Rune Linding

 

(Photo © Abhinav Mishra)

 

Co-PI

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room: 504

 

Profile

Rune Linding is the co-PI of the Klipp-Linding Lab. His research focus is how dynamic interactions that flux in space and time can causally alter nonlinear complex systems. They conduct time-series analysis of cancer associated cell signaling networks and utilize scientific machine learning (Sci-ML) to create data driven mechanistic models that aim to address grand clinical challenges.

+ - Publications Click to collapse

  1. Rein Aasland, Charles Abrams, Christophe Ampe, Linda J Ball, Mark T Bedford, Gianni Cesareni, Mario Gimona, James H Hurley, Thomas Jarchau, Veli Pekka Lehto, Mark A Lemmon, Rune Linding, Bruce J Mayer, Makoto Nagai, Marius Sudol, Ulrich Walter and Steve J Winder.
    Normalization of nomenclature for peptide motifs as ligands of modular protein domains..
    FEBS letters 513:141-4, February 2002.

  2. Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M A Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N Hunter, Rein Aasland and Toby J Gibson.
    ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins..
    Nucleic acids research 31:3625-30, July 2003.

  3. Rune Linding, Robert B Russell, Victor Neduva and Toby J Gibson.
    GlobPlot: Exploring protein sequences for globularity and disorder..
    Nucleic acids research 31:3701-8, July 2003.

  4. Konstantinos Bimpikis, Aidan Budd, Rune Linding and Toby J Gibson.
    BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases..
    Nucleic acids research 31:3792-4, July 2003.

  5. Rune Linding, Lars Juhl Jensen, Francesca Diella, Peer Bork, Toby J Gibson and Robert B Russell.
    Protein disorder prediction: implications for structural proteomics..
    Structure (London, England : 1993) 11:1453-9, November 2003.

  6. Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Kuster, Thomas Sicheritz-Pontén, Nikolaj Blom and Toby J Gibson.
    Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins..
    BMC bioinformatics 5:79, June 2004.

  7. Rune Linding, Joost Schymkowitz, Frederic Rousseau, Francesca Diella and Luis Serrano.
    A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins..
    Journal of molecular biology 342:345-53, September 2004.

  8. Tony Pawson and Rune Linding.
    Synthetic modular systems–reverse engineering of signal transduction..
    FEBS letters 579:1808-14, March 2005.

  9. Robert J Ingham, Karen Colwill, Caley Howard, Sabine Dettwiler, Caesar S H Lim, Joanna Yu, Kadija Hersi, Judith Raaijmakers, Gerald Gish, Geraldine Mbamalu, Lorne Taylor, Benny Yeung, Galina Vassilovski, Manish Amin, Fu Chen, Liudmila Matskova, Gösta Winberg, Ingemar Ernberg, Rune Linding, Paul O'donnell, Andrei Starostine, Walter Keller, Pavel Metalnikov, Chris Stark and Tony Pawson.
    WW domains provide a platform for the assembly of multiprotein networks..
    Molecular and cellular biology 25:7092-106, August 2005.

  10. Victor Neduva, Rune Linding, Isabelle Su-Angrand, Alexander Stark, Federico Masi, Toby J Gibson, Joe Lewis, Luis Serrano and Robert B Russell.
    Systematic discovery of new recognition peptides mediating protein interaction networks..
    PLoS biology 3:e405, December 2005.

  11. Rune Linding, Lars Juhl Jensen, Gerard J Ostheimer, Marcel A T M Vugt, Claus Jørgensen, Ioana M Miron, Francesca Diella, Karen Colwill, Lorne Taylor, Kelly Elder, Pavel Metalnikov, Vivian Nguyen, Adrian Pasculescu, Jing Jin, Jin Gyoon Park, Leona D Samson, James R Woodgett, Robert B Russell, Peer Bork, Michael B Yaffe and Tony Pawson.
    Systematic discovery of in vivo phosphorylation networks..
    Cell 129:1415-26, June 2007.

  12. Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B Yaffe and Tony Pawson.
    NetworKIN: a resource for exploring cellular phosphorylation networks..
    Nucleic acids research 36:D695-9, January 2008.

