PUBLICATIONS
​​          Active Genetics:
​​
  1. Li Z, You L, Hermann A, Bier E. Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier. Nat Commun. 2024 Mar 23;15(1):2629. doi: 10.1038/s41467-024-46479-2. PMID: 38521791; PMCID: PMC10960810
  2. Auradkar A, Guichard A, Kaduwal S, Sneider M, Bier E. Author Correction: tgCRISPRi: efficient gene knock-down using truncated gRNAs and catalytically active Cas9. Nat Commun. 2024 Apr 12;15(1):3183. doi: 10.1038/s41467-024-47644-3. Erratum for: Nat Commun. 2023 Sep 11;14(1):5587. PMID: 38609401; PMCID: PMC11015020
  3. Guichard, A., S . Lu, O. Kanca, D. Bressan, Y. Huang, M. Ma, S. Sanz Juste, J.C. Andrews, K.L. Jay, M. Sneider, R. Schwartz, M.C. Huang, D. Bei, H. Pan, L. Ma, W. Lin, A. Auradkar, P. Bhagwat, S. Park, K.H. Wan, … Bier, E. (2023). A comprehensive Drosophila resource to identify key functional interactions between SARS-CoV-2 factors and host proteins. Cell reports, 42(8), 112842. Advance online publication. https://doi.org/10.1016/j.celrep.2023.112842 PMID: 37480566
  4. Terradas, G., J.B. Bennett, Z. Li, J.M. Marshall and E. Bier. (2022). Genetic conversion of a split-drive into a full-drive element. Nat. Com mun.14, 191 (2023) https://www.nature.com/articles/s41467-022-35044-4​
  5. Roy, S., S.S. Juste, M. Sneider, A. Auradkar, C. Klanseck, Z. Li, A.H.F. Julio, V.L. del Amo, E. Bier* and A. Guichard*. (2022). Cas9/Nickase-induced allelic conversion by homologous chromosome-templated repair in Drosophila somatic cells. Sci Adv . 8,  eabo0721. *Co-corresponding authors. doi:10.1126/sciadv.abo0721, PMID: 35776792.
  6. Kormos, A., G.C. Lanzaro, E. Bier, V. Santos, L. Nazaré, J. Pinto, A. Aguiar, A.A. James.  (2022). Ethical Considerations for Gene Drive: Challenges of Balancing Inclusion, Power and Perspectives. Front. Bioeng & Biotech Jan 21;10:826727. doi:10.3389/fbioe.2022.826727. PMID: 35127663. 
  7. Kaduskar, B., R.B.S Kushwah, A. Auradkar, A Guichard, M. Li, J.B. Bennett, A.H.F. Julio, J.M. Marshall, C, Montell, and E. Bier.  (2022). Reversing insecticide resistance with allelic-drive in Drosophila melanogaster. Nat. Commun. 13, 291; doi:10.1038/s41467-021-27654-1. PMID: 35022402.
  8. Weitzel A.J., H.A. Grunwald, C. Weber, R. Levina, V.M. Gantz, S.M. Hedrick, E. Bier, K.L. Cooper. (2021).  Meiotic Cas9 expression mediates gene conversion in the male and female mouse germline. PLoS Biol. 19, e3001478. doi:10.1371/journal.pbio.3001478. PMID: 34941868.
  9. Terradas, G., A. Hermann, A.A. James, W. McGinnis, and E. Bier.  (2021).  High-resolution in situ analysis of Cas9 germline transcript distributions in gene-drive Anopheles mosquitoes. G3 jkab369. doi:10.1093/g3journal/jkab369. PMID: 34791161.
  10. Bier, E.  (2021). Genetic GPS system of animal development explains why limbs grow from torsos and not heads. The Conversation Nov. 10, 2021 (invited).
  11. Auradkar, A., E. Bulger, S. Devkota, W. McGinnis, and E. Bier.  (2021).  Dissecting the evolutionary role of the Hox gene proboscipedia in Drosophila mouthpart diversification by full locus replacement. Sci Adv. 7, eabk1003. doi:10.1126/sciadv.abk1003. PMID: 34757777.
