Publications
- Cheng, M. W., Mitra, M., & Coller, H. A. (2023). Pan-cancer landscape of epigenetic factor expression predicts tumor outcome. Communications Biology, 6(1). PubMed
- Mitra, M., & Coller, H. A. (2023). Screen time: An unbiased search for histone mutations that affect quiescence and chronological aging. The FEBS Journal, 290(14), 3533–3538. PubMed
- Zhao, Y., Wang, B., Tan, J., Yin, H., Huang, R., Zhu, J., Lin, S., Zhou, Y., Jelinek, D., Sun, Z., Youssef, K., Voisin, L., Horrillo, A., Zhang, K., Wu, B. M., Coller, H. A., Lu, D. C., Pei, Q., & Emaminejad, S. (2022). Soft strain-insensitive bioelectronics featuring brittle materials. Science, 378(6625), 1222–1227. PubMed
- Lin, S., Cheng, X., Zhu, J., Wang, B., Jelinek, D., Zhao, Y., Wu, T.-Y., Horrillo, A., Tan, J., Yeung, J., Yan, W., Forman, S., Coller, H. A., Milla, C., & Emaminejad, S. (2022). Wearable microneedle-based electrochemical aptamer biosensing for precision dosing of drugs with narrow therapeutic windows. Science Advances, 8(38). PubMed
- Coller H. A. (2022). Stressed-out yeast do not pass GO. The Journal of cell biology, 221(1), e202111032. PubMed
- Coller H. A. (2022). Prereplication complex proteins get caught moonlighting. PLoS biology, 20(2), e3001549. PubMed
- Erickson, O. A., Cole, R. B., Isaacs, J. M., Alvarez-Clare, S., Arnold, J., Augustus-Wallace, A., Ayoob, J. C., Berkowitz, A., Branchaw, J., Burgio, K. R., Cannon, C. H., Ceballos, R. M., Cohen, C. S., Coller, H., Disney, J., Doze, V. A., Eggers, M. J., Farina, S., Ferguson, E. L., Gray, J. J., … Dolan, E. L. (2022). "How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19. CBE life sciences education, 21(1), ar1. PubMed
- Hess, R. A., Erickson, O. A., Cole, R. B., Isaacs, J. M., Alvarez-Clare, S., Arnold, J., Augustus-Wallace, A., Ayoob, J. C., Berkowitz, A., Branchaw, J., Burgio, K. R., Cannon, C. H., Ceballos, R. M., Cohen, C. S., Coller, H., Disney, J., Doze, V. A., Eggers, M. J., Ferguson, E. L., … Dolan, E. L. (2022). Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences. BioRxiv.
- Coller, H.A. (2021). Stressed-out yeast do not pass GO. Journal of cell biology, 221(1), e202111032. PubMed
- Bonitto, K., Sarathy, K., Atai, K., Mitra, M., & Coller, H. A. (2021). Is there a histone code for cellular quiescence?. Frontiers in cell and developmental biology, 9, 739780. PubMed
- Coller H. A. (2021). Incoming Editor-in-Chief editorial. Physiological genomics, 53(7), 283–284. PubMed
- Coller, H. A. (2021). The return of quiescence metabolites. Nature cell biology, 23(4), 303–304. PubMed
- Jelinek, D., Zhang, E. R., Ambrus, A., Haley, E., Guinn, E., Vo, A., Le, P., Kesaf, A. E., Nguyen, J., Guo, L., Frederick, D., Sun, Z., Guo, N., Sevier, P., Bilotta, E., Atai, K., Voisin, L., & Coller, H. A. (2020). A mouse model to investigate the role of cancer-associated fibroblasts in tumor growth. Journal of visualized experiments : JoVE, (166). PubMed
- Tan, D. J., Mitra, M., Chiu, A. M., & Coller, H. A. (2020). Intron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinoma. NPJ genomic medicine, 5(1), 55. PubMed
- Corvalan, A. Z., & Coller, H. A. (2021). Methylation of histone 4’s lysine 20: a critical analysis of the state of the field. Physiological genomics, 53(1), 22–32. PubMed
- Rahmani, H., Archang, M.M., Jamali, B., Forghadi, M., Ambrus, A.M., Ramalingam, D., Sun, Z., Scumpia, P.O., Coller, H.A., Babakhani, A. (2020). Towards a machine-learning-assisted dielectric sensing platform for point-of-care wound monitoring. IEEE Sensors Letters, 4(6), 1-4.
