{
  "lab": "Churchman Lab",
  "institution": "Harvard Medical School",
  "source": "https://churchman.med.harvard.edu/publications",
  "fullList": "https://www.ncbi.nlm.nih.gov/myncbi/lee.churchman.1/bibliography/public/",
  "lastSynced": "2026-08-06",
  "legend": "*equal authorship; #co-corresponding authorship; Churchman Lab members in bold.",
  "count": 71,
  "publications": [
    {
      "title": "Mitochondrial RNA processing promotes translation by resolving structured precursor RNAs",
      "authors": "Nuessmeier CH, Prakash G, Hansen LN, Couvillion MT, Churchman LS",
      "labAuthors": [
        "Nuessmeier CH",
        "Prakash G",
        "Hansen LN",
        "Couvillion MT",
        "Churchman LS"
      ],
      "journal": "bioRxiv",
      "year": 2026,
      "volume": null,
      "pages": null,
      "type": "preprint",
      "section": "preprints",
      "doi": "10.64898/2026.07.30.741833",
      "pmid": null,
      "url": "https://doi.org/10.64898/2026.07.30.741833"
    },
    {
      "title": "Analog intrinsic recoding measures RNA dynamics without chemical conversion",
      "authors": "Hansen LN, Couvillion MT, McShane E, Azbukina N, Treutlein B, Churchman LS",
      "labAuthors": [
        "Hansen LN",
        "Couvillion MT",
        "McShane E",
        "Churchman LS"
      ],
      "journal": "bioRxiv",
      "year": 2026,
      "volume": null,
      "pages": null,
      "type": "preprint",
      "section": "preprints",
      "doi": "10.64898/2026.07.27.741041",
      "pmid": null,
      "url": "https://doi.org/10.64898/2026.07.27.741041"
    },
    {
      "title": "SRSF1 shapes 3'-end site selection with differential dependence on U1 snRNP",
      "authors": "Merens HE, Raicu AM, Carroll CL, Kourkoulakos M, Fiszbein A, Churchman LS",
      "labAuthors": [
        "Merens HE",
        "Raicu AM",
        "Kourkoulakos M",
        "Churchman LS"
      ],
      "journal": "bioRxiv",
      "year": 2026,
      "volume": null,
      "pages": null,
      "type": "preprint",
      "section": "preprints",
      "doi": "10.64898/2026.04.01.715904",
      "pmid": "41959273",
      "url": "https://doi.org/10.64898/2026.04.01.715904"
    },
    {
      "title": "Neuronal activity triggers widespread changes in RNA stability",
      "authors": "Duffy EE#, Patop I*#, Kalaora S, Assad EG, Koren SA, Traunmüller L, Krüttner S, Pajarillo NS, Finander B, Barsdale Z, Macias MM, Feng MY, Paulo JA, Griffith EC, Kalish BT, Gygi SP, Churchman LS#, Greenberg ME#",
      "labAuthors": [
        "Duffy EE",
        "Patop I",
        "Churchman LS",
        "Greenberg ME"
      ],
      "journal": "bioRxiv",
      "year": 2025,
      "volume": null,
      "pages": null,
      "type": "preprint",
      "section": "preprints",
      "doi": "10.1101/2025.09.05.674581",
      "pmid": "40950030",
      "url": "https://doi.org/10.1101/2025.09.05.674581"
    },
    {
      "title": "Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation",
      "authors": "Bridgers JB*, Carlström A*, Sherpa D*, Couvillion MT, Rovšnik U, Gao J, Wan B, Shao S#, Ott M#, Churchman LS#",
      "labAuthors": [
        "Bridgers JB",
        "Couvillion MT",
        "Churchman LS"
      ],
      "journal": "Nature Structural & Molecular Biology",
      "year": 2026,
      "volume": "33(2)",
      "pages": "245–258",
      "type": "research",
      "section": "research",
      "doi": "10.1038/s41594-025-01726-y",
      "pmid": "41339860",
      "url": "https://doi.org/10.1038/s41594-025-01726-y"
    },
    {
      "title": "Copper depletion boosts CNS leukemia therapy by inhibiting nucleotide synthesis through impairment of mitochondrial complex IV activity",
      "authors": "Wong AYL, Myers JW, Prakash G, Ma A, Brook JR, Petrova B, Bulut B, White R 3rd, Merz C, de Souza M, Maynard AG, Wang P, Yu A, Pohl NK, Weitman M, Silverman LB, Stegmaier K, Churchman LS, Cole PD, Brady DC, Kanarek N",
      "labAuthors": [
        "Prakash G",
        "Churchman LS"
      ],
      "journal": "Nature Cancer",
      "year": 2026,
      "volume": null,
      "pages": null,
      "type": "research",
      "section": "research",
