Author

Funda Ergün

Indiana University Bloomington

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioinformatics· 3

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:cell type annotation· 2 Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1 Research Focus:differential expression· 1 Organism:human· 1 Assay:metagenomics· 1 Organism:mouse· 1

Frequent Co-Authors

S. Cenk ŞahinalpiD· 3 shared Alejandro A. SchäfferiD· 2 shared Chi-Ping DayiD· 2 shared Erfan Sadeqi AzeriD· 2 shared Eva Pérez‐GuijarroiD· 2 shared Farid Rashidi MehrabadiiD· 2 shared Glenn T MerlinoiD· 2 shared Kerrie L. MarieiD· 2 shared

Activity by Year

2020-2022 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

S. Cenk ŞahinalpORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Strain Level Microbial Detection and Quantification with Applications to Single Cell Metagenomics

Kaiyuan Zhu, Alejandro A. Schäffer, Welles Robinson, Junyan Xu, Eytan Ruppin, Funda Ergün, Yuzhen Ye, S. Cenk Şahinalp

CAMMiQ improves microbial strain-level detection and quantification in single-cell metagenomics by using combinatorial optimization and doubly-unique substrings, outperforming existing methods in accuracy.

Nature Communications · Oct 28, 2022Peer-reviewedBioinformatics

Profiles of expressed mutations in single cells reveal subclonal expansion patterns and therapeutic impact of intratumor heterogeneity

Farid Rashidi Mehrabadi, Kerrie L. Marie, Eva Pérez‐Guijarro, Salem Malikić, Erfan Sadeqi Azer, Howard H. Yang, Can Kızılkale, Charli Gruen, Welles Robinson, Huaitian Liu, Michael C. Kelly, Christina Marcelus, Sandra Sczerba Burkett, Aydın Buluç, Funda Ergün, , S. Cenk Şahinalp

Trisicell infers subclonal expansion patterns and therapeutic impact of intratumor heterogeneity from scRNAseq data, revealing correlations between mutational composition and tumor aggressiveness.

bioRxiv · Mar 26, 2021 · PreprintBioinformatics

PhISCS-BnB: A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem

Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Salem Malikić, Xuan Cindy Li, Osnat Bartok, Kevin Litchfield, Ronen Levy, Yardena Samuels, Alejandro A. Schäffer, Edward Michael Gertz, Chi‐Ping Day, Eva Pérez‐Guijarro, Kerrie L. Marie, Maxwell P. Lee, Glenn T Merlino, , S. Cenk Şahinalp

PhISCS-BnB computes the most likely perfect tumor phylogeny from single-cell sequencing data, offering optimality guarantees and significant speed improvements over existing methods.

Bioinformatics · Jul 1, 2020Peer-reviewedBioinformatics