  13. Claus Jørgensen and Rune Linding.
    Directional and quantitative phosphorylation networks..
    Briefings in functional genomics & proteomics 7:17-26, January 2008.

  14. Tony Pawson and Rune Linding.
    Network medicine..
    FEBS letters 582:1266-70, April 2008.

  15. Martin Lee Miller, Lars Juhl Jensen, Francesca Diella, Claus Jørgensen, Michele Tinti, Lei Li, Marilyn Hsiung, Sirlester A Parker, Jennifer Bordeaux, Thomas Sicheritz-Ponten, Marina Olhovsky, Adrian Pasculescu, Jes Alexander, Stefan Knapp, Nikolaj Blom, Peer Bork, Shawn Li, Gianni Cesareni, Tony Pawson, Benjamin E Turk, Michael B Yaffe, Søren Brunak and Rune Linding.
    Linear motif atlas for phosphorylation-dependent signaling..
    Science signaling 1:ra2, September 2008.

  16. Chris Bakal, Rune Linding, Flora Llense, Elleard Heffern, Enrique Martin-Blanco, Tony Pawson and Norbert Perrimon.
    Phosphorylation networks regulating JNK activity in diverse genetic backgrounds..
    Science (New York, N.Y.) 322:453-6, October 2008.

  17. Kai Wang, Mariano J Alvarez, Brygida C Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla Favera and Andrea Califano.
    Dissecting the interface between signaling and transcriptional regulation in human B cells..
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pages 264-75, 2009.

  18. Ian W Taylor, Rune Linding, David Warde-Farley, Yongmei Liu, Catia Pesquita, Daniel Faria, Shelley Bull, Tony Pawson, Quaid Morris and Jeffrey L Wrana.
    Dynamic modularity in protein interaction networks predicts breast cancer outcome..
    Nature biotechnology 27:199-204, February 2009.

  19. Chris Soon Heng Tan, Bernd Bodenmiller, Adrian Pasculescu, Marko Jovanovic, Michael O Hengartner, Claus Jørgensen, Gary D Bader, Ruedi Aebersold, Tony Pawson and Rune Linding.
    Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases..
    Science signaling 2:ra39, July 2009.

  20. Dennis Van Hoof, Javier Muñoz, Stefan R Braam, Martijn W H Pinkse, Rune Linding, Albert J R Heck, Christine L Mummery and Jeroen Krijgsveld.
    Phosphorylation dynamics during early differentiation of human embryonic stem cells..
    Cell stem cell 5:214-26, August 2009.

  21. Chris Soon Heng Tan, Adrian Pasculescu, Wendell A Lim, Tony Pawson, Gary D Bader and Rune Linding.
    Positive selection of tyrosine loss in metazoan evolution..
    Science (New York, N.Y.) 325:1686-8, September 2009.

  22. Jing Jin, Xueying Xie, Chen Chen, Jin Gyoon Park, Chris Stark, Andrew D James, Marina Olhovsky, Rune Linding, Yongyi Mao and Tony Pawson.
    Eukaryotic protein domains as functional units of cellular evolution..
    Science signaling 2:ra76, November 2009.

  23. Chris Soon Heng Tan and Rune Linding.
    Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networks..
    Proteomics 9:5233-42, December 2009.

  24. Claus Jørgensen, Andrew Sherman, Ginny I Chen, Adrian Pasculescu, Alexei Poliakov, Marilyn Hsiung, Brett Larsen, David G Wilkinson, Rune Linding and Tony Pawson.
    Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells..
    Science (New York, N.Y.) 326:1502-9, December 2009.

  25. Cathryn M Gould, Francesca Diella, Allegra Via, Pål Puntervoll, Christine Gemünd, Sophie Chabanis-Davidson, Sushama Michael, Ahmed Sayadi, Jan Christian Bryne, Claudia Chica, Markus Seiler, Norman E Davey, Niall Haslam, Robert J Weatheritt, Aidan Budd, Tim Hughes, Jakub Pas, Leszek Rychlewski, Gilles Travé, Rein Aasland, Manuela Helmer-Citterich, Rune Linding and Toby J Gibson.
    ELM: the status of the 2010 eukaryotic linear motif resource..
    Nucleic acids research 38:D167-80, January 2010.