      "doi": "10.1038/s43018-026-01177-4",
      "pmid": "42185479",
      "url": "https://doi.org/10.1038/s43018-026-01177-4"
    },
    {
      "title": "Transcription arrest induces formation of RNA granules in mitochondria",
      "authors": "Hansen KG, Baxter-Koenigs A, Weiss CA, McShane E, Churchman LS",
      "labAuthors": [
        "Hansen KG",
        "Baxter-Koenigs A",
        "Weiss CA",
        "McShane E",
        "Churchman LS"
      ],
      "journal": "Life Science Alliance",
      "year": 2025,
      "volume": "8(9)",
      "pages": "e202403082",
      "type": "research",
      "section": "research",
      "doi": "10.26508/lsa.202403082",
      "pmid": "40523799",
      "url": "https://doi.org/10.26508/lsa.202403082"
    },
    {
      "title": "A molecular switch at the yeast mitoribosomal tunnel exit controls cytochrome b synthesis",
      "authors": "Carlström A, Bridgers JB, Couvillion M, Singh AP, Forné I, Imhof A, Churchman LS#, Ott M#",
      "labAuthors": [
        "Carlström A",
        "Bridgers JB",
        "Couvillion M",
        "Churchman LS"
      ],
      "journal": "Nucleic Acids Research",
      "year": 2025,
      "volume": "53(13)",
      "pages": null,
      "type": "research",
      "section": "research",
      "doi": "10.1093/nar/gkaf634",
      "pmid": "40637229",
      "url": "https://doi.org/10.1093/nar/gkaf634"
    },
    {
      "title": "HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy",
      "authors": "Jiang Q, Braun DA, Clauser KR, Ramesh V, Shirole NH, Duke-Cohan JE, Nabilsi N, Kramer NJ, Forman C, Lippincott IE, Klaeger S, Phulphagar KM, Chea V, Kim N, Vanasse AP, Saad E, Parsons T, Carr-Reynolds M, Carulli I, Pinjusic K, Jiang Y, Li R, Syamala S, Rachimi S, Verzani EK, Stevens JD, Lane WJ, Camp SY, Meli K, Pappalardi MB, Herbert ZT, Qiu X, Cejas P, Long HW, Shukla SA, Van Allen EM, Choueiri TK, Churchman LS, Abelin JG, Gurer C, MacBeath G, Childs RW, Carr SA, Keskin DB, Wu CJ, Kaelin WG Jr",
      "labAuthors": [
        "Kramer NJ",
        "Churchman LS"
      ],
      "journal": "Cell",
      "year": 2025,
      "volume": "188(7)",
      "pages": "1807–1827.e34",
      "type": "research",
      "section": "research",
      "doi": "10.1016/j.cell.2025.01.046",
      "pmid": "40023154",
      "url": "https://doi.org/10.1016/j.cell.2025.01.046"
    },
    {
      "title": "Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing",
      "authors": "Choquet K, Chaumont LP, Bache S, Baxter-Koenigs AR, Churchman LS",
      "labAuthors": [
        "Choquet K",
        "Chaumont LP",
        "Bache S",
        "Baxter-Koenigs AR",
        "Churchman LS"
      ],
      "journal": "Genome Research",
      "year": 2025,
      "volume": "35(4)",
      "pages": "712–724",
      "type": "research",
      "section": "research",
      "doi": "10.1101/gr.279203.124",
      "pmid": "39952678",
      "url": "https://doi.org/10.1101/gr.279203.124"
    },
    {
      "title": "Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics",
      "authors": "Bibel B, Raskar T, Couvillion M, Lee M, Kleinman JI, Takeuchi-Tomita N, Churchman LS, Fraser JS, Fujimori DG",
      "labAuthors": [
        "Couvillion M",
        "Churchman LS"
      ],
      "journal": "Nucleic Acids Research",
      "year": 2025,
      "volume": "53(3)",
      "pages": null,
      "type": "research",
      "section": "research",
      "doi": "10.1093/nar/gkaf046",
      "pmid": "39907106",
      "url": "https://doi.org/10.1093/nar/gkaf046"
    },
    {
      "title": "RNA polymerases reshape chromatin architecture and couple transcription on individual fibers",
      "authors": "Tullius TW, Isaac RS, Ranchalis J, Dubocanin D, Churchman LS#, Stergachis AB#",
      "labAuthors": [
        "Tullius TW",
        "Isaac RS",
        "Churchman LS"
      ],
      "journal": "Molecular Cell",
      "year": 2024,
      "volume": "84(17)",
      "pages": "3209–3222.e5",
      "type": "research",
      "section": "research",
      "doi": "10.1016/j.molcel.2024.08.013",
      "pmid": "39191261",
      "url": "https://doi.org/10.1016/j.molcel.2024.08.013"
