| 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 | 1566 | 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 | 458 | 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 | 352 | 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 | 306 | 2012 |
| 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 | 181 | 2019 |
| 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 | 152 | 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 | 149 | 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 | 112 | 2018 |
| 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 | 98 | 2017 |
| 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 | 92 | 2012 |
| 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 | 89 | 2020 |
| 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 | 87 | 2014 |
| Software tools for visualizing Hi-C data GG Yardımcı, WS Noble Genome biology 18, 1-9, 2017 | 76 | 2017 |
| High-content single-cell combinatorial indexing RM Mulqueen, D Pokholok, BL O’Connell, CA Thornton, F Zhang, ... Nature biotechnology 39 (12), 1574-1580, 2021 | 72 | 2021 |
| Unsupervised embedding of single-cell Hi-C data L Jie, D Lin, G Yardımcı, Galip, S Noble, William Bioinformatics 34 (13), i96–i104, 2018 | 72 | 2018 |
| 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 | 54 | 2013 |
| 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 | 41 | 2023 |
| 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 | 41 | 2019 |
| 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 | 36 | 2022 |
| Multicenter integrated analysis of noncoding CRISPRi screens D Yao, J Tycko, JW Oh, LR Bounds, SJ Gosai, L Lataniotis, ... Nature methods 21 (4), 723-734, 2024 | 28 | 2024 |