- Coller H. A. (2019). Regulation of cell cycle entry and exit: a single cell perspective. Comprehensive Physiology, 10(1), 317–344. PubMed
- Mitra, M., Lee, H. N., & Coller, H. A. (2020). Splicing busts a move: isoform switching regulates migration. Trends in cell biology, 30(1), 74–85. PubMed
- Coller H. A. (2019). The paradox of metabolism in quiescent stem cells. FEBS letters, 593(20), 2817–2839. PubMed
- Coller H. A. (2019). Fibroblasts prompt tumors to mobilize their glycogen reserves. Trends in cell biology, 29(4), 278–280. PubMed
- Lee, H. N., Bosompra, O. A., & Coller, H. A. (2019). RECK isoforms differentially regulate fibroblast migration by modulating tubulin post-translational modifications. Biochemical and biophysical research communications, 510(2), 211–218. PubMed
- Mitra, M., Johnson, E. L., Swamy, V. S., Nersesian, L. E., Corney, D. C., Robinson, D. G., Taylor, D. G., Ambrus, A. M., Jelinek, D., Wang, W., Batista, S. L., & Coller, H. A. (2018). Alternative polyadenylation factors link cellcycle to migration. Genome biology, 19(1), 176. PubMed
- Chiu, A. M., Mitra, M., Boymoushakian, L., & Coller, H. A. (2018). Integrative analysis of the inter-tumoral heterogeneity of triple-negative breast cancer. Scientific reports, 8(1), 11807. PubMed
- Jelinek, D., Flores, A., Uebelhoer, M., Pasque, V., Plath, K., Iruela-Arispe, M. L., Christofk, H. R., Lowry, W. E., & Coller, H. A. (2018). Mapping metabolism: monitoring lactate dehydrogenase activity directly in tissue. Journal of visualized experiments : JoVE, (136), 57760. PubMed
- Lee, H. N., Mitra, M., Bosompra, O., Corney, D. C., Johnson, E. L., Rashed, N., Ho, L. D., & Coller, H. A. (2018). RECK isoforms have opposing effects on cell migration. Molecular biology of the cell, 29(15), 1825–1838. PubMed
- Coller H. A. (2018). MYC sets a tumour-stroma metabolic loop. Nature cell biology, 20(5), 506–507. PubMed
- Coller H. A. (2018). DNA replication licensing in stem cells: Gatekeeping the commitment to proliferation. The Journal of cell biology, 217(5), 1563–1565. PubMed
- Mitra, M., Lee, H. N., & Coller, H. A. (2018). Determining genome-wide transcript decay rates in proliferating and quiescent human fibroblasts. Journal of visualized experiments : JoVE, (131), 56423. PubMed
- Mitra, M., Ho, L. D., & Coller, H. A. (2018). An In Vitro Model of Cellular Quiescence in Primary Human Dermal Fibroblasts. Methods in molecular biology (Clifton, N.J.), 1686, 27–47. PubMed
- Coller, H. A., & Desai, A. (2017). Cell cycle, cell division, and cell death. Molecular biology of the cell, 28(6), 693–694. PubMed
- Johnson, E. L., Robinson, D. G., & Coller, H. A. (2017). Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence. BMC genomics, 18(1), 123. PubMed
- Mitra, M., & Coller, H. A. (2016). RNAs that make a heart beat. Annals of translational medicine, 4(23), 469. PubMed
- Nouvong, A., Ambrus, A. M., Zhang, E. R., Hultman, L., & Coller, H. A. (2016). Reactive oxygen species and bacterial biofilms in diabetic wound healing. Physiological genomics, 48(12), 889–896. PubMed
- Rabinowitz, J. D., & Coller, H. A. (2016). Partners in the Warburg effect. eLife, 5, e15938. PubMed
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Mitra, M., Johnson, E. L., & Coller, H. A. (2015). Alternative polyadenylation can regulate post-translational membrane localization. Trends in cell & molecular biology, 10, 37–47. PubMed