    },
    {
      "title": "Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle",
      "authors": "Ietswaart R#*, Smalec BM*, Xu A*, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN#, Churchman LS#",
      "labAuthors": [
        "Ietswaart R",
        "Smalec BM",
        "Choquet K",
        "McShane E",
        "Guegler CK",
        "Baxter-Koenigs AR",
        "Churchman LS"
      ],
      "journal": "Molecular Cell",
      "year": 2024,
      "volume": "84",
      "pages": "2765–2784.e16",
      "type": "research",
      "section": "research",
      "doi": "10.1016/j.molcel.2024.06.008",
      "pmid": "38964322",
      "url": "https://doi.org/10.1016/j.molcel.2024.06.008"
    },
    {
      "title": "A kinetic dichotomy between mitochondrial and nuclear gene expression processes",
      "authors": "McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS",
      "labAuthors": [
        "McShane E",
        "Couvillion M",
        "Ietswaart R",
        "Prakash G",
        "Smalec BM",
        "Soto I",
        "Baxter-Koenigs AR",
        "Choquet K",
        "Churchman LS"
      ],
      "journal": "Molecular Cell",
      "year": 2024,
      "volume": "84(8)",
      "pages": "1541–1555.e11",
      "type": "research",
      "section": "research",
      "doi": "10.1016/j.molcel.2024.02.028",
      "pmid": "38503286",
      "url": "https://doi.org/10.1016/j.molcel.2024.02.028"
    },
    {
      "title": "Post-transcriptional splicing can occur in a slow-moving zone around the gene",
      "authors": "Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A",
      "labAuthors": [
        "Drexler HL",
        "Churchman LS"
      ],
      "journal": "eLife",
      "year": 2024,
      "volume": "12",
      "pages": null,
      "type": "research",
      "section": "research",
      "doi": "10.7554/eLife.91357",
      "pmid": "38577979",
      "url": "https://doi.org/10.7554/eLife.91357"
    },
    {
      "title": "Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle",
      "authors": "Litsios A, Grys BT, Kraus OZ, Friesen H, Ross C, Masinas MPD, Forster DT, Couvillion MT, Timmermann S, Billmann M, Myers C, Johnsson N, Churchman LS, Boone C, Andrews BJ",
      "labAuthors": [
        "Couvillion MT",
        "Churchman LS"
      ],
      "journal": "Cell",
      "year": 2024,
      "volume": "187",
      "pages": "1490–1507.e21",
      "type": "research",
      "section": "research",
      "doi": "10.1016/j.cell.2024.02.014",
      "pmid": "38452761",
      "url": "https://doi.org/10.1016/j.cell.2024.02.014"
    },
    {
      "title": "Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA",
      "authors": "Isaac RS, Tullius TW*, Hansen KG*, Dubocanin D, Couvillion M, Stergachis AB#, Churchman LS#",
      "labAuthors": [
        "Isaac RS",
        "Tullius TW",
        "Hansen KG",
        "Couvillion M",
        "Churchman LS"
      ],
      "journal": "Nature Structural & Molecular Biology",
      "year": 2024,
      "volume": "31",
      "pages": "568–577",
      "type": "research",
      "section": "research",
      "doi": "10.1038/s41594-024-01225-6",
      "pmid": "38347148",
      "url": "https://doi.org/10.1038/s41594-024-01225-6"
    },
    {
      "title": "Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome",
      "authors": "Singh V, Moran JC, Itoh Y, Soto IC, Fontanesi F, Couvillion M, Huynen MA, Churchman LS, Barrientos A, Amunts A",
      "labAuthors": [
        "Soto IC",
        "Couvillion M",
        "Churchman LS"
      ],
      "journal": "Nature Structural & Molecular Biology",
      "year": 2024,
      "volume": "31(12)",
      "pages": "1838–1847",
      "type": "research",
      "section": "research",
      "doi": "10.1038/s41594-024-01365-9",
      "pmid": "39134711",
      "url": "https://doi.org/10.1038/s41594-024-01365-9"
    },
    {
      "title": "Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression",
      "authors": "Kramer NJ*, Prakash G*, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS",
      "labAuthors": [
        "Kramer NJ",
        "Prakash G",
        "Choquet K",
        "Soto I",
