Selected Publications

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Shao Z, Hu J, Jandura A, Wilk R, Jachimowicz M, Ma L, Hu C, Sundquist A, Das I, Samuel-Larbi P, Brill JA, Krause HM. (2024) Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution. Nat Commun. May 7;15(1):3806.

 

Liu J, Malekoltojari A, Asokakumar A, Chow V, Li L, Li H, Grimaldi M, Dang N, Campbell J, Barrett H, Sun J, Navarre W, Wilson D, Wang H, Mani S, Balaguer P, Anakk S, Peng H, Krause HM. Diindoles produced from commensal microbiota metabolites function as endogenous CAR/Nr1i3 ligands. (2024)  Nat Commu. Mar 22;15(1):2563.

 

Dvořák Z, Vyhlídalová B, Pečinková P, Li H, Anzenbacher P, Špičáková A, Anzenbacherová E, Chow V, Liu J, Krause H, Wilson D, Berés T, Tarkowski P, Chen D, Mani S. (2024) In vitro safety signals for potential clinical development of the anti-inflammatory pregnane X receptor agonist FKK6. Bioorg Chem. Mar;144:107137.

 

Mette Lassen, Keith Pardee, Lisa H. Pedersen, Olga Kubrak, Takashi Koyama, Sasha Necakov, Suya Liu, Arnis Kuksis, Gilles Lajoie, Aled Edwards, Aurelio A. Teleman, Martin R. Larsen, Henry M. Krause, Michael J. Texada, Kim Rewitz. (2024) HR3/RORα-mediated cholesterol sensing regulates TOR signalin. bioRxi .04.09.588676.

 

Vasquez, O.E.; Allen, A.M.; So, A.K.-C.; Nguyen, Q.H.; Krause, H.M.; Levine, J.D.; Sokolowski, M.B. Characterizing the Protein Isoforms of foraging (for), the PKGI Ortholog in Drosophila melanogaster. (2023) Int. J. Mol. Sci.  24, 10219.

 

Burns AR, Baker RJ, Kitner M, Knox J, Cooke B, Volpatti JR, Vaidya AS, Puumala E, Palmeira BM, Redman EM, Snider J, Marwah S, Chung SW, MacDonald MH, Tiefenbach J, Hu C, Xiao Q, Finney CAM, Krause HM, MacParland SA, Stagljar I, Gilleard JS, Cowen LE, Meyer SLF, Cutler SR, Dowling JJ, Lautens M, Zasada I, Roy PJ. Selective control of parasitic nematodes using bioactivated nematicides. Nature. 2023 Jun;618(7963):102-109.

 

Raz AA, Vida GS, Stern SR, Mahadevaraju S, Fingerhut JM, Viveiros JM, Pal S, Grey JR, Grace MR, Berry CW, Li H, Janssens J, Saelens W, Shao Z, Hu C, Yamashita YM, Przytycka T, Oliver B, Brill JA, Krause H, Matunis EL, White-Cooper H, DiNardo S, Fuller MT. Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes. Elife. 2023 Feb 16;12:e82201.

 

Liu, J., Sahin, C., Ahmad, S., Magomedova, L., Zhang, M., Jia, Z., Metherel, H., Orellana, A., Poda, G.,    Bazinet, R., Attisano, L., Cummins, C., Peng, H. and Krause, H.M. (2022) The omega-3 hydroxy fatty acid 7(S)-HDHA is a high-affinity PPAR ligand that regulates brain neuronal morphology. Science Signaling, 15, eabo 1857: 1-12.  

 

Li, H. et al (Fly Cell Atlas Consortium). (2022). Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly. Science 375   (6584), eabk2432.

 

Witt E, Shao Z, Hu C, Krause HM, Zhao L. Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis. PLoS Genet. 2021 Aug 17;17(8):e1009728.

