Publications | Purvis Lab

Latest Preprints

Mihailovic S, Wolff SC, Kedziora KM, Smiddy NM, Redick MA, Wang Y, Lin GK, Zikry TM, Simon J, Ptacek T, Allbritton NL, Beltran AS, Purvis JE. Single-cell dynamics of core pluripotency factors in human pluripotent stem cells. (2022) bioRxiv 2022.12.13.520282.
Luo H, Purvis JE, Li D. Spherical Rotation Dimension Reduction with Geometric Loss Functions. (2023) arXiv:2204.10975.

Zikry TM, Wolff SC, Ranek JS, Davis H, Naugle A, Whitman AA, Kosorok MR, Spanheimer PM, Purvis JE. Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells. (2023) bioRxiv 2023.05.22.541831.
Ranek JS, Stallaert W, Milner J, Stanley N, Purvis JE. Feature selection for preserving biological trajectories in single-cell data. (2023) bioRxiv 2023.05.09.540043.
Shahir JA, Stanley N, Purvis JE. Cellograph: A Semi-supervised Approach to Analyzing Multi-condition Single-cell RNA-sequencing Data Using Graph Neural Networks. (2022) bioRxiv 2023.02.24.528672.

Cho M, Kumar RJ, Lin C, Boyer JA, Shahir JA, Fagan-Solis K, Simpson DA, Fan C, Foster CE, Goddard AM, Wang Q, Wang Y, Ho AY, Liu P, Perou CM, Zhang Q, McGinty RK, Purvis JE, Gupta GP. Mre11 liberates cGAS from nucleosome sequestration during tumorigenesis. (2023) Accepted at Nature (July 31, 2023) bioRxiv 2022.12.09.519750v1
Adler FR, Anderson ARA, Bhushan A, Bogdan P, Bravo-Cordero JJ, Brock A, Chen Y, Cukierman E, DelGiorno KE, Denis GV, Ferrall-Fairbanks MC, Gartner ZJ, Germain RN, Gordon DM, Hunter G, Jolly MK, Karacosta LG, Mythreye K, Katira P, Kulkarni RP, Kutys ML, Lander AD, Laughney AM, Levine H, Lou E, Lowenstein PR, Masters KS, Pe’er D, Peyton SR, Platt MO, Purvis JE, Quon G, Richer JK, Riddle NC, Rodriguez A, Snyder JC, Szeto GL, Tomlin CJ, Yanai I, Zervantonakis IK, Dueck H. Modeling collective cell behavior in cancer: perspectives from an interdisciplinary conversation (2023) Cell Systems 14(4):252-257. PMID: 37080161

Stallaert W, Taylor SR, Kedziora KM, Johnson MS, Taylor CD, Sobon HK, Young CL, Limas JC, Varblow-Holloway J, Cook JG, Purvis JE. The molecular architecture of cell cycle arrest (2022). Molecular Systems Biology 18(9):e11087. PMID: 36161508
Ranek JS, Stanley N, Purvis JE. Integrating temporal single-cell gene expression modalities for trajectory inference and disease prediction (2022). Genome Biology 23(1):186. PMID: 36064614
Burclaff J, Bliton RJ, Breau KA, Ok MT, Gomez-Martinez I, Ranek JS, Bhatt AP, Purvis JE, Woosley JT, Magness ST. A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics. (2022) Cellular and Molecular Gastroenterology and Hepatology Feb 14:S2352-345X(22)00034-0. PMID: 35176508.
Mei L, Kedziora KM, Song EA, Purvis JE, Cook JG. The consequences of differential origin licensing dynamics in distinct chromatin environments. (2022) Nucleic Acids Research Jan 26:gkac003. PMID: 35079814.

Enrico TP, Stallaert W, Wick ET, Ngoi P, Wang X, Rubin SM, Brown NG, Purvis JE, Emanuele MJ. Cyclin F drives proliferation through SCF-dependent degradation of the retinoblastoma-like tumor suppressor p130/RBL2. (2021) Elife 10:e70691. PMID: 34851822.
Stallaert W, Kedziora KM, Taylor CD, Zikry TM, Ranek JS, Sobon HK, Taylor SR, Young CL, Cook JG, Purvis JE. The structure of the human cell cycle. (2021) Cell Systems S2405-4712(21)00418-X. PMID: 34800361.
Haggerty RA, Purvis JE. Inferring the structures of signaling motifs from paired dynamic traces of single cells. (2021) PLoS Computational Biology 17(2):e1008657. PMID: 33539338.