  12. Bier, E.  (2021 online).  Gene-drives: gaining speed. (2022 printed). Nat. Rev. Genet. 23, 5-22. doi:10.1038/s41576-021-00386-0. PMID: 34363067.
  13.  Bier, E. with V. Gantz and Z. Li (2021). Efficient interhomolog gene conversion in both somatic and germline cells of Drosophila. Nature Community Behind the Paper Blog (invited).
  14.  Li, Z. N. Marcel, S. Devkota, A. Auradkar, S.M. Hedrick, V.M. Gantz, E. Bier.  (2021).  CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion. Nat. Commun. 12, 2625; doi.org/10.1038/s41467-021-22927-1. PMID: 33976171
  15.  Bier, E. and V. Nizet.  (2021).  Driving to safety: CRISPR-based genetic approaches to reducing antibiotic resistance.  Trends in Genet. Mar 18:S0168-9525(21)00052-4. doi:10.1016/j.tig.2021.02.007.  PMID: 33745750.
  16.  Terradas, G., A.B. Buchman, J.B. Bennett, I. Shriner, J.M. Marshall, O.S. Akbari, and E. Bier.  (2021). Inherently confinable split-drive systems in Drosophila. Nat. Commun. 12, 1480; doi:10.1038/s41467-021-21771-7.
  17.  Chakraborty, M., A. Ramaiah., A. Adolfi., P. Halas., B. Kaduskar., L.T. Ngo, S. Jayaprasad, K. Paul, S. Whadgar, S. Srinivasan, S. Subramani, E. Bier, A.A. James, and J.J. Emerson. (2021).  Hidden features of the malaria vector mosquito, Anopheles stephensi, revealed by a high-quality reference genome.  BMC Biology 19, 28. doi:10.1186/s12915-021-00963-z.  PMID: 33568145
  18.  Kormos, A., G.C. Lanzaro, E. Bier, G.D. Dimopoulos, J.M. Marshall, J. Pinto., A. Aguiar dos Santos., A. Bacar, H.S. Pontes Sacramento Rompão, and A.A. James (2020). Application of the relationship-based model to engagement for field trials of genetically engineered malaria vectors. Amer. J. Trop. Med. Hyg. doi: 10.4269/ajtmh.20-0868. PMID: 33350374.
  19.  Adolfi, A., V.M. Gantz, N. Jasinskiene, H-F. Lee, K. Hwang, E.A. Bulger, A. Ramaiah, J.B. Bennett, G. Terradas, J.J. Emerson, J.M. Marshall, E. Bier, A.A. James.  (2020). Efficient population modification by a gene-drive rescue system in the malaria mosquito Anopheles stephensi.  Nat. Commun. 11, 5553; doi:10.1038/s41467-020-19426-0. PMID: 33144570.
  20.  Xu, X-R.S., E.A. Bulger†, V.M. Gantz†,  C. Klanseck, S.R. Heimler, A. Auradkar, J.B.B Bennett, L.A. Miller, S. Leahy, S.S Juste, A. Buchman, O.S. Akbari, J.M. Marshall, and E. Bier.  (2020).  Active-genetic neutralizing elements for halting or deleting gene-drives. Molecular Cell 80, 246-262. doi:10.1016/j.molcel.2020.09.003.  † Equal contributions. PMID: 32949493.
  21.  Bier, E and E. Sober.  (2020).  Gene editing and the war against malaria.  American Scientist 108, 162-169. doi:10.1511/2020.108.3.162.
  22.  López Del Amo, V., A. L. Bishop, H. M. Sánchez, J. B. Bennett, X. Feng, J. M. Marshall, E. Bier, and V. Gantz.  (2020). A trans-complementing split-gene drive system provides a flexible platform for laboratory investigation and potential field deployment.  Nat. Commun. 11, 352; doi:10.1038/s41467-019-13977-7.  PMID: 31953404.
  23.  Kandul, N., L. Liu, A. Buchman, V.M. Gantz, E. Bier, and O. Akbari.  (2019).  Assessment of a split homing-based drive for efficient knockout of multiple genes.  G3 10, 827-37; doi:0.1534/g3.119.400985. PMID: 31882406.
