2020
Jelinek D, Zhang ER, Ambrus A, Haley E, Guinn E, Vo A, Le P, Kesaf AE, Nguyen J, Guo L, Frederick D, Sun Z, Guo N, Sevier P, Bilotta E, Atai K, Voisin L, Coller HA (2020). A Mouse Model to Investigate the Role of Cancer-associated Fibroblasts in Tumor Growth. J Vis Exp. 2020 Dec 22;(166)
Tan DJ, Mitra M, Chiu AM, Coller HA (2020) Intron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinoma NPJ Genom Med. 2020 Dec 11;5(1):55.
Corvalan AZ, Coller HA (2020) Methylation of histone 4’s lysine 20: a critical analysis of the state of the field. Physiol Genomics 53(1):22-32
H. Rahmani et al., “Towards a Machine-Learning-Assisted Dielectric Sensing Platform for Point-of-Care Wound Monitoring,” in IEEE Sensors Letters, vol. 4, no. 6, pp. 1-4, June 2020, Art no. 5501004, doi: 10.1109/LSENS.2020.2999031.
Coller HA (2020) Regulation of cell cycle entry and exit: A single cell perspective. Compr Physiol 10L 2020, 317-344
2019
Mitra M, Lee HN, Coller HA (2019) Splicing Busts a Move: Isoform Switching Regulates Migration. Trends Cell Biol (19):30182-5
Coller HA (2019) The paradox of metabolism in quiescent stem cells. FEBS Letters 593(20):2817-2839
Coller HA (2019) Fibroblasts prompt tumors to mobilize their glycogen reserves. Trends Cell Biol 29(4):278-280
Lee HN et al (2019) RECK isoforms differentially regulate fibroblast migration by modulating tubulin post-translational modifications Biochem Biophys Res Commun 520:211-218
2018
Mitra M et al (2018) Alternative polyadenylation factors link cellcycle to migration. Genome Biology 19:176
Chiu A, Mitra M, Boymoushakian L, Coller HA (2018) Integrative analysis of the inter-tumoral heterogeneity of triple-negative breast cancer. Scientific Reports
Jelinek D, Flores A, Uebelhoer M, Pasque V, Plath K, Iruela-Arispe ML, Christofk HR, Lowry WE, Coller HA (2018) Mapping Metabolism: Monitoring Lactate Dehydrogenase Activity Directly in Tissue. J Vis Exp.
Lee HN, Mitra M, Bosompra O, Corney DC, Johnson EL, Rashed N, Ho LD, Coller HA. RECK isoforms have opposing effects on cell migration. Mol Biol Cell. mbcE17120708
Coller HA. MYC sets a tumour-stroma metabolic loop. Nat Cell Biol. 20(5):506-507.
Coller HA. DNA replication licensing in stem cells: Gatekeeping the commitment to proliferation. J Cell Biol. 217(5):1563-1565
Mitra M, Lee HN, Coller HA (2018) Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts. J Vis Exp. (131)
Mitra M, Ho LD, Coller HA. (2018) An In Vitro Model of Cellular Quiescence in Primary Human Dermal Fibroblasts. Methods Mol Biol. 1686:27-47
2017
Coller HA, Desai A (2017) Cell cycle, cell division, and cell death. Mol Biol Cell 28 (6) 693-694
Johnson EL, Robinson DG, Coller HA (2017) Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence. BMC Genomics 18 (1):123
2016
Mitra M, Coller HA (2016) RNAs that make a heart beat. Ann Transl Med 4(23):469
Nouvong A, Ambrus AM, Zhang ER, Hultman L, Coller HA (2016) Reactive oxygen species and bacterial biofilms in diabetic wound healing. Physiol Genomics 48 (12):889-896
Rabinowitz JD, Coller HA (2015) Partners in the Warburg effect. Elife (5) e15938
2015
Mitra M, Johnson EL, Coller HA (2015) Alternative Polyadenylation can regulate post-translational membrane localization. Trends Cell Mol Bio 10:37-47
2014
Coller HA (2014) The Runt-related transcription factor 1 in prostate cancer- associated fibroblasts. PNAS 111 (46) 16238-9
Courney DC, Coller HA (2014) On form and function: does chromatin packing regulate the cell cycle? Physiological Genomics 46 (6) 191-194
Coller HA (2014) Is cancer a metabolic disease? American Journal of Pathology 184 (1) 4-17
2013
Evertts AG, Manning AL, Wang X, Dyson NJ, Garcia BA, Coller HA (2013) H4K20me3 methylation regulates quiescence and chromatin compaction. Mol Biol Cell (19) 3025-37
Jiang P, Singh M, Coller HA (2013) Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay. PLoS Comput Biol 9(5): e1003075. doi:10.1371/journal.pcbi.1003075. (Selected for Faculty of 100
Coller, H.A. (2013) Introducing the Systems Biology of Cell State Regulation Section of Physiological Genomics. Physiological Genomics, April 30.