        "Merens HE",
        "Churchman LS"
      ],
      "journal": "Nature Cell Biology",
      "year": 2023,
      "volume": "25",
      "pages": "1575–1589",
      "type": "research",
      "section": "research",
      "doi": "10.1038/s41556-023-01244-3",
      "pmid": "37770567",
      "url": "https://doi.org/10.1038/s41556-023-01244-3"
    },
    {
      "title": "RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation",
      "authors": "Martell DJ, Merens HE, Caulier A, Fiorini C, Ulirsch J, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NBA, Babbs C, Higgs DR, Sankaran VG#, Churchman LS#",
      "labAuthors": [
        "Martell DJ",
        "Merens HE",
        "Ietswaart R",
        "Choquet K",
        "Churchman LS"
      ],
      "journal": "Developmental Cell",
      "year": 2023,
      "volume": "58",
      "pages": "2112–2127.e4",
      "type": "research",
      "section": "research",
      "doi": "10.1016/j.devcel.2023.07.018",
      "pmid": "37586368",
      "url": "https://doi.org/10.1016/j.devcel.2023.07.018"
    },
    {
      "title": "Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts",
      "authors": "Choquet K, Baxter-Koenigs AR, Dülk SL, Smalec BM, Rouskin S, Churchman LS",
      "labAuthors": [
        "Choquet K",
        "Baxter-Koenigs AR",
        "Smalec BM",
        "Churchman LS"
      ],
      "journal": "Nature Structural & Molecular Biology",
      "year": 2023,
      "volume": "30",
      "pages": "1064–1076",
      "type": "research",
      "section": "research",
      "doi": "10.1038/s41594-023-01035-2",
      "pmid": "37443198",
      "url": "https://doi.org/10.1038/s41594-023-01035-2"
    },
    {
      "title": "Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences",
      "authors": "Bergeron D, Faucher-Giguère L, Emmerichs A-K, Choquet K, Song KS, Deschamps-Francoeur G, Fafard-Couture É, Rivera A, Couture S, Churchman LS, Heyd F, Abou Elela S, Scott MS",
      "labAuthors": [
        "Choquet K",
        "Churchman LS"
      ],
      "journal": "Genome Biology",
      "year": 2023,
      "volume": "24",
      "pages": "160",
      "type": "research",
      "section": "research",
      "doi": "10.1186/s13059-023-03002-y",
      "pmid": "37415181",
      "url": "https://doi.org/10.1186/s13059-023-03002-y"
    },
    {
      "title": "Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs",
      "authors": "Khitun A, Brion C, Moqtaderi Z, Geisberg JV, Churchman LS, Struhl K",
      "labAuthors": [
        "Churchman LS"
      ],
      "journal": "Journal of Biological Chemistry",
      "year": 2023,
      "volume": "299(11)",
      "pages": "105289",
      "type": "research",
      "section": "research",
      "doi": "10.1016/j.jbc.2023.105289",
      "pmid": "37748648",
      "url": "https://doi.org/10.1016/j.jbc.2023.105289"
    },
    {
      "title": "Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes",
      "authors": "Soto I*, Couvillion M*, Hansen KG, McShane E, Moran JC, Barrientos A, Churchman LS",
      "labAuthors": [
        "Soto I",
        "Couvillion M",
        "Hansen KG",
        "McShane E",
        "Churchman LS"
      ],
      "journal": "Genome Biology",
      "year": 2022,
      "volume": "23(1)",
      "pages": "170",
      "type": "research",
      "section": "research",
      "doi": "10.1186/s13059-022-02732-9",
      "pmid": "35945592",
      "url": "https://doi.org/10.1186/s13059-022-02732-9"
    },
    {
      "title": "Transcription elongation is finely tuned by dozens of regulatory factors",
      "authors": "Couvillion M*, Harlen KM*, Lachance KC*, Trotta KL, Smith E, Brion C, Smalec BM, Churchman LS",
      "labAuthors": [
        "Couvillion M",
        "Harlen KM",
        "Lachance KC",
        "Trotta KL",
        "Smith E",
        "Smalec BM",
        "Churchman LS"
      ],
      "journal": "eLife",
      "year": 2022,
      "volume": "11",
      "pages": null,
      "type": "research",
      "section": "research",
      "doi": "10.7554/eLife.78944",
      "pmid": "35575476",
      "url": "https://doi.org/10.7554/eLife.78944"
    },
    {