  26. Janine T Erler and Rune Linding.
    Network-based drugs and biomarkers..
    The Journal of pathology 220:290-6, January 2010.

  27. Marcel A T M Vugt, Alexandra K Gardino, Rune Linding, Gerard J Ostheimer, Christian H Reinhardt, Shao-En Ong, Chris S Tan, Hua Miao, Susan M Keezer, Jeijin Li, Tony Pawson, Timothy A Lewis, Steven A Carr, Stephen J Smerdon, Thijn R Brummelkamp and Michael B Yaffe.
    A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint..
    PLoS biology 8:e1000287, January 2010.

  28. Claus Jørgensen and Rune Linding.
    Simplistic pathways or complex networks?.
    Current opinion in genetics & development 20:15-22, February 2010.

  29. Chris Soon Heng Tan, Claus Jørgensen and Rune Linding.
    Roles of “junk phosphorylation” in modulating biomolecular association of phosphorylated proteins?.
    Cell cycle (Georgetown, Tex.) 9:1276-80, April 2010.

  30. Rune Linding.
    Multivariate signal integration..
    Nature reviews. Molecular cell biology 11:391, June 2010.

  31. Rune Linding.
    (R)evolution of complex regulatory systems..
    In Science signaling 3. June 2010, eg4.

  32. Christian H Reinhardt, Pia Hasskamp, Ingolf Schmedding, Sandra Morandell, Marcel A T M Vugt, Xiaozhe Wang, Rune Linding, Shao-En Ong, David Weaver, Steven A Carr and Michael B Yaffe.
    DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization..
    Molecular cell 40:34-49, October 2010.

  33. Marina Olhovsky, Kelly Williton, Anna Yue Dai, Adrian Pasculescu, John Paul Lee, Marilyn Goudreault, Clark D Wells, Jin Gyoon Park, Anne-Claude Gingras, Rune Linding, Tony Pawson and Karen Colwill.
    OpenFreezer: a reagent information management software system..
    July 2011.

  34. Pablo Meyer, Leonidas G Alexopoulos, Thomas Bonk, Andrea Califano, Carolyn R Cho, Alberto Fuente, David Graaf, Alexander J Hartemink, Julia Hoeng, Nikolai V Ivanov, Heinz Koeppl, Rune Linding, Daniel Marbach, Raquel Norel, Manuel C Peitsch, Jeremy J Rice, Ajay Royyuru, Frank Schacherer, Joerg Sprengel, Katrin Stolle, Dennis Vitkup and Gustavo Stolovitzky.
    Verification of systems biology research in the age of collaborative competition..
    Nature biotechnology 29:811-5, September 2011.

  35. Christopher R Kinsinger, James Apffel, Mark Baker, Xiaopeng Bian, Christoph H Borchers, Ralph Bradshaw, Mi-Youn Brusniak, Daniel W Chan, Eric W Deutsch, Bruno Domon, Jeff Gorman, Rudolf Grimm, William Hancock, Henning Hermjakob, David Horn, Christie Hunter, Patrik Kolar, Hans-Joachim Kraus, Hanno Langen, Rune Linding, Robert L Moritz, Gilbert S Omenn, Ron Orlando, Akhilesh Pandey, Peipei Ping, Amir Rahbar, Robert Rivers, Sean L Seymour, Richard J Simpson, Douglas Slotta, Richard D Smith, Stephen E Stein, David L Tabb, Danilo Tagle, John 3rd R Yates and Henry Rodriguez.
    Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)..
    December 2011.

  36. Christopher R Kinsinger, James Apffel, Mark Baker, Xiaopeng Bian, Christoph H Borchers, Ralph Bradshaw, Mi-Youn Brusniak, Daniel W Chan, Eric W Deutsch, Bruno Domon, Jeff Gorman, Rudolf Grimm, William Hancock, Henning Hermjakob, David Horn, Christie Hunter, Patrik Kolar, Hans-Joachim Kraus, Hanno Langen, Rune Linding, Robert L Moritz, Gilbert S Omenn, Ron Orlando, Akhilesh Pandey, Peipei Ping, Amir Rahbar, Robert Rivers, Sean L Seymour, Richard J Simpson, Douglas Slotta, Richard D Smith, Stephen E Stein, David L Tabb, Danilo Tagle, John 3rd R Yates and Henry Rodriguez.
    Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)..
    December 2011.