 

 Han J, Yang D, Hall DR, Liu J, Sun J, Gu W, Tang S, Alharbi HA, Jones PD, Krause HM, Peng H. Toxicokinetics of Brominated Azo Dyes in the Early Life Stages of Zebrafish (Danio rerio) Is Prone to Aromatic Substituent Changes. Environ Sci Technol. 2020 Apr 7;54(7):4421-4431.

 

Burgess J, Burrows JT, Sadhak R, Chiang S, Weiss A, D'Amata C, Molinaro AM, Zhu S, Long M, Hu C, Krause HM, Pearson BJ. (2020) An optimized QF-binary expression system for use in zebrafish. Dev Biol. 15;465 (2):144-156.

 

Lee, H., Zhang, Z. and Krause, H.M. (2019) Long noncoding RNAs and repetitive elements: junk or intimate partners in evolution. TIGs, 35(12), 892-902. 

 

Krause, H.M., (2018) New and prospective roles for lncRNAs in organelle formation and function. Trends in Genetics, 34(10):736-745.

Tiefenbach, J., Magomedova, L., Liu, J., Tsai, R., Nislow, C., Cummins, C.L.and Krause, H.M., (2018) Idebenone and CoQ10 are novel PPARa/g ligands, with potential for treatment of fatty liver diseases. Disease Models and Mechanisms, 11(9).

Jandura, A. and Krause, H.M. (2017) The new RNA world - what to make of noncoding RNA expansion and function. Trends in Genetics, 33, 665-676.

 

Jandura, A. Hu, J., Wilk, R. and Krause, H.M. (2017) High resolution fluorescent in situ hybridization in Drosophila embryos and tissues using tyramide signal amplification. JoVE, 128, e56281.

Wilk R., Hu J., Blotsky D., and Krause H. M. (2016) Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs. Genes Dev. March 1, 2016 30: 594-609.

Wilk R., Hu J., and Krause H. M. (2013) Spatial Profiling of Nuclear Receptor Transcription Patterns over the Course of Drosophila Development. G3 - Genes/Genomes/Genetics (Bethesda). July 8;3(7):1177-1189.

Yoo, J., Ko, S., Kim, H., Sampson, H., Yun, J., Chang, I., Arrowsmith, C., Krause, HM, CHO, S-G. and Lee, W. (2011) Crystal structure of the FTZ-F1 LBD/FTZ peptide complex identifies a new class of nuclear receptor structures. JBC 286: 31225-31231.

Cáceres, L. Necakov, A., Schwartz, C. Roberts, I. and Krause, H.M. (2011) Nitric oxide coordinates metabolism, growth, and development via the nuclear receptor E75. Genes Dev. 25: 1476-1485.

Delvecchio C, Tiefenbach J, Krause HM. (2011) The Zebrafish: A Powerful Platform for In Vivo, HTS Drug Discovery. Assay Drug Dev Technol. 9 (4): 354-361.

Pardee K, Necakov AS, Krause H. (2011) Nuclear Receptors: Small Molecule Sensors that Coordinate Growth, Metabolism and Reproduction. in A handbook for transcription factors. ed: Timothy Hughes, Ch 6, 123-153.

Tiefenbach J, Moll PR, Nelson MR, Hu C, Baev L, Kislinger T, Krause HM. (2010) A live zebrafish-based screening system for human nuclear receptor ligand and cofactor discovery. PLoS One. 5(3):e9797.

Wilk R, Murthy S, Yan H, and Krause HM. (2010) In Situ Hybridization: Fruit Fly Embryos and Tissues. Current Protocols Essential Laboratory Technique.  9.3.1-24, Wiley.

Horner, M.A., Pardee, K., Liu, S., King-Jones, K., Lajoie, G., Krause, H.M. and Thummel, C.S. (2010) The Drosophila DHR96 Nuclear Receptor Binds Cholesterol and Regulates Cholesterol Homeostasis. Genes Dev; 23: 2711-2716.

