MGH Lab Publications

Featured Publications

Research

O’Neill, K., Shaw, R., Bolger, I., NYGC ALS Consortium, Tam, O.H., Phatnani, H., Gale Hammell, M. (2025) ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers. Cell Reports 44(3). pp. 115402.

Krupp, S, Hubbard, I, Tam, O, Gale Hammell, M, Dubnau, J. (2023) TDP-43 pathology in Drosophila induces glial-cell type specific toxicity that can be ameliorated by knock-down of SF2/SRSF1. PLoS Genet. 19:e1010973.

Garza R, Sharma Y, Atacho D, Thiruvalluvan A, Hamdeh SA, Jönsson M, Horvath V, Adami A, Ingelsson M, Jern P, Hammell MG, Englund E, Kirkeby A, Jakobsson J, Marklund N. (2023) Single-Cell Transcriptomics of Resected Human Traumatic Brain Injury Tissues Reveals Acute Activation of Endogenous Retroviruses in Oligodendroglia. Cell Reports 42(11):113395.

Garza R, Atacho DAM, Adami A, Gerdes P, Vinod M, Hsieh P, Karlsson O, Horvath V, Johansson PA, Pandiloski N, Matas-Fuentes J, Quaegebeur A, Kouli A, Sharma Y, Jönsson ME, Monni E, Englund E, Eichler EE, Gale Hammell M, Barker RA, Kokaia Z, Douse CH, Jakobsson J. (2023) LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification. Sci Adv. 9(44):eadh9543.

Torre D, Fstkchyan YS, Ho JSY, Cheon Y, Patel RS, Degrace EJ, Mzoughi S, Schwarz M, Mohammed K, Seo JS, Romero-Bueno R, Demircioglu D, Hasson D, Tang W, Mahajani SU, Campisi L, Zheng S, Song WS, Wang Y chih, Shah H, Francoeur N, Soto J, Salfati Z, Weirauch MT, Warburton P, Beaumont K, Smith ML, Mulder L, Villalta SA, Kessenbrock K, Jang C, Lee D, De Rubeis S, Cobos I, Tam O, Hammell MG, Seldin M, Shi Y, Basu U, Sebastiano V, Byun M, Sebra R, Rosenberg BR, Benner C, Guccione E, Marazzi I. (2023) Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Molecular Cell. 83(23):4255-4271.e9.

Tam, O. H., Rozhkov, N. V., Shaw, R., Kim, D., Hubbard, I., Fennessey, S., Propp, N., Fagegaltier, D., Harris, B. T., Ostrow, L. W., Phatnani, H., Ravits, J., Dubnau, J. , Gale Hammell, M. (2019) Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Reports, 29(5) pp. 1164-1177.e5.

Stein CB, Genzor P, Mitra S, Elchert AR, Ipsaro JJ, Benner L, Sobti S, Su Y, Hammell M, Joshua-Tor L, Haase AD. (2019) Decoding the 5′ nucleotide bias of PIWI-interacting RNAs. Nat Commun. 10(1):828.

Ho, Y. J., Anaparthy, N., Molik, D., Mathew, G., Aicher, T., Patel, A., Hicks, J., Gale Hammell, M. (2018) Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome Res, 28 (9). pp. 1353-1363.

O’Neill K, Liao WW, Patel A, Hammell MG. (2018) TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma. Front Genet. 9:461.

Hwang DW, Jaganathan A, Shrestha P, Jin Y, El-Amine N, Wang SH, Hammell M, Mills AA. (2018) Chromatin-mediated translational control is essential for neural cell fate specification. Life Sci Alliance. 1(4):e201700016.

Krug L, Chatterjee N, Borges-Monroy R, Hearn S, Liao WW, Morrill K, Prazak L, Rozhkov N, Theodorou D, Hammell M, Dubnau J. (2017) Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet. 13(3):e1006635.

Jin, Y., Tam, O. H., Paniagua, E., Hammell, M. (2015) TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics, 31 (22). pp. 3593-3599.

Petsch K, Manzotti PS, Tam OH, Meeley R, Hammell M, Consonni G, Timmermans MCP. (2015) Novel Dicer-like1 siRNAs bypass the requirement for Dicer-like4 in maize development. Plant Cell. 27(8):2163-2177.

Feigin ME, Xue B, Hammell MC, Muthuswamy SK. (2014) G-protein–coupled receptor GPR161 is overexpressed in breast cancer and is a promoter of cell proliferation and invasion. PNAS. 111(11):4191-4196.