  37. Christopher R Kinsinger, James Apffel, Mark Baker, Xiaopeng Bian, Christoph H Borchers, Ralph Bradshaw, Mi-Youn Brusniak, Daniel W Chan, Eric W Deutsch, Bruno Domon, Jeff Gorman, Rudolf Grimm, William Hancock, Henning Hermjakob, David Horn, Christie Hunter, Patrik Kolar, Hans-Joachim Kraus, Hanno Langen, Rune Linding, Robert L Moritz, Gilbert S Omenn, Ron Orlando, Akhilesh Pandey, Peipei Ping, Amir Rahbar, Robert Rivers, Sean L Seymour, Richard J Simpson, Douglas Slotta, Richard D Smith, Stephen E Stein, David L Tabb, Danilo Tagle, John R Yates and Henry Rodriguez.
    Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)..
    January 2012.

  38. Pau Creixell and Rune Linding.
    Cells, shared memory and breaking the PTM code..
    2012.

  39. Christopher R Kinsinger, James Apffel, Mark Baker, Xiaopeng Bian, Christoph H Borchers, Ralph Bradshaw, Mi-Youn Brusniak, Daniel W Chan, Eric W Deutsch, Bruno Domon, Jeff Gorman, Rudolf Grimm, William Hancock, Henning Hermjakob, David Horn, Christie Hunter, Patrik Kolar, Hans-Joachim Kraus, Hanno Langen, Rune Linding, Robert L Moritz, Gilbert S Omenn, Ron Orlando, Akhilesh Pandey, Peipei Ping, Amir Rahbar, Robert Rivers, Sean L Seymour, Richard J Simpson, Douglas Slotta, Richard D Smith, Stephen E Stein, David L Tabb, Danilo Tagle, John R Yates and Henry Rodriguez.
    Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)..
    February 2012.

  40. Janine T Erler and Rune Linding.
    Network medicine strikes a blow against breast cancer..
    Cell 149:731-3, May 2012.

  41. Pau Creixell, Erwin M Schoof, Chris Soon Heng Tan and Rune Linding.
    Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues..
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 367:2584-93, September 2012.

  42. Pau Creixell, Erwin M Schoof, Janine T Erler and Rune Linding.
    Navigating cancer network attractors for tumor-specific therapy..
    Nature biotechnology 30:842-8, September 2012.

  43. Sara Zanivan, Alexander Meves, Kristina Behrendt, Erwin M Schoof, Lisa J Neilson, Jürgen Cox, Hao R Tang, Gabriela Kalna, Janine H Ree, Jan M Deursen, Carol S Trempus, Laura M Machesky, Rune Linding, Sara A Wickström, Reinhard Fässler and Matthias Mann.
    In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis..
    Cell reports 3:552-66, February 2013.

  44. Sarah F Martin, Heiner Falkenberg, Thomas F Dyrlund, Guennadi A Khoudoli, Craig J Mageean and Rune Linding.
    PROTEINCHALLENGE: crowd sourcing in proteomics analysis and software development..
    Journal of proteomics 88:41-6, August 2013.

  45. Abel Gonzalez-Perez, Ville Mustonen, Boris Reva, Graham R S Ritchie, Pau Creixell, Rachel Karchin, Miguel Vazquez, Lynn J Fink, Karin S Kassahn, John V Pearson, Gary D Bader, Paul C Boutros, Lakshmi Muthuswamy, Francis B F Ouellette, Jüri Reimand, Rune Linding, Tatsuhiro Shibata, Alfonso Valencia, Adam Butler, Serge Dronov, Paul Flicek, Nick B Shannon, Hannah Carter, Li Ding, Chris Sander, Josh M Stuart, Lincoln D Stein and Nuria Lopez-Bigas.
    Computational approaches to identify functional genetic variants in cancer genomes..
    Nature methods 10:723-9, August 2013.