  24.  Valderamma, A.J., S.S. Kulkarni, V. Nizet, and E. Bier.  (2019).  A bacterial gene-drive system efficiently edits and inactivates a high copy number antibiotic resistance locus.  Nat. Comm. 10, 5726; doi:10.1038/s41467-019-13649-6. PMID: 31844051.
  25.  Grunwald, H.A.†, V.M. Gantz†, G. Poplawski†, X-R.S. Xu, E. Bier, and K.L. Cooper.  (2019).  Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline.  Nature 566, 105-109. † Equal contributions. PMID: 30675057.
  26.  Guichard, A., T. Haque, M. Bobik, X-R.S. Xu, C. Klanseck, R. Kushwah, M. Berni, B. Kaduskar, V.M. Gantz, and E. Bier.  (2019).  Efficient allelic-drive in Drosophila.  Nat. Comm. 10, Article number: 1640; doi: https://doi.org/10.1038/s41467-019-09694-w. PMID: 28945820.
  27.  Bier, E., M.M. Harrison, K.M. O'Connor-Giles, and J. Wildonger.  (2018).  Advances in Engineering the Fly Genome with the CRISPR-Cas System.  Genetics 208, 1-18; doi:10.1534/genetics.117.1113. PMID: 29301946.
  28.  Bier, E.  (2017).  Two lines of research converge to create immunizing gene-drive mosquitoes.  Authorea: https://www.authorea.com/users/176044/articles/233842-two-lines-of-research-converge-to-create-immunizing-gene-drive-mosquitoes
  29.  Aldeman, Z., O. Akbari, J. Bauer, E. Bier (+29 other authors).  (2017).  Rules of the road for insect gene drive research and testing.  Nature Biotech. 35, 716-18.  PMID:28787415
  30.  Xu, X-R.S., V.M. Gantz, N. Siomava, and E. Bier. (2017). CRISPR/Cas9 and Active Genetics-based trans-species replacement of the endogenous Drosophila kni-L2 CRM reveals unexpected complexity.  eLife 6, e30281; doi:10.7554/eLife.30281.  PMID: 29274230.
  31.  Gantz, V., and E Bier.  (2016).  The dawn of active genetics.  BioEssays 38, 50-63; Epub 12/10/15; DOI: 10.1002/bies.201500102.   PMID: 26660392
  32.  Akbari, O.S., H.J. Bellen, E. Bier, et al., (+24 other authors).  (2015).  Safeguarding gene drive experiments in the laboratory.  Science 349, 927-29; Epub 7/30/2015 ScienceExpress DOI: 10.1126/science.aac7932. PMID: 26229113.
  33.  Gantz, V., N. Jasinskiene, O. Tatarenkova, A. Fazekas, V.M. Macias, E. Bier*, and A.A. James*.  (2015).  Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito, Anopheles stephensi. PNAS 112, E6736-43; doi: 10.1073/pnas.1521077112.  *Co-corresponding authors.  PMID: 26598698.
  34.  Gantz, V. and E. Bier.  (2015).  The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science 348, 442-4; Epub 3/19/15 ScienceExpress DOI:10.1126/science.aaa5945. PMID: 25908821

    Host-Pathogen Interactions:

  35. Schwartz, R., A. Guichard, N.C. Franc, and E. Bier.  (2020).  A Drosophila model for Clostridium difficile toxin CDTa reveals interactions with multiple effector pathways.  iScience 23, 100865. doi:10.1016/j.isci.2020.100865.  PMID: 32058973.
  36. Guichard, A., P. Jain, M. Moayeri, R. Schwartz, S. Chin, L. Zhu, B. Cruz-Moreno, J. Liu, B. Aguilar, A. Hollands, S. H. Leppla, V. Nizet, and E. Bier.  (2017).  Anthrax Edema Toxin disrupts distinct steps in Rab11-dependent junctional transport.  PLoS Path. 13, e1006603.  PMID: 28945820.
  37. Smelkinson, M.G, A. Guichard, J. Teijaro, M. Malur, M.E. Loureiro, P. Jain, E.I. Zúñiga, S. Ganesan, R.M. Krug, M.B. Oldstone, and E. Bier.  (2017).  Influenza NS1 directly modulates Hedgehog signaling during infection. PLoS Path. 13, e1006588. PMID: 28837667.
