Access
On Datacenter-Network-Aware Load Balancing in MapReduce
2015· 3 cited
On the monotonicity of a data stream
COMBINATORICA·2014· 5 cited
Online load balancing for MapReduce with skewed data input
2014· 56 cited
Network design for tolerating multiple link failures using Fast Re-route (FRR)
2014· 16 cited
Palindrome Recognition In The Streaming Model
DROPS (Schloss Dagstuhl – Leibniz Center for Informatics)·2014· 3 citedOpen Access
Palindrome Recognition In The Streaming Model
arXiv (Cornell University)·2013· 1 citedOpen Access
Periodicity testing with sublinear samples and space
ACM Transactions on Algorithms·2010· 4 cited
Periodicity in Streams
Lecture notes in computer science·2010· 35 cited
On distance to monotonicity and longest increasing subsequence of a data stream
Symposium on Discrete Algorithms·2008· 30 cited
Statistical Identification Of Uniformly Mutated Segments within Repeats
2007
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Frequent Co-authors

Ronitt Rubinfeld(12), Erfan Sadeqi Azer(11), S. Cenk Şahinalp(8), S. Ravi Kumar(6), Farid Rashidi Mehrabadi(5), Salem Malikić(5), Chi‐Ping Day(5), Eva Pérez‐Guijarro(5), Kerrie L. Marie(5), Maxwell P. Lee(5), Glenn Merlino(5), Petra Berenbrink(5), Tuğkan Batu(4), Avner Magen(4), Rakesh Sinha(4), Elena Grigorescu(4), Samson Zhou(4), Joe Kilian(3), Cenk Sahinalp(3), Dan Wang(3)