Year |
Citation |
Score |
2024 |
Tegtmeyer M, Arora J, Asgari S, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Connor L, et al. High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature Communications. 15: 347. PMID 38184653 DOI: 10.1038/s41467-023-44045-w |
0.781 |
|
2023 |
Serrano E, Chandrasekaran SN, Bunten D, Brewer KI, Tomkinson J, Kern R, Bornholdt M, Fleming S, Pei R, Arevalo J, Tsang H, Rubinetti V, Tromans-Coia C, Becker T, Weisbart E, ... ... Way GP, et al. Reproducible image-based profiling with Pycytominer. Arxiv. PMID 38045474 |
0.524 |
|
2023 |
Davidson NR, Barnard ME, Hippen AA, Campbell A, Johnson C, Way GP, Dalley BK, Berchuck A, Salas LA, Peres LC, Marks JR, Schildkraut JM, Greene CS, Doherty JA. Molecular subtypes of high grade serous ovarian cancer across racial groups and gene expression platforms. Biorxiv : the Preprint Server For Biology. PMID 37961178 DOI: 10.1101/2023.11.01.565179 |
0.542 |
|
2023 |
Carragher NO, Wardwell-Swanson J, Way GP. High-content imaging 2023: A joint special collection with the society for biomolecular imaging. Slas Discovery : Advancing Life Sciences R & D. PMID 37821045 DOI: 10.1016/j.slasd.2023.10.001 |
0.406 |
|
2023 |
Kelley ME, Berman AY, Stirling DR, Cimini BA, Han Y, Singh S, Carpenter AE, Kapoor TM, Way GP. High-content microscopy reveals a morphological signature of bortezomib resistance. Elife. 12. PMID 37753907 DOI: 10.7554/eLife.91362 |
0.762 |
|
2023 |
Way GP, Sailem H, Shave S, Kasprowicz R, Carragher NO. Evolution and impact of high content imaging. Slas Discovery : Advancing Life Sciences R & D. PMID 37666456 DOI: 10.1016/j.slasd.2023.08.009 |
0.464 |
|
2023 |
Ramezani M, Bauman J, Singh A, Weisbart E, Yong J, Lozada M, Way GP, Kavari SL, Diaz C, Haghighi M, Batista TM, Pérez-Schindler J, Claussnitzer M, Singh S, Cimini BA, et al. A genome-wide atlas of human cell morphology. Biorxiv : the Preprint Server For Biology. PMID 37609130 DOI: 10.1101/2023.08.06.552164 |
0.788 |
|
2023 |
Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, Rathi KS, Zhu Y, Egolf LE, Farrow BK, Miller DP, Yang Y, Koganti T, Noureen N, Koptyra MP, ... ... Way GP, et al. OpenPBTA: The Open Pediatric Brain Tumor Atlas. Cell Genomics. 3: 100340. PMID 37492101 DOI: 10.1016/j.xgen.2023.100340 |
0.751 |
|
2023 |
Laber S, Strobel S, Mercader JM, Dashti H, Dos Santos FRC, Kubitz P, Jackson M, Ainbinder A, Honecker J, Agrawal S, Garborcauskas G, Stirling DR, Leong A, Figueroa K, Sinnott-Armstrong N, ... ... Way GP, et al. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. Cell Genomics. 3: 100346. PMID 37492099 DOI: 10.1016/j.xgen.2023.100346 |
0.745 |
|
2022 |
Way GP, Natoli T, Adeboye A, Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban MH, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, et al. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Systems. 13: 911-923.e9. PMID 36395727 DOI: 10.1016/j.cels.2022.10.001 |
0.766 |
|
2022 |
Chow YL, Singh S, Carpenter AE, Way GP. Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. Plos Computational Biology. 18: e1009888. PMID 35213530 DOI: 10.1371/journal.pcbi.1009888 |
0.724 |
|
2022 |
Way GP, Spitzer H, Burnham P, Raj A, Theis F, Singh S, Carpenter AE. Image-based profiling: a powerful and challenging new data type. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27: 407-411. PMID 34890168 |
0.774 |
|
2021 |
Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley S, Gosline SJC, Lȇ Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, et al. A field guide to cultivating computational biology. Plos Biology. 19: e3001419. PMID 34618807 DOI: 10.1371/journal.pbio.3001419 |
0.648 |
|
2021 |
Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM. Sharing biological data: why, when, and how. Febs Letters. 595: 847-863. PMID 33843054 DOI: 10.1002/1873-3468.14067 |
0.301 |
|
2021 |
Way GP, Kost-Alimova M, Shibue T, Harrington WF, Gill S, Piccioni F, Becker T, Shafqat-Abbasi H, Hahn WC, Carpenter AE, Vazquez F, Singh S. Predicting cell health phenotypes using image-based morphology profiling. Molecular Biology of the Cell. mbcE20120784. PMID 33534641 DOI: 10.1091/mbc.E20-12-0784 |
0.775 |
|
2021 |
Cousminer DL, Wagley Y, Pippin JA, Elhakeem A, Way GP, Pahl MC, McCormack SE, Chesi A, Mitchell JA, Kindler JM, Baird D, Hartley A, Howe L, Kalkwarf HJ, Lappe JM, et al. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual. Genome Biology. 22: 1. PMID 33397451 DOI: 10.1186/s13059-020-02207-9 |
0.531 |
|
2020 |
Way GP, Zietz M, Rubinetti V, Himmelstein DS, Greene CS. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations. Genome Biology. 21: 109. PMID 32393369 DOI: 10.1186/S13059-020-02021-3 |
0.765 |
|
2020 |