  46. Brigid C Browne, Falko Hochgräfe, Jianmin Wu, Ewan K A Millar, Jane Barraclough, Andrew Stone, Rachael A McCloy, Christine S Lee, Caroline Roberts, Naveid A Ali, Alice Boulghourjian, Fabian Schmich, Rune Linding, Lynn Farrow, Julia M W Gee, Robert I Nicholson, Sandra A O'Toole, Robert L Sutherland, Elizabeth A Musgrove, Alison J Butt and Roger J Daly.
    Global characterization of signalling networks associated with tamoxifen resistance in breast cancer..
    The FEBS journal 280:5237-57, November 2013.

  47. X Robin, P Creixell, O Radetskaya, C C Santini, J Longden and R Linding.
    Personalized network-based treatments in oncology..
    Clinical pharmacology and therapeutics 94:646-50, December 2013.

  48. Erwin M Schoof and Rune Linding.
    Experimental and computational tools for analysis of signaling networks in primary cells..
    Current protocols in immunology 104:11.11.1-11.11.23, February 2014.

  49. Adrian Pasculescu, Erwin M Schoof, Pau Creixell, Yong Zheng, Marina Olhovsky, Ruijun Tian, Jonathan So, Rachel D Vanderlaan, Tony Pawson, Rune Linding and Karen Colwill.
    CoreFlow: a computational platform for integration, analysis and modeling of complex biological data..
    Journal of proteomics 100:167-73, April 2014.

  50. Marie-Claude Djidja, Joan Chang, Andreas Hadjiprocopis, Fabian Schmich, John Sinclair, Martina Mršnik, Erwin M Schoof, Holly E Barker, Rune Linding, Claus Jørgensen and Janine T Erler.
    Identification of hypoxia-regulated proteins using MALDI-mass spectrometry imaging combined with quantitative proteomics..
    Journal of proteome research 13:2297-313, May 2014.

  51. Heiko Horn, Erwin M Schoof, Jinho Kim, Xavier Robin, Martin L Miller, Francesca Diella, Anita Palma, Gianni Cesareni, Lars Juhl Jensen and Rune Linding.
    KinomeXplorer: an integrated platform for kinome biology studies..
    June 2014.

  52. Alessio Maiolica, Maria Medina-Redondo, Erwin M Schoof, Apirat Chaikuad, Fabrizio Villa, Marco Gatti, Siva Jeganathan, Hua Jane Lou, Karel Novy, Simon Hauri, Umut H Toprak, Franz Herzog, Patrick Meraldi, Lorenza Penengo, Benjamin E Turk, Stefan Knapp, Rune Linding and Ruedi Aebersold.
    Modulation of the chromatin phosphoproteome by the Haspin protein kinase..
    Molecular & cellular proteomics : MCP 13:1724-40, July 2014.

  53. Jonathan So, Adrian Pasculescu, Anna Y Dai, Kelly Williton, Andrew James, Vivian Nguyen, Pau Creixell, Erwin M Schoof, John Sinclair, Miriam Barrios-Rodiles, Jun Gu, Aldis Krizus, Ryan Williams, Marina Olhovsky, James W Dennis, Jeffrey L Wrana, Rune Linding, Claus Jorgensen, Tony Pawson and Karen Colwill.
    Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy..
    Science signaling 8:rs3, April 2015.

  54. Pau Creixell, Jüri Reimand, Syed Haider, Guanming Wu, Tatsuhiro Shibata, Miguel Vazquez, Ville Mustonen, Abel Gonzalez-Perez, John Pearson, Chris Sander, Benjamin J Raphael, Debora S Marks, Francis B F Ouellette, Alfonso Valencia, Gary D Bader, Paul C Boutros, Joshua M Stuart, Rune Linding, Nuria Lopez-Bigas and Lincoln D Stein.
    Pathway and network analysis of cancer genomes..
    Nature methods 12:615-621, July 2015.