Pardee KI1, Xu X, Reinking J, Schuetz A, Dong A, Liu S, Zhang R, Tiefenbach J, Lajoie G, Plotnikov AN, Botchkarev A, Krause, H.M. * and Edwards A.*(2009). The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta. PLoS Biology, 7(2), 384-398. * co-senior authors.

Lecuyer, E., Yoshida, H. and Krause, H.M. (2009) Global implications of mRNA localization pathways in cellular organization. Current Opinions in Cell Biology, 21: 409-415. 

Lécuyer, E. Necakov, A. Cáceres, L., Krause, H. M. (2008) High-Resolution Fluorescent In situ Hybridization in Drosophila Embryos and Tissues. CSH Protocols.

dos Santos, G. and Krause, H.M. (2008) A stem-loop structure in the wingless transcript defines a consensus motif for apical RNA transport. Development, 135, 133-143.

Lécuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Babak, T., Cerovina, T., Hughes, T.R., Tomancak, P.and Krause, H.M. (2007) Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function. Cell, 131, 174-187.

Palanker, L., Sampson, H., Necakov, S., Ni, R., Hu, C., Thummel, C.S. and Krause, H.M. (2006) Dynamic regulation of Drosophila nuclear receptor activity in vivo. Development, 133, 3549-3562.

Reinking, J., Lam, M., Pardee, K., Yang, P., Williams, S., Yudin, A., Edwards A., and Krause, H.M. (2005) The nuclear receptor E75 binds heme and is regulated by Nitric oxide. Cell, 122, 195-207.

Dietrich, B.H., Yang, P. and Krause, H.M. (2005) Tantalus, a link between Notch signaling and chromatin remodeling. Genes, Development and Evolution. 215: 255-260.

 

Pardee, K., Reinking, J. and Krause, H.M. (2004) Nuclear hormone receptors, metabolism and aging; what goes around comes around. SAGE KE 47:24, re8.

Baker, K., Shewchuk, L., Kozlova, T. Makishima, M., Hassell, A., Wisely, B., Lambert, M., Reinking, J., Krause, H.M., Thummel, C., Willson, T., and Mangelsdorf , D. (2003). The Drosophila orphan nuclear receptor DHR38 mediates an atypical ecdysteroid signaling pathway. Cell.113, 731-742.

Nasiadka, A. and Krause, H.M. (2002) Transcriptional regulation during early Drosophila development. In: Advances in Developmental Biology and Biochemistry: Regulation of Gene Expression at the Beginning of Development. 12, Elsevier Science, Melvin DePamphilis, editor, 155-204.

Simmonds, A.J., dos Santos, G., Livne-Bar, I. and Krause, H.M., (2001) Apical localization of wingless transcripts is required for wingless signaling. Cell, 105, 197-201.

Hughes, S.C. and Krause, H.M. (2001) Establishment and maintenance of parasegmental compartments in Drosophila embryos. Development, 128, 1109-1118.

Schwartz, C.J.E., Sampson, H.M., Hlousek, D., Percival-Smith, A., Copeland, J.W.R. and Krause, H.M. (2001) FTZ-Factor1 and Fushi tarazu interact via conserved nuclear receptor and coactivator interaction motifs. EMBO J., 20, 510-519.

Nasiadka, A., Grill, A. and Krause, H.M. (2000) Mechanisms regulating target gene selection by the homeodomain-containing protein Fushi tarazu. Development, 127, 2965-2976.

Nasiadka, A. and Krause, H.M. (1999) Kinetic analysis of segmentation gene interactions in Drosophila embryos. Development, 126:1515-1526.

Saulier-Le Drean, B., Nasiadka, A., Dong, J. and Krause, H.M. (1998) Dynamic changes in the functions of Odd-skipped during early Drosophila development. Development, 125, 4851-4861.

Simmonds AJ, Liu X, Soanes KH, Krause HM, Irvine KD and Bell JB (1998) Molecular interactions between Vestigial and Scalloped promote wing formation in Drosophila. Genes and Development, 12, 3815-3820.

