Galip Gürkan Yardımcı
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Expanded encyclopaedias of DNA elements in the human and mouse genomes
JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ...
Nature 583 (7818), 699-710, 2020
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
T Yang, F Zhang, GG Yardımcı, F Song, RC Hardison, WS Noble, F Yue, ...
Genome research 27 (11), 1939-1949, 2017
Integrative detection and analysis of structural variation in cancer genomes
JR Dixon, J Xu, V Dileep, Y Zhan, F Song, VT Le, GG Yardımcı, ...
Nature genetics 50 (10), 1388-1398, 2018
Predicting cell-type–specific gene expression from regions of open chromatin
A Natarajan, GG Yardımcı, NC Sheffield, GE Crawford, U Ohler
Genome research 22 (9), 1711-1722, 2012
Transcriptional control of tissue formation throughout root development
MA Moreno-Risueno, R Sozzani, GG Yardımcı, JJ Petricka, T Vernoux, ...
Science 350 (6259), 426-430, 2015
Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory
A Bertero, PA Fields, V Ramani, G Bonora, GG Yardimci, H Reinecke, ...
Nature communications 10 (1), 1538, 2019
Measuring the reproducibility and quality of Hi-C data
GG Yardımcı, H Ozadam, MEG Sauria, O Ursu, KK Yan, T Yang, ...
Genome biology 20, 1-19, 2019
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs
O Ursu, N Boley, M Taranova, YXR Wang, GG Yardimci, W Stafford Noble, ...
Bioinformatics 34 (16), 2701-2707, 2018
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
AK Tewari, GG Yardimci, Y Shibata, NC Sheffield, L Song, BS Taylor, ...
Genome biology 13, 1-17, 2012
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection
GG Yardımcı, CL Frank, GE Crawford, U Ohler
Nucleic acids research 42 (19), 11865-11878, 2014
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps
KK Yan, GG Yardımcı, C Yan, WS Noble, M Gerstein
Bioinformatics 33 (14), 2199-2201, 2017
Measuring the reproducibility and quality of Hi-C data
GG Yardimci, H Ozadam, BR Lajoie, Y Zhan, J Dekker, WS Noble
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data
HJ Kim, GG Yardımcı, G Bonora, V Ramani, J Liu, R Qiu, C Lee, J Hesson, ...
PLoS computational biology 16 (9), e1008173, 2020
Software tools for visualizing Hi-C data
GG Yardımcı, WS Noble
Genome biology 18, 1-9, 2017
Unsupervised embedding of single-cell Hi-C data
L Jie, D Lin, G Yardımcı, Galip, S Noble, William
Bioinformatics 34 (13), i96–i104, 2018
High-content single-cell combinatorial indexing
RM Mulqueen, D Pokholok, BL O’Connell, CA Thornton, F Zhang, ...
Nature biotechnology 39 (12), 1574-1580, 2021
Statistical evaluation of the Rodin–Ohno hypothesis: Sense/antisense coding of ancestral Class I and II aminoacyl-tRNA synthetases
SN Chandrasekaran, GG Yardimci, O Erdogan, J Roach, CW Carter Jr
Molecular Biology and Evolution 30 (7), 1588-1604, 2013
Computational methods for analyzing and modeling genome structure and organization
D Lin, G Bonora, GG Yardımcı, WS Noble
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 11 (1), e1435, 2019
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types
V Agarwal, F Inoue, M Schubach, BK Martin, PM Dash, Z Zhang, A Sohota, ...
bioRxiv, 2023
GoPeaks: histone modification peak calling for CUT&Tag
WM Yashar, G Kong, J VanCampen, BM Curtiss, DJ Coleman, L Carbone, ...
Genome biology 23 (1), 144, 2022
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