Dotto MC, Petsch KA, Aukerman MJ, Beatty M, Hammell M*, Timmermans MCP. (2014) Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development. PLoS Genet. 10(12):e1004826.

Rozhkov NV, Hammell M, Hannon GJ. (2013) Multiple roles for Piwi in silencing Drosophila transposons. Genes Dev. 27(4):400-412.

Li W, Jin Y, Prazak L, Hammell* M, Dubnau* J. (2012) Transposable elements in TDP-43-mediated neurodegenerative disorders. PLoS ONE. 7(9):e44099.

Post-doctoral Work

Burke SL, Hammell M, Ambros V. (2015) Robust distal tip cell pathfinding in the face of temperature stress is ensured by two conserved microRNAs in Caenorhabditis Elegans. Genetics. 200(4):1201-1218.

Karp X, Hammell M, Ow MC, Ambros V. (2011) Effect of life history on microRNA expression during C. elegans development. RNA. 17(4):639-651.

Zhang L, Hammell M, Kudlow BA, Ambros V, Han M. (2009) Systematic analysis of dynamic miRNA-target interactions during C. elegans development. Development. 136(18):3043-3055.

Hong* X, Hammell* M, Ambros V, Cohen SM. (2009) Immunopurification of Ago1 miRNPs selects for a distinct class of microRNA targets. PNAS. 106(35):15085-15090.

Hammell M, Long D, Zhang L, Lee A, Carmack CS, Han M, Ding Y, Ambros V. (2008) MirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts. Nature Meth. 5(9):813-819.

Martinez NJ, Ow MC, Barrasa MI, Hammell M, Sequerra R, Doucette-Stamm L, Roth FP, Ambros VR, Walhout AJM. (2008) A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev. 22(18):2535-2549.

Astrophysics Work

Fesen RA, Zastrow JA, Hammell MC, Shull JM, Silvia DW. (2011) Ejecta knot flickering, mass ablation, and fragmentation in Cassiopeia A. The Astrophysical Journal. 736(2):109.

Hammell MC, Fesen RA. (2008) A catalog of outer ejecta knots in the Cassiopeia A supernova remnant. Astrophysical Journal Supplement Series 179(1):195-208.

Fesen RA, Hoflich PA, Hamilton AJS, Hammell MC, Gerardy CL, Khokhlov AM, Wheeler JC. (2007) The chemical distribution in a subluminous Type Ia Supernova: Hubble Space Telescope images of the SN 1885 remnant. The Astrophysical Journal. 658(1):396-409.

Fesen RA, Hammell MC, Morse J, Chevalier RA, Borkowski KJ, Dopita MA, Gerardy CL, Lawrence SS, Raymond JC, Van Den Bergh S. (2006) The expansion asymmetry and age of the Cassiopeia A supernova remnant. The Astrophysical Journal. 645(1):283-292.

Fesen RA, Hammell MC, Morse J, Chevalier RA, Borkowski KJ, Dopita MA, Gerardy CL, Lawrence SS, Raymond JC, Van Den Bergh S. (2006) Discovery of outlying high‐velocity oxygen‐rich ejecta in Cassiopeia a. The Astrophysical Journal. 636(2):859-872.

Immler S, Fesen RA, Van Dyk SD, Weiler KW, Petre R, Lewin WHG, Pooley D, Pietsch W, Aschenbach B, Hammell MC, Rudie GC. (2005) Late‐time X‐ray, UV, and optical monitoring of Supernova 1979c. The Astrophysical Journal. 632(1):283-293.

MacDonald EC, Allen P, Dalton G, Moustakas LA, Heymans C, Edmondson E, Blake C, Clewley L, Hammell MC, Olding E, Miller L, Rawlings S, Wall J, Wegner G, Wolf C. (2004) The Oxford-Dartmouth Thirty degree survey - i. Observations and calibration of a wide-field multiband survey. Monthly Notices of the Royal Astronomical Society. 352(4):1255-1272.

Reviews

Rupert, D.D., Nowlan, A.C., Tam, O. H. , Gale Hammell, M. (2020) Ten Simple Rules for Running a Successful women-in-STEM Organization on an Academic Campus. PLoS Comput Biol, 16(5) pp. e1007754.

O'Neill, K., Brocks, D. , Gale Hammell, M. (2020) Mobile Genomics: Tools and Techniques for Tackling Transposons. Philos Trans R Soc Lond B Biol Sci, 375(1795)

Bourque, G., Burns, K. H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvak, Z., Levin, H. L., Macfarlan, T. S., Mager, D. L., Feschotte, C. (2018) Ten things you should know about transposable elements. Genome Biol, 19 p. 199.