Dong, J., Hung, L.-H., Strome, R. and Krause, H.M. (1998) A phosphorylation site in the Ftz homeodomain is required for activity. EMBO J. 17, 2308-2318.

Hughes, S. and Krause, H.M. (1998) Single and double FISH protocols for Drosophila. in: Methods in Molecular Biology, vol. 122: Protocols in Confocal Microscopy., ed. Stephen Paddock, Humana Press Inc., 93-101.

A. Guichet, J. W. R. Copeland, M. Erdélyi, D. Hlousek, P. Zavorszky, J. Ho, S. Brown, A. Percival-Smith, H. M. Krause and A. Ephrussi (1997) The nuclear receptor homologue Ftz-F1 and the homeodomain protein Ftz are mutually dependent cofactors. Nature, 385, 548-552.

 

Copeland, J., Dietrich, B., Nasiadka, A. and Krause, H.M. (1996) Patterning of the Drosophila embryo by a homeodomain-deleted Ftz polypeptide. Nature, 379, 162-165.

 

Armen S Manoukian, Henry M Krause. (1993) Control of segmental asymmetry in Drosophila embryos. Development.  118 (3): 785–796.

 

Manoukian, A. S., & Manoukian, H. M. (1992). Concentration-dependent activities of the even-skipped protein in Drosophila embryos. Genes & Development., 6(9), 1740–1751.

 

Armen S Manoukian, Henry M Krause, Ellen W Larsen. (1992). Modifiers of bx1 alter the distribution of Ubx proteins in haltere imaginal discs of Drosophila. Developmental Biology., 151(2): 611-616.  

 

V Danial Fitzpatrick, Anthony Percival-Smith, C James Ingles, Henry M Krause. (1992). Homeodomain-independent activity of the fushi tarazu polypeptide in Drosophila embryos. Nature., 356(6370): 610-612.                  

 

Henry M Krause, Walter J Gehring. (1989). Stage‐specific phosphorylation of the fushi tarazu protein during Drosophila development. The EMBO Journal., 8(4): 1197-1204.

 

N Patrick Higgins, David A Collier, Michael W Kilpatrick, HM Krause. (1989). Supercoiling and integration host factor change the DNA conformation and alter the flow of convergent transcription in phage Mu. The Journal of Biological Chemistry., 264(5): 3035-3042.

 

Krause, H. M., Krause, R., & Klemenz, W. J. (1988). Expression, modification, and localization of the fushi tarazu protein in Drosophila embryos. Genes & Development., 2(8), 1021–1036.

 

HM Krause, WJ Gehring. (1988). The location, modification, and function of the fushi tarazu protein during Drosophila embryogenesis. Progress in clinical and biological research, 105–123.

 

Marek Mlodzik, Catherine M DeMontrion, Yasushi Hiromi, Henry M Krause, Walter J Gehring. (1987). The influence on the blastoderm fate map of maternal-effect genes that affect the antero-posterior pattern in Drosophila. Genes & Development., 1: 603-614.

 

Henry M Krause, N Patrick Higgins. (1986). Positive and negative regulation of the Mu operator by Mu repressor and Escherichia coli integration host factor. The Journal of Biological Chemistry., 261(8): 3744-3752.

 

Krause, H. M. (1985). A Model For The Transcriptional Regulation Of The Lytic And Lysogenic Pathways Of Bacteriophage Mu (early Genes, Promoters, Integration Host Factor (ihf), Supercoiling, Repressor).

 

HM Krause, NP Higgins. (1984). On the Mu repressor and early DNA intermediates of transposition. Cold Spring Harbor Symposia on Quantitative Biology, 49: 827-834.

 

HM Krause, MR Rothwell, NP Higgins. (1983). The early promoter of bacteriophage Mu: definition of the site of transcript initiation. Nucleic Acids Research., 11(16): 5483-5495.