Evertts, A. and Coller, H.A. (2012) Back to the origin: Reconsidering replication, transcription, epigenetics and cell cycle control, Genes and Cancer,
3 (11/12): 679 – 697.
Evertts AG, Zee BM, Dimaggio PA, Gonzales-Cope M, Coller HA, Garcia BA. (2013) Quantitative Dynamics of the Link Between Cellular Metabolism and Histone Acetylation, J Biol Chem , 2013 Mar 12.
2012
Suh, E.J., Remillard, M.Y., Legesse-Miller, A., Johnson, E.L. Lemons, J.M.S., Chapman, T.R., Forman, J.J., Kojima, M., Silberman, E.S., and Coller, H.A. (2012) A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts, Genome Biology, 13: R121.
Legesse-Miller A, Raitman I, Haley EM, Liao A, Sun LL, Wang DJ, Krishnan N, Lemons JM, Suh EJ, Johnson EL, Lund BA, Coller HA (2012) Quiescent fibroblasts are protected from proteasome inhibition-mediated toxicity. Mol Biol Cell. 2012 Sep; 23(18):3566-81
Valcourt, J.R., Lemons, J.M.S., Haley, E.M., Kojima, M., Demuren, O.O., and Coller, H.A. (2012) Staying alive: metabolic adaptations to quiescence. Cell Cycle 11(9).
Ventura-Clapier R, Coller HA, A Step Toward Systems Metabolomics, Physiol Genomics, 2012 Feb 14
Wang DJ, Legesse-Miller A, Johnson EL, Coller HA (2012) Regulation of the let-7a-3 Promoter by NF-κB. PLoS ONE 7(2): e31240. doi:10.1371/journal.pone.0031240
Waldron, L, Coller, H.A., and Huttenhower, C. (2012) Integrative approaches for microarray data analysis. Methods in Molecular Biology, 802: 157-182.
2011
Coller HA (2011) The essense of quiescence. Science 334: 1074-1075.
Guo JY, Chen HY, Mathew R, Fan J, Strohecker AM, Karsli-Uzunbas G, Kamphorst JJ, Chen G, Lemmons JM, Karantza V, Coller HA, Dipaola RS, Gelinas C, Rabinowitz JD, White E. (2011) Activated Ras requires autophagy to maintain oxidative metabolism and tumorigenesis. Genes Dev. 25:460-470
2010
Wellen, K.E., Lu, C., Mancuso, A., Lemons, J.M., Ryczko, M., Dennis, J.W., Rabinowitz, J.D., Coller, H.A. and Thompson, C.B. (2010) The hexosamine biosynthetic pathway coordinates glucose and glutamine metabolism through regulation of IL-3Ra, Genes and Development, 24(24) 2784-2799
Lemons, J.M.L., Feng, X.-J., Bennett, B.D., Legesse-Miller, A., Johnson, E.L., Raitman, I., Pollina, E.A., Rabitz, H.A., Rabinowitz, J.D. and Coller, H.A. (2010) Quiescent fibroblasts exhibit active metabolism, PloS Biology, 8(10): e1000514. (Selected for Nature Research Highlights and Faculty of 1000).
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., Rabinowtiz, J.D., Carroll, M., Su, S.M., Sharp, K.A., Levine, R.L. and 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.
Forman JJ, Coller HA. (2010) The code within the code: MicroRNAs target coding regions. Cell Cycle. 9(8): 1533-1541.
Sang, L., Roberts, J.M. and Coller, H.A. (2010) Hijacking Hes1: Tumors co-opt the anti-differentiation strategies of quiescent cells, Trends in Molecular Medicine, 16(1): 17-26.
Huttenhower, C.*, Mutungu, K.T.*, Indik, N., Yang, W., Schroeder, M. Forman, J.J., Troyanskaya, O.G.* and Coller, H.A.* (2009) Detailing regulatory networks through large scale data integration, Bioinformatics, 25(24): 3267-3274.
2009
Sang, L. and Coller, H.A. (2009) Fear of commitment: Hes1 protects quiescent fibroblasts from irreversible cellular fates, Cell Cycle, 8(14): 2161-2167.
Huttenhower, C.*, Haley, E.M.*, Hibbs, M.A., Dumeaux, V., Coller, H.A.* and Troyanskaya, O.G.* (2009) A functional map of the human genome, Genome Research, 9(6):1093-106.