Upton K, Modi A, Patel K, Kendsersky NM, Conkrite KL, Sussman RT, Way GP, Adams RN, Sacks GI, Fortina P, Diskin SJ, Maris JM, Rokita JL. Epigenomic profiling of neuroblastoma cell lines. Scientific Data. 7: 116. PMID 32286315 DOI: 10.1038/S41597-020-0458-Y |
0.34 |
|
2019 |
Martinez-Lage M, Lynch TM, Bi Y, Cocito C, Way GP, Pal S, Haller J, Yan RE, Ziober A, Nguyen A, Kandpal M, O'Rourke DM, Greenfield JP, Greene CS, Davuluri RV, et al. Immune landscapes associated with different glioblastoma molecular subtypes. Acta Neuropathologica Communications. 7: 203. PMID 31815646 DOI: 10.1186/S40478-019-0803-6 |
0.544 |
|
2019 |
Lin YT, Way GP, Barwick BG, Mariano MC, Marcoulis M, Ferguson ID, Driessen C, Boise LH, Greene CS, Wiita AP. Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma. Blood Advances. 3: 3214-3227. PMID 31698452 DOI: 10.1182/Bloodadvances.2019000303 |
0.561 |
|
2019 |
Rokita JL, Rathi KS, Cardenas MF, Upton KA, Jayaseelan J, Cross KL, Pfeil J, Egolf LE, Way GP, Farrel A, Kendsersky NM, Patel K, Gaonkar KS, Modi A, Berko ER, et al. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Reports. 29: 1675-1689.e9. PMID 31693904 DOI: 10.1016/J.Celrep.2019.09.071 |
0.563 |
|
2019 |
Way GP, Greene CS. Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning Annual Review of Biomedical Data Science. 2: 1-17. DOI: 10.1146/ANNUREV-BIODATASCI-072018-021348 |
0.605 |
|
2018 |
Way GP, Greene CS. Bayesian deep learning for single-cell analysis. Nature Methods. 15: 1009-1010. PMID 30504887 DOI: 10.1038/S41592-018-0230-9 |
0.582 |
|
2018 |
Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS. PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. Biodata Mining. 11: 14. PMID 29988723 DOI: 10.1186/S13040-018-0175-7 |
0.648 |
|
2018 |
Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, ... ... Way GP, et al. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 173: 321-337.e10. PMID 29625050 DOI: 10.1016/J.Cell.2018.03.035 |
0.566 |
|
2018 |
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, et al. Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface. 15. PMID 29618526 DOI: 10.1098/Rsif.2017.0387 |
0.725 |
|
2018 |
Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, et al. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Reports. 23: 239-254.e6. PMID 29617664 DOI: 10.1016/J.Celrep.2018.03.076 |
0.563 |
|
2018 |
Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Reports. 23: 172-180.e3. PMID 29617658 DOI: 10.1016/J.Celrep.2018.03.046 |
0.57 |
|
2018 |
Harrington LX, Way GP, Doherty JA, Greene CS. Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 157-167. PMID 29218878 |
0.571 |
|
2018 |
Way GP, Greene CS. Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 80-91. PMID 29218871 |
0.615 |
|
2017 |
Doherty JA, Peres LC, Wang C, Way GP, Greene CS, Schildkraut JM. Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes. Current Epidemiology Reports. 4: 211-220. PMID 29226065 DOI: 10.1007/S40471-017-0115-Y |
0.573 |
|
2017 |
Titus AJ, Way GP, Johnson KC, Christensen BC. Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes. Scientific Reports. 7: 11594. PMID 28912426 DOI: 10.1038/s41598-017-10199-z |
0.305 |
|
2017 |
Way GP, Youngstrom DW, Hankenson KD, Greene CS, Grant SF. Implicating candidate genes at GWAS signals by leveraging topologically associating domains. European Journal of Human Genetics : Ejhg. PMID 28792001 DOI: 10.1038/Ejhg.2017.108 |
0.576 |
|
2017 |
Way GP, Allaway RJ, Bouley SJ, Fadul CE, Sanchez Y, Greene CS. A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. Bmc Genomics. 18: 127. PMID 28166733 DOI: 10.1186/S12864-017-3519-7 |
0.552 |
|
2016 |
Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny GE, Goode EL, Greene CS, Doherty JA. Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. G3 (Bethesda, Md.). PMID 27729437 DOI: 10.1534/G3.116.033514 |
0.559 |
|
2016 |
Way GP, Southwell M, McRobert SP. Boldness, Aggression, and Shoaling Assays for Zebrafish Behavioral Syndromes. Journal of Visualized Experiments : Jove. PMID 27684060 DOI: 10.3791/54049 |
0.249 |
|
2015 |
McRobert SP, Moss S, Tittaferrante S, Way GP, Fuller A, Sullivan N, Ruhl N. Interactions between aggression, boldness and shoaling within a brood of convict cichlids (Amatitlania nigrofasciatus). Behavioural Processes. PMID 26497098 DOI: 10.1016/j.beproc.2015.10.012 |
0.205 |
|
2015 |
Way GP, Ruhl N, Snekser JL, Kiesel AL, McRobert SP. A comparison of methodologies to test aggression in zebrafish. Zebrafish. 12: 144-51. PMID 25621988 DOI: 10.1089/zeb.2014.1025 |
0.247 |
|
2015 |
Way GP, Kiesel AL, Ruhl N, Snekser JL, McRobert SP. Sex differences in a shoaling-boldness behavioral syndrome, but no link with aggression. Behavioural Processes. 113: 7-12. PMID 25562194 DOI: 10.1016/J.Beproc.2014.12.014 |
0.206 |
|
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