  38. Bier, E. and V. Nizet.  (2015).  Hedgehog: Linking uracil to innate defense. Cell Host & Microbe 17,146-48.  PMID: 25674980.
  39. Guichard, A., V. Nizet, and E. Bier.  (2014).  Rab11-mediated trafficking in host-pathogen interactions. Nat. Rev. Microbiol.12, 624-634.  PMID: 28945820.
  40. Guichard, A., B. Cruz-Moreno, B. Aguilar, J. Kuang, A.A. Kurkciyan, Z. Wang, S. Hang, G.P. Pineton de Chambrun, D.F. McCole, P. Watnick, N.M. van Sorge, V. Nizet, and E. Bier.  (2013). Cholera toxin disrupts barrier function by inhibiting exocyst-mediated trafficking of host proteins to intestinal cell junctions.  Cell Host & Microbe 14, 294-305.  PMID: 24034615.
  41. Guichard, A., V. Nizet and E. Bier.  (2012).  New insights into the biological effects of anthrax toxins: linking cellular to organismal responses. Microbes & Infect. 14, 97-118.  PMID: 21930233.
  42. Guichard, A., S.M. McGillivray, B. Cruz-Moreno, N.M. van Sorge, V. Nizet, and E. Bier.  (2010).  Anthrax toxins cooperatively inhibit endocytic recycling by the Rab11/Sec15 exocyst.  Nature 467, 854-859. PMID: 20944747.
  43. Guichard, A., J-M. Park, B. Cruz-Moreno, M. Karin, and E. Bier.  (2006).  Anthrax Lethal Factor and Edema Factor act on conserved targets in Drosophila.  PNAS 103, 3244-3249.  PMID: 16455799.
  44. Bier, E.  (2005).  Drosophila, the golden bug, emerges as a tool for human genetics.  Nat. Rev. Genet. 6, 9-23.  PMID: 15630418.
  45. Reiter, L.T., L. Potocki, S. Chien, M. Gribskov, and E. Bier.  (2001).  A systematic analysis of human disease-associated genes in Drosophila melanogaster. Genome Res. 11, 1114-1125.  PMID: 11381037.

    Evo-Devo:
    Vein Patterning:

  46.  Xu, X-R.S., V.M. Gantz, N. Siomava, and E. Bier. (2017).  CRISPR/Cas9 and Active Genetics-based trans-species replacement of the endogenous Drosophila kni-L2 CRM reveals unexpected complexity.  eLife 6, e30281; doi:10.7554/eLife.30281.  PMID: 29274230.
  47.  Cook, O., B. Biehs, and E. Bier.  (2004).  brinker and optomotor-blind act coordinately to initiate development of the L5 wing vein primordium in Drosophila.  Development 131, 2113-2124.  PMID: 15073155.
  48.  Lunde, K., J. Trimble, A. Guichard, K. Guss, U. Nauber, and E. Bier.  (2003).  Activation of the knirps locus links patterning to morphogenesis of the second wing vein in Drosophila.  Development 130, 235-248. PMID: 12466192.
  49.  Biehs, B., M.A. Sturtevant, and E. Bier.  (1998).  Boundaries in the Drosophila wing imaginal discs organize vein-specific genetic programs.  Development 125, 4245-4257. PMID: 9753679.
  50.  Lunde, K., B. Biehs, and E. Bier.  (1998).  The knirps and knirps-related genes organize development of the second wing vein in Drosophila.  Development 125, 4145-4154.  PMID: 9753669.
  51.  Sturtevant, M.A., B. Biehs, E. Marin, and E. Bier.  (1997).  The spalt gene links the A/P compartment boundary to a linear adult structure in the Drosophila wing.  Development 124, 21-32.  PMID: 9006064.
  52.  Yu, K., M.A. Sturtevant, B. Biehs, V. François, R. Padgett, R. Blackman, and E. Bier.  (1996).  The Drosophila decapentaplegic and short gastrulation genes function antagonistically during adult wing vein development.  Development 122, 4033-4044.  PMID: 9012523.
