| Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow H Ma, LC Tu, A Naseri, M Huisman, S Zhang, D Grunwald, T Pederson Nature biotechnology 34 (5), 528-530, 2016 | 488 | 2016 |
| Multicolor CRISPR labeling of chromosomal loci in human cells H Ma, A Naseri, P Reyes-Gutierrez, SA Wolfe, S Zhang, T Pederson Proceedings of the National Academy of Sciences 112 (10), 3002-3007, 2015 | 472 | 2015 |
| CRISPR-Cas9 nuclear dynamics and target recognition in living cells H Ma, LC Tu, A Naseri, M Huisman, S Zhang, D Grunwald, T Pederson Journal of Cell Biology 214 (5), 529-537, 2016 | 208 | 2016 |
| CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging H Ma, LC Tu, A Naseri, YC Chung, D Grunwald, S Zhang, T Pederson Nature methods 15 (11), 928-931, 2018 | 148 | 2018 |
| Epigenetic regulation of microRNA-375 and its role in melanoma development in humans J Mazar, D DeBlasio, SS Govindarajan, S Zhang, RJ Perera FEBS letters 585 (15), 2467-2476, 2011 | 122 | 2011 |
| Netlist reverse engineering for high-level functionality reconstruction T Meade, S Zhang, Y Jin 2016 21st Asia and South Pacific Design Automation Conference (ASP-DAC), 655-660, 2016 | 103 | 2016 |
| Revisit Sequential Logic Obfuscation: Attacks and Defenses T Meade, Z Zhao, S Zhang, D Pan, Y Jin IEEE International Symposium on Circuits and Systems (ISCAS), 2017 | 99 | 2017 |
| Epigenetic regulation of microRNA genes and the role of miR-34b in cell invasion and motility in human melanoma J Mazar, D Khaitan, D DeBlasio, C Zhong, SS Govindarajan, S Kopanathi, ... PloS one 6 (9), e24922, 2011 | 99 | 2011 |
| Cas9 effector-mediated regulation of transcription, differentiation and gene editing/labeling SA Wolfe, H Ma, T Pederson, MSK Enuameh, NA Kearns, RMJ Genga, ... US Patent App. 14/571,818, 2015 | 95 | 2015 |
| Searching genomes for noncoding RNA using FastR S Zhang, B Haas, E Eskin, V Bafna IEEE/ACM Transactions on Computational Biology and Bioinformatics 2 (4), 366-379, 2005 | 76 | 2005 |
| Gate-level netlist reverse engineering for hardware security: Control logic register identification T Meade, Y Jin, M Tehranipoor, S Zhang 2016 IEEE International Symposium on Circuits and Systems (ISCAS), 1334-1337, 2016 | 71 | 2016 |
| RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment C Zhong, H Tang, S Zhang Nucleic acids research 38 (18), e176-e176, 2010 | 64 | 2010 |
| RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts A Naseri, X Liu, K Tang, S Zhang, D Zhi Genome biology 20, 1-15, 2019 | 58 | 2019 |
| A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements S Zhang, I Borovok, Y Aharonowitz, R Sharan, V Bafna Bioinformatics 22 (14), e557-e565, 2006 | 50 | 2006 |
| Consensus folding of unaligned RNA sequences revisited V Bafna, H Tang, S Zhang Research in Computational Molecular Biology: 9th Annual International
, 2005 | 50 | 2005 |
| FIGHT-metric: Functional identification of gate-level hardware trustworthiness D Sullivan, J Biggers, G Zhu, S Zhang, Y Jin Proceedings of the 51st Annual Design Automation Conference, 1-4, 2014 | 49 | 2014 |
| Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription Y Feng, Y Wang, X Wang, X He, C Yang, A Naseri, T Pederson, J Zheng, ... Genome biology 21, 1-24, 2020 | 48 | 2020 |
| FastR: Fast database search tool for non-coding RNA V Bafna, S Zhang Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004
, 2004 | 47 | 2004 |
| Cell cycleand genomic distancedependent dynamics of a discrete chromosomal region H Ma, LC Tu, YC Chung, A Naseri, D Grunwald, S Zhang, T Pederson Journal of Cell Biology 218 (5), 1467-1477, 2019 | 46 | 2019 |
| Structural alignment of pseudoknotted RNA B Han, B Dost, V Bafna, S Zhang Journal of Computational Biology 15 (5), 489-504, 2008 | 45 | 2008 |