      "title": "Hsf1 activation by proteotoxic stress requires concurrent protein synthesis",
      "authors": "Tye BW, Churchman LS",
      "labAuthors": [
        "Tye BW",
        "Churchman LS"
      ],
      "journal": "Molecular Biology of the Cell",
      "year": 2021,
      "volume": "32(19)",
      "pages": "1800–1806",
      "type": "research",
      "section": "research",
      "doi": "10.1091/mbc.E21-01-0014",
      "pmid": "34191586",
      "url": "https://doi.org/10.1091/mbc.E21-01-0014"
    },
    {
      "title": "Essential histone chaperones collaborate to regulate transcription and chromatin integrity",
      "authors": "Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F",
      "labAuthors": [
        "Churchman LS"
      ],
      "journal": "Genes & Development",
      "year": 2021,
      "volume": "35(9-10)",
      "pages": "698–712",
      "type": "research",
      "section": "research",
      "doi": "10.1101/gad.348431.121",
      "pmid": "33888559",
      "url": "https://doi.org/10.1101/gad.348431.121"
    },
    {
      "title": "GeneWalk identifies relevant gene functions for a biological context using network representation learning",
      "authors": "Ietswaart R, Gyori BM, Bachman JA, Sorger PK, Churchman LS",
      "labAuthors": [
        "Ietswaart R",
        "Churchman LS"
      ],
      "journal": "Genome Biology",
      "year": 2021,
      "volume": "22(1)",
      "pages": "55",
      "type": "research",
      "section": "research",
      "doi": "10.1186/s13059-021-02264-8",
      "pmid": "33526072",
      "url": "https://doi.org/10.1186/s13059-021-02264-8"
    },
    {
      "title": "Single-molecule regulatory architectures captured by chromatin fiber sequencing",
      "authors": "Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA",
      "labAuthors": [
        "Stergachis AB",
        "Churchman LS"
      ],
      "journal": "Science",
      "year": 2020,
      "volume": "368",
      "pages": "1449–1454",
      "type": "research",
      "section": "research",
      "doi": "10.1126/science.aaz1646",
      "pmid": "32587015",
      "url": "https://doi.org/10.1126/science.aaz1646"
    },
    {
      "title": "The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions",
      "authors": "Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M",
      "labAuthors": [
        "di Iulio J",
        "Churchman LS"
      ],
      "journal": "Journal of Biological Chemistry",
      "year": 2020,
      "volume": "295",
      "pages": "11435–11454",
      "type": "research",
      "section": "research",
      "doi": "10.1074/jbc.RA120.013426",
      "pmid": "32518159",
      "url": "https://doi.org/10.1074/jbc.RA120.013426"
    },
    {
      "title": "Splicing kinetics and coordination revealed by direct nascent RNA sequencing through nanopores",
      "authors": "Drexler HL, Choquet K, Churchman LS",
      "labAuthors": [
        "Drexler HL",
        "Choquet K",
        "Churchman LS"
      ],
      "journal": "Molecular Cell",
      "year": 2020,
      "volume": "77(5)",
      "pages": "985–998.e8",
      "type": "research",
      "section": "research",
      "doi": "10.1016/j.molcel.2019.11.017",
      "pmid": "31839405",
      "url": "https://doi.org/10.1016/j.molcel.2019.11.017"
    },
    {
      "title": "Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness",
      "authors": "Tye BW, Commins N, Ryazanova LV, Wühr M, Springer M, Pincus D, Churchman LS",
      "labAuthors": [
        "Tye BW",
        "Churchman LS"
      ],
      "journal": "eLife",
      "year": 2019,
      "volume": "8",
      "pages": null,
      "type": "research",
      "section": "research",
      "doi": "10.7554/eLife.43002",
      "pmid": "30843788",
      "url": "https://doi.org/10.7554/eLife.43002"
    },
    {
      "title": "Spt6 is required for the fidelity of promoter selection",
      "authors": "Doris SM, Chuang J, Viktorovskaya O, Murawska M, Spatt D, Churchman LS, Winston F",
      "labAuthors": [
        "Churchman LS"
      ],
      "journal": "Molecular Cell",
      "year": 2018,
      "volume": "72(4)",
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