Publications
2023
Cheng, M. W., Mitra, M., & Coller, H. A. (2023). Pan-cancer landscape of epigenetic factor expression predicts tumor outcome. Communications Biology, 6(1).
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.
2022
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.
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).
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.
2021
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
2020
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.
2019
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
2018
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
2017
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
2016
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
2015
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
2014
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
2013
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
2012
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
2011
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
2010
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
2009
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
2008
Coller, H. A., & Kruglyak, L. (2008). Genetics. It's the sequence, stupid!. Science (New York, N.Y.), 322(5900), 380–381.
PubMed
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
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
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.
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
2007
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
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
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
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
2006
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
Coller, H. A., Sang, L., & Roberts, J. M. (2006). A new description of cellular quiescence. PLoS biology, 4(3), e83.
PubMed
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
2005
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
2003
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
2001
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
2000
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
1999
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
1998
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