  53.  Sturtevant, M.A. and E. Bier.  (1995).  Analysis of the genetic hierarchy guiding wing vein formation in Drosophila.  Development 121, 785-801.  PMID: 7720583.

    Dorsal-Ventral Embryonic Patterning:

  54.  Bier, E. and E.M. De Robertis.  (2015).  BMP gradients: a paradigm for morphogen-mediated developmental patterning. (Review Summary) Science 348, 1443; Full Online Review: aaa5838: 1-12.  PMID: 26113727.
  55.  Esteves, F.F., A. Springhorn, E. Kague, E. Taylor, G. Pyrowolakis, S. Fisher, and E. Bier.  (2014). BMPs regulate msx gene expression in the dorsal neuroectoderm of Drosophila and vertebrates by distinct mechanisms. PLoS Genetics 10, e1004625.  PMID: 25210771.
  56.  McHale, P., C. M. Mizutani, D. Kosman, D. L. MacKay, M. Belu, A. Hermann, W. McGinnis, E. Bier and T. Hwa.  (2011).  Gene length may contribute to graded transcriptional responses in the Drosophila embryo.  Dev. Biol. 360, 230-240.  PMID: 21920356.
  57.  Bier, E.  (2011).  Evolution of Development: Diversified Dorsoventral Patterning. Curr. Biol. 21, R591-594.  PMID: 21820625.
  58.  Mizutani, C.M. and E. Bier.  (2008).  EvoD/Vo: the origins of BMP signalling in the neuroectoderm. Nat. Rev. Genet. 9, 663-677, doi:10.1038/nrg2417.  PMID: 18679435.
  59.  Mizutani, C.M., N. Meyer, H. Roelink, and E. Bier.  (2006).  Threshold dependent BMP mediated repression: a model for a conserved mechanism that patterns the neuroectoderm.  PLoS Biol. 4, e313.  PMID: 16968133.
  60.  Mizutani, C.M., Q. Nie, F.-Y.M. Wan, Y.-T. Zhang, P. Vilmos, R. Sousa-Neves, E. Bier, J. L. Marsh, and A. D. Lander. (2005).  Formation of the BMP activity gradient in the Drosophila embryo. Dev. Cell 8, 915-924.  PMID: 15935780.
  61.  Kosman, D., C.M. Mizutani, D. Lemons, G. Cox, W. McGinnis, and E. Bier.  Multiplex detection of RNA expression in Drosophila embryos. (2004).  Science 305, 846.  PMID: 15297669.
  62.  Srinivasan, S., K. E. Rashka and E. Bier.  (2002).  Creation of a Sog morphogen gradient in the Drosophila embryo. Dev. Cell 2, 91-101.  PMID: 11782317.
  63.  Biehs, B., François, V., and E. Bier.  (1996).  The Drosophila short gastrulation gene prevents Dpp signaling from autoactivating and suppressing neurogenesis in the neuroectoderm.  Genes and Dev. 10, 2922-2934.  PMID: 8918893.
  64.  Schmidt, J., V. François, E. Bier, and D. Kimelman.  (1995).  The Drosophila short gastrulation gene induces an ectopic axis in Xenopus: evidence for conserved mechanisms of dorsal-ventral patterning.  Development 121, 4319-4328.  PMID: 8575332.
  65.  François, V. and E. Bier.  (1995).  The Xenopus chordin and the Drosophila short gastrulation genes encode homologous proteins functioning in dorsal-ventral axis formation.  Cell 80, 19-20.  PMID: 7813014.
  66.  François, V., M. Solloway, J.W. O'Neill, J. Emery, and E. Bier.  (1994).  Dorsal-ventral patterning of the Drosophila embryo depends on a putative negative growth factor encoded by the short gastrulation gene.  Genes and Dev. 8, 2602-2616.  PMID: 7958919.
  67.  Sturtevant, M.A, M. Roark, and E. Bier.  (1993).  The Drosophila rhomboid gene mediates the localized formation of wing veins and interacts genetically with components of the EGF-R signaling pathway.  Genes and Dev. 7, 961-973.  PMID: 8504935.