  55. Pau Creixell, Erwin M Schoof, Craig D Simpson, James Longden, Chad J Miller, Hua Jane Lou, Lara Perryman, Thomas R Cox, Nevena Zivanovic, Antonio Palmeri, Agata Wesolowska-Andersen, Manuela Helmer-Citterich, Jesper Ferkinghoff-Borg, Hiroaki Itamochi, Bernd Bodenmiller, Janine T Erler, Benjamin E Turk and Rune Linding.
    Kinome-wide decoding of network-attacking mutations rewiring cancer signaling..
    Cell 163:202-17, September 2015.

  56. Pau Creixell, Antonio Palmeri, Chad J Miller, Hua Jane Lou, Cristina C Santini, Morten Nielsen, Benjamin E Turk and Rune Linding.
    Unmasking determinants of specificity in the human kinome..
    Cell 163:187-201, September 2015.

  57. Thomas R Cox, Erwin M Schoof, Alison Gartland, Janine T Erler and Rune Linding.
    Dataset for the proteomic inventory and quantitative analysis of the breast cancer hypoxic secretome associated with osteotropism..
    Data in brief 5:621-5, December 2015.

  58. Simon Koplev, James Longden, Jesper Ferkinghoff-Borg, Mathias Blicher Bjerregård, Thomas R Cox, Janine T Erler, Jesper T Pedersen, Franziska Voellmy, Morten O A Sommer and Rune Linding.
    Dynamic Rearrangement of Cell States Detected by Systematic Screening of Sequential Anticancer Treatments..
    Cell reports 20:2784-2791, September 2017.

  59. Gaye Saginc, Franziska Voellmy and Rune Linding.
    Cancer systems biology: Harnessing off-target effects..
    Nature chemical biology 13:1204-1205, November 2017.

  60. Mathias Engel, James Longden, Jesper Ferkinghoff-Borg, Xavier Robin, Gaye Saginc and Rune Linding.
    Bowhead: Bayesian modelling of cell velocity during concerted cell migration..
    PLoS computational biology 14:e1005900, January 2018.

  61. Becky Inkster, Andy Simmons, James H Cole, Erwin Schoof, Rune Linding, Tom Nichols, Pierandrea Muglia, Florian Holsboer, Philipp G Sämann, Peter McGuffin, Cynthia H Y Fu, Kamilla Miskowiak, Paul M Matthews, Gwyneth Zai and Kristin Nicodemus.
    Unravelling the GSK3β-related genotypic interaction network influencing hippocampal volume in recurrent major depressive disorder..
    Psychiatric genetics 28:77-84, October 2018.

  62. Lars Sjögren, Maïna Floris, Andrea Barghetti, Franziska Völlmy, Rune Linding and Peter Brodersen.
    Farnesylated heat shock protein 40 is a component of membrane-bound RISC in Arabidopsis..
    The Journal of biological chemistry 293:16608-16622, October 2018.

  63. Chad J Miller, Hua Jane Lou, Craig Simpson, Bert Kooij, Byung Hak Ha, Oriana S Fisher, Natasha L Pirman, Titus J Boggon, Jesse Rinehart, Michael B Yaffe, Rune Linding and Benjamin E Turk.
    Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output..
    PLoS biology 17:e2006540, March 2019.

  64. Bert Kooij, Pau Creixell, Anne Vlimmeren, Brian A Joughin, Chad J Miller, Nasir Haider, Craig D Simpson, Rune Linding, Vuk Stambolic, Benjamin E Turk and Michael B Yaffe.
    Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs..
    eLife 8, May 2019.

  65. Cristina C Santini, James Longden, Erwin M Schoof, Craig D Simpson, Grace R Jeschke, Pau Creixell, Jinho Kim, Xuewei Wu, Benjamin E Turk, Neal Rosen, Poulikos I Poulikakos and Rune Linding.
    Global view of the RAF-MEK-ERK module and its immediate downstream effectors..
    Scientific reports 9:10865, July 2019.

  66. B Goldenbogen, SO Adler, O Bodeit, JAH Wodke, A Korman, L Bonn, X Escalera-Fanjul, JEL Haffner, M Karnetzki, M Krantz, I Maintz, L Mallis, RU Moran Torres, H Prawitz, PS Segelitz, M Seeger, R Linding and E Klipp.
    Geospatial precision simulations of community confined human interactions during SARS-CoV-2 transmission reveals bimodal intervention outcomes.
    medRxiv, 2020.
    URL, DOI

  67. James Longden, Xavier Robin, Mathias Engel, Jesper Ferkinghoff-Borg, Ida Kjær, Ivan D Horak, Mikkel W Pedersen and Rune Linding.
    Deep neural networks identify signaling mechanisms of ErbB-family drug resistance from a continuous cell morphology space..
    Cell reports 34:108657, January 2021.

