Match!
Boris N. Kholodenko
University College Dublin
266Publications
49H-index
10.4kCitations
Publications 266
Newest
#1Susan Kennedy (UCD: University College Dublin)H-Index: 6
#2Mohamed-Ali Jarboui (University of Tübingen)H-Index: 2
Last.Aleksandar Krstic (UCD: University College Dublin)H-Index: 9
view all 41 authors...
Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming le...
Source
#1Daniel Lill (UCD: University College Dublin)
#2Oleksii S. Rukhlenko (UCD: University College Dublin)H-Index: 5
Last.Boris N. KholodenkoH-Index: 49
view all 6 authors...
Modular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of both the directions and strengths of connections between network modules from network responses to perturbations. Standard MRA assumes that modules are insulated, thereby neglecting the existence of inter-modular protein complexes. Such complexes sequester proteins from different modules and propagate perturbations to the protein abundance of a downstream module retroactivel...
Source
#1Vadim ZhernovkovH-Index: 1
#2Tapesh SantraH-Index: 6
Last.Boris N. KholodenkoH-Index: 49
view all 9 authors...
Source
#1Keesha E. Erickson (LANL: Los Alamos National Laboratory)H-Index: 7
#2Oleksii S. Rukhlenko (UCD: University College Dublin)H-Index: 5
Last.Boris N. Kholodenko (UCD: University College Dublin)H-Index: 49
view all 5 authors...
Abstract RAS is the most frequently mutated gene across human cancers, but developing inhibitors of mutant RAS has proven to be challenging. Given the difficulties of targeting RAS directly, drugs that impact the other components of pathways where mutant RAS operates may potentially be effective. However, the system-level features, including different localizations of RAS isoforms, competition between downstream effectors, and interlocking feedback and feed-forward loops, must be understood to f...
2 CitationsSource
#1Caterina Thomaseth (University of Stuttgart)H-Index: 3
#2Dirk Fey (UCD: University College Dublin)H-Index: 12
Last.Boris N. Kholodenko (Yale University)H-Index: 49
view all 6 authors...
Modular Response Analysis (MRA) is a method to reconstruct signalling networks from steady-state perturbation data which has frequently been used in different settings. Since these data are usually noisy due to multi-step measurement procedures and biological variability, it is important to investigate the effect of this noise onto network reconstruction. Here we present a systematic study to investigate propagation of noise from concentration measurements to network structures. Therefore, we de...
1 CitationsSource
#1Keesha E. Erickson (LANL: Los Alamos National Laboratory)H-Index: 7
#2Oleksii S. Rukhlenko (UCD: University College Dublin)H-Index: 5
Last.William S. Hlavacek (LANL: Los Alamos National Laboratory)H-Index: 34
view all 12 authors...
Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may compete for binding to a common ...
5 CitationsSource
#1Jens RauchH-Index: 15
Last.Boris N. KholodenkoH-Index: 49
view all 3 authors...
Source
#1Brian MunskyH-Index: 17
#2Karen Tkach TuzmanH-Index: 1
Last.Lev S. TsimringH-Index: 48
view all 75 authors...
An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilit...
2 Citations
#1Oleksii S. Rukhlenko (UCD: University College Dublin)H-Index: 5
#2Fahimeh Khorsand (UCD: University College Dublin)H-Index: 2
Last.Boris N. KholodenkoH-Index: 49
view all 16 authors...
Summary Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can be chosen. We built a next-generation mechanistic dynamic model to analyze combinations of structurally d...
8 CitationsSource
#1Vadim Zhernovkov (UCD: University College Dublin)H-Index: 1
#2Tapesh Santra (UCD: University College Dublin)H-Index: 6
Last.Boris N. Kholodenko (UCD: University College Dublin)H-Index: 49
view all 9 authors...
Carbon nanotubes (CNTs) usage has rapidly increased in the last few decades due to their unique properties, exploited in various industrial and commercial products. Certain types of CNTs cause adverse health effects, including chronic inflammation and fibrosis. Despite the large number of in vitro and in vivo studies evaluating these effects, many important questions remain unanswered due to a lack of mechanistic understanding of how CNTs induce cellular stress responses. In order to predict CNT...
Source
12345678910