Publications

20 items matching your search terms.

SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms

O'Donoghue, S. I.; Schafferhans, A.; Sikta, N.; Stolte, C.; Kaur, S.; Ho, B. K.; Anderson, S.; Procter, J. B.; Dallago, C.; Bordin, N.; Adcock, M.; Rost, B.

Molecular Systems Biology 17 (9) :e10079, 2021 10.15252/msb.202010079

PredictProtein - Predicting Protein Structure and Function for 29 Years

Bernhofer, M.; Dallago, C.; Karl, T.; Satagopam, V.; Heinzinger, M.; Littmann, M.; Olenyi, T.; Qiu, J.; Schutze, K.; Yachdav, G.; Ashkenazy, H.; Ben-Tal, N.; Bromberg, Y.; Goldberg, T.; Kajan, L.; O'Donoghue, S.; Sander, C.; Schafferhans, A.; Schlessinger, A.; Vriend, G.; Mirdita, M.; Gawron, P.; Gu, W.; Jarosz, Y.; Trefois, C.; Steinegger, M.; Schneider, R.; Rost, B.

NUCLEIC ACIDS RESEARCH 49 (W1) :W535-W540, 2021 10.1093/nar/gkab354

Single-cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtype

Valdes-Mora, F.; Salomon, R.; Gloss, B. S.; Law, A. M. K.; Venhuizen, J.; Castillo, L.; Murphy, K. J.; Magenau, A.; Papanicolaou, M.; Rodriguez de la Fuente, L.; Roden, D. L.; Colino-Sanguino, Y.; Kikhtyak, Z.; Farbehi, N.; Conway, J. R. W.; Sikta, N.; Oakes, S. R.; Cox, T. R.; O'Donoghue, S. I.; Timpson, P.; Ormandy, C. J.; Gallego-Ortega, D.

Cell Reports 35 (2) :108945, 2021 10.1016/j.celrep.2021.108945

Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Martinez, X.; Krone, M.; Alharbi, N.; Rose, A. S.; Laramee, R. S.; O'Donoghue, S.; Baaden, M.; Chavent, M.

STRUCTURE 27 (11) :1617-1623, 2019 10.1016/j.str.2019.09.001

SnapShot: S-Phase Entry and Exit

Burgess, A.; Vuong, J.; Marzec, K. A.; Nicolai de Lichtenberg, U.; O'Donoghue, S. I.; Jensen, L. J.

CELL 179 (3) :802-802 e1, 2019 10.1016/j.cell.2019.09.031

A benchmark dataset for analyzing and visualizing the dynamic epiproteome

Kaur, S.; Baldi, B.; Vuong, J.; O'Donoghue, S. I.

Data in Brief 25 :104000, 2019 10.1016/j.dib.2019.104000

Visualization and Analysis of Epiproteome Dynamics

Kaur, S.; Baldi, B.; Vuong, J.; O'Donoghue, S. I.

JOURNAL OF MOLECULAR BIOLOGY 431 (8) :1519-1539, 2019 10.1016/j.jmb.2019.01.044

Dark Proteins Important for Cellular Function

Schafferhans, A.; O'Donoghue, S. I.; Heinzinger, M.; Rost, B.

PROTEOMICS :e1800227, 2018 10.1002/pmic.201800227

The Dark Proteome Database

Perdigao, N.; Rosa, A. C.; O'Donoghue, S. I.

BioData Mining 10 :24, 2017 10.1186/s13040-017-0144-6

SnapShot: Phosphoregulation of Mitosis

Burgess, A.; Vuong, J.; Rogers, S.; Malumbres, M.; O'Donoghue, S. I.

CELL 169 (7) :1358-1358.e1, 2017 10.1016/j.cell.2017.06.003

Monogenic and polygenic determinants of sarcoma risk: an international genetic study

Ballinger, M. L.; Goode, D. L.; Ray-Coquard, I.; James, P. A.; Mitchell, G.; Niedermayr, E.; Puri, A.; Schiffman, J. D.; Dite, G. S.; Cipponi, A.; Maki, R. G.; Brohl, A. S.; Myklebost, O.; Stratford, E. W.; Lorenz, S.; Ahn, S. M.; Ahn, J. H.; Kim, J. E.; Shanley, S.; Beshay, V.; Randall, R. L.; Judson, I.; Seddon, B.; Campbell, I. G.; Young, M. A.; Sarin, R.; Blay, J. Y.; O'Donoghue, S. I.; Thomas, D. M.; International Sarcoma Kindred, Study;

LANCET ONCOLOGY 17 (9) :1261-71, 2016

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

Taberlay, P. C. ; Achinger-Kawecka, J. ; Lun, A. T. ; Buske, F. A. ; Sabir, K. ; Gould, C. M. ; Zotenko, E. ; Bert, S. A. ; Giles, K. A. ; Bauer, D. C. ; Smyth, G. K. ; Stirzaker, C. ; O'Donoghue, S. I. ; Clark, S. J.;

GENOME RESEARCH 26 (6) :719-31, 2016

Unexpected features of the ‘dark’ proteome

Perdigao, N.; Heinrich, J.; Stolte, C.; Sabir, K.S.; Buckley, M.J.; Tabor, B; Signal, B; Gloss, B.S.; Hammang, C.J.; Rost, B.; Schafferhans, A.; O'Donoghue, S.I.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112 (52) :15898-903, 2015

Aquaria: Simplifying discovery and insight from protein structures

O'Donoghue, S. I.; Sabir, K. S.; Kalemanov, M.; Stolte, C.; Wellmann, B.; Ho, V.; Roos, M.; Perdigao, N.; Buske, F. A.; Heinrich, J.; Rost, B.; Schafferhans, A.

NATURE METHODS 12 (2) :98-99, 2015

How to learn about gene function: text-mining or ontologies?

Soldatos, T. G.; Perdigao, N.; Brown, N. P.; Sabir, K. S.; O'Donoghue, S. I.

METHODS 74 :3-15, 2015

Unexpected features of the dark proteome

Perdigao, N. ; Heinrich, J. ; Stolte, C. ; Sabir, K. S. ; Buckley, M. J. ; Tabor, B. ; Signal, B. ; Gloss, B. S. ; Hammang, C. J. ; Rost, B. ; Schafferhans, A. ; O'Donoghue, S. I.;

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112 (52) :15898-903, 2015