- Coller H. A. (2014). The Runt-related transcription factor 1 in prostate cancer- associated fibroblasts. Proceedings of the National Academy of Sciences of the United States of America, 111(46), 16238–16239. PubMed
- Corney, D. C., & Coller, H. A. (2014). On form and function: does chromatin packing regulate the cell cycle?. Physiological genomics, 46(6), 191–194. PubMed
- Coller H. A. (2014). Is cancer a metabolic disease?. The American journal of pathology, 184(1), 4–17. PubMed
- Evertts, A. G., Manning, A. L., Wang, X., Dyson, N. J., Garcia, B. A., & Coller, H. A. (2013). H4K20me3 methylation regulates quiescence and chromatin compaction. Molecular biology of the cell, 24(19), 3025–3037. PubMed
- Jiang, P., Singh, M., & Coller, H. A. (2013). Computational assessment of the cooperativity between RNA binding proteins and microRNAs in transcript decay. PLoS computational biology, 9(5), e1003075. PubMed
- Coller, H. A., & Systems Biology of Cell State Regulation Editorial Board (2013). Introducing the systems biology of cell state regulation section of Physiological Genomics. Physiological genomics, 45(11), 407–408. PubMed
- Evertts, A. G., & Coller, H. A. (2012). Back to the origin: reconsidering replication, transcription, epigenetics and cell cycle control. Genes & cancer, 3(11-12), 678–696. PubMed
- Evertts, A. G., Zee, B. M., Dimaggio, P. A., Gonzales-Cope, M., Coller, H. A., & Garcia, B. A. (2013). Quantitative dynamics of the link between cellular metabolism and histone acetylation. The Journal of biological chemistry, 288(17), 12142–12151. PubMed
- Suh, E. J., Remillard, M. Y., Legesse-Miller, A., Johnson, E. L., Lemons, J. M., Chapman, T. R., Forman, J. J., Kojima, M., Silberman, E. S., & Coller, H. A. (2012). A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts. Genome biology, 13(12), R121. PubMed
- Legesse-Miller, A., Raitman, I., Haley, E. M., Liao, A., Sun, L. L., Wang, D. J., Krishnan, N., Lemons, J. M., Suh, E. J., Johnson, E. L., Lund, B. A., & Coller, H. A. (2012). Quiescent fibroblasts are protected from proteasome inhibition-mediated toxicity. Molecular biology of the cell, 23(18), 3566–3581. PubMed
- Valcourt, J. R., Lemons, J. M., Haley, E. M., Kojima, M., Demuren, O. O., & Coller, H. A. (2012). Staying alive: metabolic adaptations to quiescence. Cell cycle (Georgetown, Tex.), 11(9), 1680–1696. PubMed
- Ventura-Clapier, R., & Coller, H. A. (2012). A step toward systems metabolomics. Physiological genomics, 44(7), 383–385. PubMed
- Wang, D. J., Legesse-Miller, A., Johnson, E. L., & Coller, H. A. (2012). Regulation of the let-7a-3 promoter by NF-κB. PloS one, 7(2), e31240. PubMed
- Waldron, L., Coller, H. A., & Huttenhower, C. (2012). Integrative approaches for microarray data analysis. Methods in Molecular Biology (Clifton, N.J.), 802, 157–182. PubMed
- Coller H. A. (2011). Cell biology. The essence of quiescence. Science (New York, N.Y.), 334(6059), 1074–1075. PubMed
- Guo, J. Y., Chen, H. Y., Mathew, R., Fan, J., Strohecker, A. M., Karsli-Uzunbas, G., Kamphorst, J. J., Chen, G., Lemons, J. M., Karantza, V., Coller, H. A., Dipaola, R. S., Gelinas, C., Rabinowitz, J. D., & White, E. (2011). Activated Ras requires autophagy to maintain oxidative metabolism and tumorigenesis. Genes & development, 25(5), 460–470. PubMed
- Wellen, K. E., Lu, C., Mancuso, A., Lemons, J. M., Ryczko, M., Dennis, J. W., Rabinowitz, J. D., Coller, H. A., & Thompson, C. B. (2010). The hexosamine biosynthetic pathway coordinates glucose and glutamine metabolism through regulation of IL-3Ra. Genes & development, 24(24), 2784–2799.