Legesse-Miller, A., Elemento, O., Pfau, S., Forman, J.J., Tavazoie, S. and Coller, H.A. (2009) let-7 overexpression leads to G2/M arrest, direct down-regulation of Cdc34 and stabilization of Wee1 kinase in primary fibroblasts, Journal of Biological Chemistry, 284(11): 6605-6609.
2008
Coller, H.A. and Kruglyak, L. (2008) It’s the sequence, stupid! Science, 322(5900): 380-381.
Forman, J.J., Legesse-Miller, A. and Coller, H.A. (2008) A search for highly conserved sequences in coding regions finds that let-7 targets Dicer within its coding sequence, Proc. Natl. Acad. Sci. USA, 105(39): 14879-14884.
Sang, L., Coller, H.A., and Roberts, J.M. (2008) HES1 regulates the reversibility of cellular quiescence, Science, 321(5892): 1095-1100.
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., Aisner, S., Randolph-Habecker, J. and Coller, H.A. (2008) An immunohistochemical method for identifying fibroblasts, Journal of Histochemistry and Cytochemistry, 56(4): 347-358.
2007
Coller, H.A., Forman, J.J. and Legesse-Miller, A. (2007) “Myc’ed” messages: Myc induces transcription of E2Fs while inhibiting their translation via a microRNA polycistron that may serve as a signal integrator, PLoS Genetics, 3(8): e146. PMC1959363.
Huttenhower, C., Flamholz, A., Landis, J., Sahi, S., Myers, C., Hibbs, M., Siemers, N., Troyanskaya, O. and Coller, H.A. (2007) Nearest Neighbor Networks: Clustering expression data based on gene neighborhoods, BMC Bioinformatics, 8(1): 250. PMC1941745.
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.
Miller, D.L., Myers, C., Rickards, B., Coller, H. and Flint, S.J. (2007) Adenovirus type 5 exerts genome-wide control over cellular programs governing cell proliferation, quiescence and survival, Genome Biology, 8(4): R58. PMC1896011.
2006
Munger, J., Bajad, S.U., Coller, H.A., Shenk, T. and Rabinowitz, J.D. (2006) Dynamics of the cellular metabolome during HCMV infection, PLoS Pathogens, 2(12): e132. PMC1698944.
Coller, H.A.*, Sang, L.* and Roberts, J.M. (2006) A new description of cellular quiescence. PLoS Biol. 4: e83. PMC1393757.
Zheng, W., Khrapko, K., Coller, H.A., Thilly, W.G. and Copeland, W.C. (2006) Origins of human mitochondrial point mutations as DNA polymerase gamma-mediated errors. Mutat Res. 599: 11-20.
2005
Coller, H.A., Khrapko, K., Herrero-Jimenez, P., Vatland, J.A., Li-Sucholeiki, X.C. and Thilly W.G. (2005) Clustering of mutant mitochondrial DNA copies suggests stem cells are common in human bronchial epithelium. Mutat Res, 578: 256-271.
2003
Smith, L.L.,* Coller, H.A.* and Roberts, J. (2003) Telomerase modulates expression of growth-controlling genes and enhances cell proliferation. Nat Cell Biol. 5: 474-479.
2001
Staunton, J.E., Slonim, D.K., Coller, H.A., Tamayo, P., Angelo, M.J., Scherf, U., Weinstein, J.N., Park, J., Mesirov, J.P., Lander, E.S. and Golub, T.R. (2001) Chemomsensitivity prediction by transcriptional profiling. Proc. Natl. Acad. Sci. USA, 98:10787-10792. PMC58553.
Coller H.A., Khrapko, K., Bodyak, N.D., Nekhaeva, E., Herrero-Jimenez, P., and Thilly, W.G. (2001) High frequency of homoplasmic mitochondrial DNA mutations in human tumors can be explained without selection. Nature Genetics 28:147-50.
Khrapko, K., Coller, H.A., Li-Sucholeiki, X.C., Andre, P.C., Thilly, W.G. (2001) High resolution analysis of point mutations by constant denaturant capillary electrophoresis (CDCE). Methods Mol. Biol. 163: 57-72.
2000
Coller, H.A.,* Grandori, C.,* Tamayo, P., Colbert, T., Lander, E.S., Eisenman, R.N., and Golub, T. (2000) Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc. Natl. Acad. Sci. USA 97: 3260-3265. PMC16226.
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. and Lander, E.S. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537.
1998
Coller, H.A., Khrapko, K., Torres, A., Frampton, M., Utell, M. and Thilly, W. (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: 1268-1277.
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.