| An integrated encyclopedia of DNA elements in the human genome. EP Consortium. Nature 6 (489), 7414, 2012 | 13857* | 2012 |
| An integrated map of genetic variation from 1,092 human genomes 1000 Genomes Project Consortium Nature 491 (7422), 56, 2012 | 8241 | 2012 |
| Pan-cancer analysis of whole genomes Nature 578 (7793), 82-93, 2020 | 1668* | 2020 |
| Architecture of the human regulatory network derived from ENCODE data MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, ... Nature 489 (7414), 91-100, 2012 | 1642 | 2012 |
| Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel O Delaneau, J Marchini Nature communications 5 (1), 3934, 2014 | 434 | 2014 |
| Integrative annotation of variants from 1092 humans: application to cancer genomics E Khurana, Y Fu, V Colonna, XJ Mu, HM Kang, T Lappalainen, A Sboner, ... Science 342 (6154), 1235587, 2013 | 423 | 2013 |
| AlleleSeq: analysis of allele‐specific expression and binding in a network framework J Rozowsky, A Abyzov, J Wang, P Alves, D Raha, A Harmanci, J Leng, ... Molecular systems biology 7 (1), 522, 2011 | 393 | 2011 |
| Comparative analysis of the transcriptome across distant species MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, ... Nature 512 (7515), 445-448, 2014 | 328 | 2014 |
| Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign AO Harmanci, G Sharma, DH Mathews BMC bioinformatics 8, 1-21, 2007 | 146 | 2007 |
| HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models TTT Nguyen, Y Zhang, E Shang, C Shu, C Torrini, J Zhao, E Bianchetti, ... The Journal of clinical investigation 130 (7), 3699-3716, 2020 | 119 | 2020 |
| CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data A Serin Harmanci, AO Harmanci, X Zhou Nature communications 11 (1), 89, 2020 | 116 | 2020 |
| Passenger mutations in more than 2,500 cancer genomes: overall molecular functional impact and consequences S Kumar, J Warrell, S Li, PD McGillivray, W Meyerson, L Salichos, ... Cell 180 (5), 915-927. e16, 2020 | 114 | 2020 |
| TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences AO Harmanci, G Sharma, DH Mathews BMC bioinformatics 12, 1-22, 2011 | 113 | 2011 |
| An integrative ENCODE resource for cancer genomics J Zhang, D Lee, V Dhiman, P Jiang, J Xu, P McGillivray, H Yang, J Liu, ... Nature communications 11 (1), 3696, 2020 | 106 | 2020 |
| A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals J Chen, J Rozowsky, TR Galeev, A Harmanci, R Kitchen, J Bedford, ... Nature communications 7 (1), 11101, 2016 | 99 | 2016 |
| Quantification of private information leakage from phenotype-genotype data: linking attacks A Harmanci, M Gerstein Nature methods 13 (3), 251-256, 2016 | 99 | 2016 |
| Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression DD Pervouchine, S Djebali, A Breschi, CA Davis, PP Barja, A Dobin, ... Nature communications 6 (1), 5903, 2015 | 89 | 2015 |
| VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment L Habegger, S Balasubramanian, DZ Chen, E Khurana, A Sboner, ... Bioinformatics 28 (17), 2267-2269, 2012 | 84 | 2012 |
| MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework A Harmanci, J Rozowsky, M Gerstein Genome biology 15, 1-15, 2014 | 65 | 2014 |
| PARTS: probabilistic alignment for RNA joinT secondary structure prediction AO Harmanci, G Sharma, DH Mathews Nucleic acids research 36 (7), 2406-2417, 2008 | 61 | 2008 |