- Lemons, J. M., Feng, X. J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., & Coller, H. A. (2010). Quiescent fibroblasts exhibit high metabolic activity. PLoS biology, 8(10), e1000514. PubMed
- Ward, P. S., Patel, J., Wise, D. R., Abdel-Wahab, O., Bennett, B. D., Coller, H. A., Cross, J. R., Fantin, V. R., Hedvat, C. V., Perl, A. E., Rabinowitz, J. D., Carroll, M., Su, S. M., Sharp, K. A., Levine, R. L., & Thompson, C. B. (2010). The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzymatic activity that convert a-ketoglutarate to 2-hydroxyglutarate. Cancer cell, 17(3), 225–234. PubMed
- Forman, J. J., & Coller, H. A. (2010). The code within the code: microRNAs target coding regions. Cell cycle (Georgetown, Tex.), 9(8), 1533–1541. PubMed
- Sang, L., Roberts, J. M., & Coller, H. A. (2010). Hijacking Hes1: tumors co-opt the anti-differentiation strategies of quiescent cells. Trends in molecular medicine, 16(1), 17–26. PubMed
- Sang, L., & Coller, H. A. (2009). Fear of commitment: Hes1 protects quiescent fibroblasts from irreversible cellular fates. Cell cycle (Georgetown, Tex.), 8(14), 2161–2167. PubMed
- Huttenhower, C., Haley, E. M., Hibbs, M. A., Dumeaux, V., Barrett, D. R., Coller, H. A., & Troyanskaya, O. G. (2009). Exploring the human genome with functional maps. Genome research, 19(6), 1093–1106. PubMed
- Huttenhower, C., Mutungu, K. T., Indik, N., Yang, W., Schroeder, M., Forman, J. J., Troyanskaya, O. G., & Coller, H. A. (2009). Detailing regulatory networks through large scale data integration. Bioinformatics (Oxford, England), 25(24), 3267–3274. PubMed
- Legesse-Miller, A., Elemento, O., Pfau, S. J., Forman, J. J., Tavazoie, S., & Coller, H. A. (2009). let-7 overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts. The Journal of biological chemistry, 284(11), 6605–6609. PubMed
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Coller, H. A., & Kruglyak, L. (2008). Genetics. It's the sequence, stupid!. Science (New York, N.Y.), 322(5900), 380–381. PubMed
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Forman, J. J., Legesse-Miller, A., & Coller, H. A. (2008). A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proceedings of the National Academy of Sciences of the United States of America, 105(39), 14879–14884. PubMed
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Sang, L., Coller, H. A., & Roberts, J. M. (2008). Control of the reversibility of cellular quiescence by the transcriptional repressor HES1. Science (New York, N.Y.), 321(5892), 1095–1100. PubMed
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Pollina, E., Legesse-Miller, A., Haley, E., Goodpaster, T., Randolph-Habecker, J. and Coller, H.A. (2008). Regulating the angiogenic balance in tissues: A potential role for the proliferative state of fibroblasts, Cell Cycle, 7(13), 2056-2070.
