| Evolutionary constraint and innovation across hundreds of placental mammals MJ Christmas, IM Kaplow, DP Genereux, MX Dong, GM Hughes, X Li, ... Science 380 (6643), eabn3943, 2023 | 171 | 2023 |
| Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements J Tycko, M Wainberg, GK Marinov, O Ursu, GT Hess, BK Ego, Aradhana, ... Nature communications 10 (1), 4063, 2019 | 128 | 2019 |
| Population-specific neuromodulation prolongs therapeutic benefits of deep brain stimulation TA Spix, S Nanivadekar, N Toong, IM Kaplow, BR Isett, Y Goksen, ... Science 374 (6564), 201-206, 2021 | 124 | 2021 |
| Integrating gene annotation with orthology inference at scale BM Kirilenko, C Munegowda, E Osipova, D Jebb, V Sharma, M Blumer, ... Science 380 (6643), eabn3107, 2023 | 95 | 2023 |
| A genomic timescale for placental mammal evolution NM Foley, VC Mason, AJ Harris, KR Bredemeyer, J Damas, HA Lewin, ... Science 380 (6643), eabl8189, 2023 | 93 | 2023 |
| Leveraging base-pair mammalian constraint to understand genetic variation and human disease PF Sullivan, JRS Meadows, S Gazal, BDN Phan, X Li, DP Genereux, ... Science 380 (6643), eabn2937, 2023 | 80 | 2023 |
| Fine-mapping cis-regulatory variants in diverse human populations A Tehranchi, B Hie, M Dacre, I Kaplow, K Pettie, P Combs, HB Fraser Elife 8, e39595, 2019 | 76 | 2019 |
| Insights into mammalian TE diversity through the curation of 248 genome assemblies AB Osmanski, NS Paulat, J Korstian, JR Grimshaw, M Halsey, ... Science 380 (6643), eabn1430, 2023 | 66 | 2023 |
| Three-dimensional genome rewiring in loci with human accelerated regions KC Keough, S Whalen, F Inoue, PF Przytycki, T Fair, C Deng, M Steyert, ... Science 380 (6643), eabm1696, 2023 | 63 | 2023 |
| Mammalian evolution of human cis-regulatory elements and transcription factor binding sites G Andrews, K Fan, HE Pratt, N Phalke, Zoonomia Consortium §, ... Science 380 (6643), eabn7930, 2023 | 58 | 2023 |
| The contribution of historical processes to contemporary extinction risk in placental mammals AP Wilder, MA Supple, A Subramanian, A Mudide, R Swofford, ... Science 380 (6643), eabn5856, 2023 | 56 | 2023 |
| Relating enhancer genetic variation across mammals to complex phenotypes using machine learning IM Kaplow, AJ Lawler, DE Schäffer, C Srinivasan, HH Sestili, ME Wirthlin, ... Science 380 (6643), eabm7993, 2023 | 53 | 2023 |
| A pooling-based approach to mapping genetic variants associated with DNA methylation IM Kaplow, JL MacIsaac, SM Mah, LM McEwen, MS Kobor, HB Fraser Genome research 25 (6), 907-917, 2015 | 43 | 2015 |
| The functional and evolutionary impacts of human-specific deletions in conserved elements JR Xue, A Mackay-Smith, K Mouri, MF Garcia, MX Dong, JF Akers, ... Science 380 (6643), eabn2253, 2023 | 39 | 2023 |
| RNAiCut: automated detection of significant genes from functional genomic screens IM Kaplow, R Singh, A Friedman, C Bakal, N Perrimon, B Berger Nature methods 6 (7), 476-477, 2009 | 33 | 2009 |
| A Classifier-based approach to identify genetic similarities between diseases MA Schaub, IM Kaplow, M Sirota, CB Do, AJ Butte, S Batzoglou Bioinformatics 25 (12), i21-i29, 2009 | 29 | 2009 |
| Addiction-associated genetic variants implicate brain cell type-and region-specific cis-regulatory elements in addiction neurobiology C Srinivasan, BDN Phan, AJ Lawler, E Ramamurthy, M Kleyman, ... Journal of Neuroscience 41 (43), 9008-9030, 2021 | 26 | 2021 |
| HALPER facilitates the identification of regulatory element orthologs across species X Zhang, IM Kaplow, M Wirthlin, TY Park, AR Pfenning Bioinformatics 36 (15), 4339-4340, 2020 | 22 | 2020 |
| Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements ME Wirthlin, TA Schmid, JE Elie, X Zhang, A Kowalczyk, R Redlich, ... Science 383 (6690), eabn3263, 2024 | 20 | 2024 |
| Machine learning sequence prioritization for cell type-specific enhancer design AJ Lawler, E Ramamurthy, AR Brown, N Shin, Y Kim, N Toong, IM Kaplow, ... Elife 11, e69571, 2022 | 20 | 2022 |
Andreas R PfenningAssociate Professor, Carnegie Mellon UniversityVerified email at cmu.edu