Kumar RJ, Chao HX, Simpson DA, Feng W, Cho MG, Roberts VR, Sullivan AR, Shah SJ, Wozny AS, Fagan-Solis K, Kumar S, Luthman A, Ramsden DA, Purvis JE, Gupta GP. Dual inhibition of DNA-PK and DNA polymerase theta overcomes radiation resistance induced by p53 deficiency. (2020) Nucleic Acids Research Cancer 2(4):zcaa038. PMID: 33385162.
Coryell PR, Goraya SK, Griffin KA, Redick MA, Sisk SR, Purvis JE. Autophagy regulates the localization and degradation of p16INK4a. (2020) Aging Cell 19(7):e13171. PMID: 32662244.

Stallaert W, Kedziora KM, Chao HX, Purvis JE. Bistable switches as integrators and actuators during cell cycle progression. (2019) FEBS Letters 593(20):2805. PMID: 31566708.
Feng W, Simpson DA, Carvajal-Garcia J, Price BA, Kumar RJ, Mose LE, Wood RD, Rashid N, Purvis JE, Parker JS, Ramsden DA, Gupta GP. Genetic determinants of cellular addiction to DNA polymerase theta. (2019) Nature Communications 10(1):4286. PMID: 31537809.
Headley KM, Kedziora KM, Alejo A, Lai EZ, Purvis JE, Hathaway NA. Chemical screen for epigenetic barriers to single allele activation of Oct4. (2019) Stem Cell Research 38:101470. PMID: 31170660.
Zikry TM, Kedziora KM, Kosorok MR, Purvis JE. In and out of the nucleus: CNN based segmentation of cell nuclei from images of a translocating sensor. (2019) Proceedings of the Practice and Experience in Advanced Research Computing. View PDF.
Wolff SC, Purvis JE. Reprogramming favors the elite. (2019) Science 364(6438):330-331. PMID: 31023911.

Chao HX, Fakhreddin RI, Shimerov HK, Kedziora KM, Kumar RJ, Perez J, Limas JC, Grant GD, Cook JG, Gupta GP, Purvis JE. Evidence that the human cell cycle is a series of uncoupled, memoryless phases. (2018) Molecular Systems Biology 15(3):e8604. PMID: 30886052.
Grant GD, Kedziora KM, Limas JC, Cook JG, Purvis JE. Accurate delineation of cell cycle phase transitions in living cells with PIP-FUCCI. (2018) Cell Cycle17(21-22):2496-2516. PMID: 30421640.
Wolff SC, Kedziora KM, Dumitru R, Dungee CD, Zikry TM, Beltran AS, Haggerty RA, Cheng J, Redick MA, Purvis JE. Inheritance of OCT4 predetermines fate choice in human embryonic stem cells. (2018) Molecular Systems Biology 14(9):e8140. PMID: 30177503.
Borland D, Yi H, Grant GD, Kedziora KM, Chao HX, Haggerty RA, Kumar J, Wolff SC, Cook JG, Purvis JE. The Cell Cycle Browser: An Interactive Tool for Visualizing, Simulating, and Perturbing Cell-Cycle Progression. (2018) Cell Systems 7(2):180-184.e4. PMID: 30077635.

Haggerty RA, Purvis JE. Natural language processing: put your model where your mouth is. (2017) Molecular Systems Biology 13(12):958. PMID: 29254950. View PDF
Chao HX, Poovey CE, Privette AA, Grant GD, Chao HY, Cook JG, Purvis JE. Orchestration of DNA Damage Checkpoint Dynamics across the Human Cell Cycle. (2017) Cell Systems 5(5):445-459.e5. PMID: 29102360. View PDF
Matson JP, Dumitru R, Coryell P, Baxley RM, Chen W, Twaroski K, Webber BR, Tolar J, Bielinsky AK, Purvis JE, Cook JG. Rapid DNA replication origin licensing protects stem cell pluripotency. (2017) Elife 6. pii: e30473. PMID: 29148972. View PDF
Kedziora KM, Purvis JE. Cell biology: The persistence of memory. (2017) Nature 549(7672):343-344. PMID: 28869963. View PDF

Baran-Gale J, Purvis JE*, Sethupathy P*. An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response in MCF-7 breast cancer cells. (2016) RNA 22(10):1592-603. PMID: 27539783. View PDF

Coleman KE, Grant GD, Haggerty RA, Brantley K, Shibata E, Workman BD, Dutta A, Varma D, Purvis JE, Cook JG. Sequential replication-coupled destruction at G1/S ensures genome stability. (2015) Genes and Development 29(16):1734. PMCID: PMC4561482. View PDF
Davis DM, Purvis JE. Computational analysis of signaling patterns in single cells (2015) Seminars in Cell and Developmental Biology Jan; 37:35-43. View PDF

Gorman BR, Lu J, Baccei A, Lowry NC, Purvis JE, Mangoubi RS, Lerou PH. Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis. (2014) PLoS ONE 9(12):e116037. PMID: 25551762. View PDF