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Goodpaster, T., Legesse-Miller, A., Hameed, M. R., Aisner, S. C., Randolph-Habecker, J., & Coller, H. A. (2008). An immunohistochemical method for identifying fibroblasts in formalin-fixed, paraffin-embedded tissue. The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society, 56(4), 347–358. PubMed
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Coller, H. A., Forman, J. J., & Legesse-Miller, A. (2007). "Myc'ed messages": myc induces transcription of E2F1 while inhibiting its translation via a microRNA polycistron. PLoS genetics, 3(8), e146. PubMed
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Huttenhower, C., Flamholz, A. I., Landis, J. N., Sahi, S., Myers, C. L., Olszewski, K. L., Hibbs, M. A., Siemers, N. O., Troyanskaya, O. G., & Coller, H. A. (2007). Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC bioinformatics, 8, 250. PubMed
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Coller H. A. (2007). What's taking so long? S-phase entry from quiescence versus proliferation. Nature reviews. Molecular cell biology, 8(8), 667–670. PubMed
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Miller, D. L., Myers, C. L., Rickards, B., Coller, H. A., & Flint, S. J. (2007). Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival. Genome biology, 8(4), R58. PubMed
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Munger, J., Bajad, S. U., Coller, H. A., Shenk, T., & Rabinowitz, J. D. (2006). Dynamics of the cellular metabolome during human cytomegalovirus infection. PLoS pathogens, 2(12), e132. PubMed
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Coller, H. A., Sang, L., & Roberts, J. M. (2006). A new description of cellular quiescence. PLoS biology, 4(3), e83. PubMed
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Zheng, W., Khrapko, K., Coller, H. A., Thilly, W. G., & Copeland, W. C. (2006). rigins of human mitochondrial point mutations as DNA polymerase gamma-mediated errors. Mutation research, 599(1-2), 11–20. PubMed
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Coller, H. A., Khrapko, K., Herrero-Jimenez, P., Vatland, J. A., Li-Sucholeiki, X. C., & Thilly, W. G. (2005). Clustering of mutant mitochondrial DNA copies suggests stem cells are common in human bronchial epithelium. Mutation research, 578(1-2), 256–271. PubMed
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Smith, L. L., Coller, H. A., & Roberts, J. M. (2003). Telomerase modulates expression of growth-controlling genes and enhances cell proliferation. Nature cell biology, 5(5), 474–479. PubMed
- Staunton, J. E., Slonim, D. K., Coller, H. A., Tamayo, P., Angelo, M. J., Park, J., Scherf, U., Lee, J. K., Reinhold, W. O., Weinstein, J. N., Mesirov, J. P., Lander, E. S., & Golub, T. R. (2001). Chemomsensitivity prediction by transcriptional profiling. Proceedings of the National Academy of Sciences of the United States of America, 98(19), 10787–10792. PubMed
- Coller, H. A., Khrapko, K., Bodyak, N. D., Nekhaeva, E., Herrero-Jimenez, P., & Thilly, W. G. (2001). High frequency of homoplasmic mitochondrial DNA mutations in human tumors can be explained without selection. Nature genetics, 28(2), 147–150. PubMed
- Khrapko, K., Coller, H. A., Li-Sucholeiki, X. C., André, P. C., & Thilly, W. G. (2001). High resolution analysis of point mutations by constant denaturant capillary electrophoresis (CDCE). Methods in molecular biology (Clifton, N.J.), 163, 57–72. PubMed
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Coller, H. A., Grandori, C., Tamayo, P., Colbert, T., Lander, E. S., Eisenman, R. N., & Golub, T. R. (2000). Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proceedings of the National Academy of Sciences of the United States of America, 97(7), 3260–3265. PubMed
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Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D., & Lander, E. S. (1999). Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (New York, N.Y.), 286(5439), 531–537. PubMed
- Coller, H. A., Khrapko, K., Torres, A., Frampton, M. W., Utell, M. J., & Thilly, W. G. (1998). Mutational spectra of a 100 base pair mitochondrial DNA target sequence in bronchial epithelial cells: a comparison of smoking and nonsmoking twins. Cancer research, 58(6), 1268–1277. PubMed
- Khrapko, K., Coller, H.A., Hanekamp, J. and Thilly, W. (1998). Identification of sequence variants in mixtures by capillary electrophoresis hybridization. Nucleic Acids Research 26: 5738-5740.
- Khrapko, K., Coller, H. A., Hanekamp, J. S., & Thilly, W. G. (1998). Identification of point mutations in mixtures by capillary electrophoresis hybridization. Nucleic acids research, 26(24), 5738–5740. PubMed