  68. Ralitsa R Madsen, James Longden, Rachel G Knox, Xavier Robin, Franziska Völlmy, Kenneth G Macleod, Larissa S Moniz, Neil O Carragher, Rune Linding, Bart Vanhaesebroeck and Robert K Semple.
    NODAL/TGFβ signalling mediates the self-sustained stemness induced by PIK3CAH1047R homozygosity in pluripotent stem cells..
    Disease models & mechanisms 14, March 2021.

  69. Martin Seeger, James Longden, Edda Klipp and Rune Linding.
    Deep Hidden Physics Modeling of Cell Signaling Networks..
    Current genomics 22:239-243, December 2021.
    URL, DOI

  70. Björn Goldenbogen, Stephan O Adler, Oliver Bodeit, Judith A H Wodke, Ximena Escalera-Fanjul, Aviv Korman, Maria Krantz, Lasse Bonn, Rafael Morán-Torres, Johanna E L Haffner, Maxim Karnetzki, Ivo Maintz, Lisa Mallis, Hannah Prawitz, Patrick S Segelitz, Martin Seeger, Rune Linding and Edda Klipp.
    Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination.
    Advanced Science n/a(n/a):2200088, 2022.
    URL, DOI

  71. Jared L Johnson, Tomer M Yaron, Emily M Huntsman, Alexander Kerelsky, Junho Song, Amit Regev, Ting-Yu Lin, Katarina Liberatore, Daniel M Cizin, Benjamin M Cohen, Neil Vasan, Yilun Ma, Konstantin Krismer, Jaylissa Torres Robles, Bert Kooij, Anne E Vlimmeren, Nicole Andrée-Busch, Norbert F Käufer, Maxim V Dorovkov, Alexey G Ryazanov, Yuichiro Takagi, Edward R Kastenhuber, Marcus D Goncalves, Benjamin D Hopkins, Olivier Elemento, Dylan J Taatjes, Alexandre Maucuer, Akio Yamashita, Alexei Degterev, Mohamed Uduman, Jingyi Lu, Sean D Landry, Bin Zhang, Ian Cossentino, Rune Linding, John Blenis, Peter V Hornbeck, Benjamin E Turk, Michael B Yaffe and Lewis C Cantley.
    An atlas of substrate specificities for the human serine/threonine kinome..
    Nature 613:759-766, January 2023.

  72. Thomas R Cox, Robin M H Rumney, Erwin M Schoof, Lara Perryman, Anette M Høye, Ankita Agrawal, Demelza Bird, Norain Ab Latif, Hamish Forrest, Holly R Evans, Iain D Huggins, Georgina Lang, Rune Linding, Alison Gartland and Janine T Erler.
    Retraction Note: The hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase..
    May 2023.

News

Our newest publications:

  1. Gabriele Schreiber, Facundo Rueda, Florian Renner, Asya Fatima Polat, Philipp Lorenz and Edda Klipp.
    Expression Dynamics and Genetic Compensation of Cell Cycle Paralogues in Saccharomyces cerevisiae..
    Cells 14, March 2025.
    URL, DOI

  1. Stephan O Adler, Anastasia Kitashova, Ana Bulović, Thomas Nägele and Edda Klipp.
    Plant cold acclimation and its impact on sensitivity of carbohydrate metabolism..
    NPJ systems biology and applications 11:28, March 2025.
    URL, DOI

  1. Pattarawan Intasian, Chalermroj Sutthaphirom, Oliver Bodeit, Duangthip Trisrivirat, Ninlapan Kimprasoot, Juthamas Jaroensuk, Barbara Bakker, Edda Klipp and Pimchai Chaiyen.
    Enhancement of essential cofactors for in vivo biocatalysis..
    Faraday discussions, June 2024.
    URL, DOI