Browse by Research Team

Bioinformatics

JAMM: a peak finder for joint analysis of NGS replicates.
Ibrahim, M.M., Lacadie, S.A. and Ohler, U.
Bioinformatics 31 (1): 48-55. 1 January 2015

Cell Genomics

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C., Kopp, W., Vučićević, D., Mattonet, K., Kempfer, R., Hirsekorn, A., Bilić, I., Gil, M., Trinks, A., Merks, A.M., Panáková, D., Pombo, A., Akalin, A., Junker, J.P., Stainier, D.Y.R., Garfield, D., Ohler, U. and Lacadie, S.A.
Cell Genomics 2 (1): 100083. 13 January 2022

Cell Stem Cell

The transcriptional landscape of hematopoietic stem cell ontogeny.
McKinney-Freeman, S., Cahan, P., Li, H., Lacadie, S.A., Huang, H.T., Curran, M., Loewer, S., Naveiras, O., Kathrein, K.L., Konantz, M., Langdon, E.M., Lengerke, C., Zon, L.I., Collins, J.J. and Daley, G.Q.
Cell Stem Cell 11 (5): 701-714. 2 November 2012

Developmental Cell

FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells.
Kolundzic, E., Ofenbauer, A., Bulut, S.I., Uyar, B., Baytek, G., Sommermeier, A., Seelk, S., He, M., Hirsekorn, A., Vucicevic, D., Akalin, A., Diecke, S., Lacadie, S.A. and Tursun, B.
Developmental Cell 46 (5): 611-626. 10 September 2018

EMBO Journal

Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes.
Abruzzi, K.C., Lacadie, S. and Rosbash, M.
EMBO Journal 23 (13): 2620-2631. 7 July 2004

Genes & Development

The ERGonomics of hematopoietic stem cell self-renewal.
Lacadie, S.A. and Zon, L.I.
Genes & Development 25 (4): 289-293. 15 February 2011

In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants.
Lacadie, S.A., Tardiff, D.F., Kadener, S. and Rosbash, M.
Genes & Development 20 (15): 2055-2066. 1 August 2006

Molecular Cell

Human promoters are intrinsically directional.
Duttke, S.H.C., Lacadie, S.A., Ibrahim, M.M., Glass, C.K., Corcoran, D.L., Benner, C., Heinz, S., Kadonaga, J.T. and Ohler, U.
Molecular Cell 57 (4): 674-684. 19 February 2015

A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional.
Tardiff, D.F., Lacadie, S.A. and Rosbash, M.
Molecular Cell 24 (6): 917-929. 28 December 2006

Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5'ss base pairing in yeast.
Lacadie, S.A. and Rosbash, M.
Molecular Cell 19 (1): 65-75. 1 July 2005

Nature Communications

Determinants of promoter and enhancer transcription directionality in metazoans.
Ibrahim, M.M., Karabacak, A., Glahs, A., Kolundzic, E., Hirsekorn, A., Carda, A., Tursun, B., Zinzen, R.P., Lacadie, S.A. and Ohler, U.
Nature Communications 9 (1): 4472. 26 October 2018

Nature Ecology & Evolution

Redundant regulation.
Lacadie, S.A. and Ohler, U.
Nature Ecology & Evolution 2 (3): 418-419. March 2018

Nature Genetics

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C, Daub, C.O., Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. July 2022

Science

NextGen speaks.
Lacadie, S.A.
Science 340 (6128): 29. April 2013

Wiley Interdisciplinary Reviews: Developmental Biology

Small molecule screening in zebrafish: swimming in potential drug therapies.
Tamplin, O.J., White, R.M., Jing, L., Kaufman, C.K., Lacadie, S.A., Li, P., Taylor, A.M. and Zon, L.I.
Wiley Interdisciplinary Reviews: Developmental Biology 1 (3): 459-468. May 2012

bioRxiv

Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation.
Vučićević, D., Hsu, C.W., Lopez Zepeda, L.S., Burkert, M., Hirsekorn, A., Bilić, I., Kastelić, N., Landthaler, M., Lacadie, S.A. and Ohler, U.
bioRxiv : 2024.09.12.612198. 12 September 2024