input stringlengths 28k 164k | pubmedid stringlengths 8 8 | output stringlengths 321 41.9k |
|---|---|---|
Predicting Essential Components of Signal
Transduction Networks: A Dynamic Model
of Guard Cell Abscisic Acid Signaling
Song Li1, Sarah M. Assmann1, Re´ka Albert2*
1 Biology Department, Pennsylvania State University, University Park, Pennsylvania, United States of America, 2 Physics Department, Pennsylvania State Univer... | 16968132 | ROS = ( Atrboh )
PEPC = NOT ( ( ABA ) )
PLD = ( GPA1 )
HTPase = NOT ( ( pH ) OR ( Ca2_c ) OR ( ROS ) )
Ca2_c = ( ( CIS ) AND NOT ( Ca2_ATPase ) ) OR ( ( CaIM ) AND NOT ( Ca2_ATPase ) )
ROP10 = ( ERA1 )
RAC1 = NOT ( ( ABA ) OR ( ABI1 ) )
OST1 = ( ABA )
ROP2 = ( PA )
InsP6 = ( InsPK )
SphK = ( ABA )
De... |
A Logical Model Provides Insights into T Cell
Receptor Signaling
Julio Saez-Rodriguez1, Luca Simeoni2, Jonathan A. Lindquist2, Rebecca Hemenway1, Ursula Bommhardt2,
Boerge Arndt2, Utz-Uwe Haus3, Robert Weismantel3, Ernst D. Gilles1, Steffen Klamt1*, Burkhart Schraven2*
1 Max Planck Institute for Dynamics of Complex Tec... | 17722974 | tcrlig = ( tcrlig )
vav1 = ( zap70 AND ( ( ( sh3bp2 ) ) ) ) OR ( xx )
lat = ( zap70 )
pi3k = ( ( xx ) AND NOT ( cblb ) ) OR ( ( lckp2 ) AND NOT ( cblb ) )
gap = ( unknown_input3 )
rac1r = ( unknown_input )
Dummy = ( ( plcgb AND ( ( ( vav1 AND zap70 AND itk AND slp76 ) ) ) ) AND NOT ( ccblp2 ) )
... |
BioMed Central
Page 1 of 26
(page number not for citation purposes)
BMC Bioinformatics
Open Access
Methodology article
A methodology for the structural and functional analysis of signaling
and regulatory networks
Steffen Klamt*†1, Julio Saez-Rodriguez†1, Jonathan A Lindquist2,
Luca Simeoni2 and Ernst D Gilles1
Addres... | 16464248 | Lck = ( ( CD45 AND ( ( ( CD8 ) ) ) ) AND NOT ( PAGCsk ) )
ZAP70 = ( ( TCRphos AND ( ( ( Lck ) ) ) ) AND NOT ( cCbl ) )
Itk = ( ZAP70 AND ( ( ( SLP76 ) ) ) )
SEK = ( PKCth )
RasGRP1 = ( PKCth AND ( ( ( DAG ) ) ) )
SLP76 = ( Gads )
CREB = ( Rsk )
Rlk = ( Lck )
ERK = ( MEK )
Gads = ( LAT )
IkB = ... |
BioMed Central
Page 1 of 18
(page number not for citation purposes)
Theoretical Biology and Medical
Modelling
Open Access
Research
A method for the generation of standardized qualitative dynamical
systems of regulatory networks
Luis Mendoza* and Ioannis Xenarios
Address: Serono Pharmaceutical Research Institute, 14, ... | 16542429 | IL4 = ( ( GATA3 ) AND NOT ( STAT1 ) )
SOCS1 = ( Tbet ) OR ( STAT1 )
IFNg = ( ( STAT4 ) AND NOT ( STAT3 ) ) OR ( ( IRAK ) AND NOT ( STAT3 ) ) OR ( ( Tbet ) AND NOT ( STAT3 ) ) OR ( ( NFAT ) AND NOT ( STAT3 ) )
STAT3 = ( IL10R )
IRAK = ( IL18R )
IFNgR = ( IFNg )
STAT1 = ( IFNbR ) OR ( JAK1 )
NFAT = ... |
Emergent decision-making in biological signal
transduction networks
Toma´sˇ Helikar*, John Konvalina†, Jack Heidel†, and Jim A. Rogers*†‡
*Department of Pathology and Microbiology, University of Nebraska Medical Center, 983135 Nebraska Medical Center, Omaha, NE 68198; and †Department
of Mathematics, University of Nebra... | 18250321 | PTP1b = ( NOT ( ( EGFR AND ( ( ( EGF ) ) ) ) OR ( Stress ) ) ) OR NOT ( EGFR OR EGF OR Stress )
Csk = ( Cbp AND ( ( ( Gbg_i OR PKA OR Gbg_1213 OR Gbg_q ) ) OR ( ( NOT Gbg_i AND NOT PKA AND NOT SHP2 AND NOT Gbg_1213 AND NOT Gbg_q ) ) ) ) OR ( ( Fak AND ( ( ( Src AND Cbp ) ) ) ) AND NOT ( SHP2 ) ... |
Global control of cell cycle transcription by coupled CDK and
network oscillators
David A. Orlando1,2, Charles Y. Lin1, Allister Bernard3, Jean Y. Wang1, Joshua E. S.
Socolar4, Edwin S. Iversen5, Alexander J. Hartemink3, and Steven B. Haase1,*
1Department of Biology, Duke University
2Program in Computational Biology an... | 18463633 | MBF = ( CLN3 )
HCM1 = ( MBF AND ( ( ( SBF ) ) ) )
SWI5 = ( SFF )
YOX1 = ( MBF AND ( ( ( SBF ) ) ) )
SFF = ( SBF AND ( ( ( HCM1 ) ) ) )
ACE2 = ( SFF )
YHP1 = ( MBF ) OR ( SBF )
SBF = ( ( ( MBF ) AND NOT ( YHP1 ) ) AND NOT ( YOX1 ) ) OR ( ( ( CLN3 ) AND NOT ( YHP1 ) ) AND NOT ( YOX1 ) )
CLN3 = ... |
BioMed Central
Page 1 of 15
(page number not for citation purposes)
BMC Systems Biology
Open Access
Research article
A logic-based diagram of signalling pathways central to macrophage
activation
Sobia Raza1, Kevin A Robertson1,3, Paul A Lacaze1, David Page1,
Anton J Enright2, Peter Ghazal*1,3 and Tom C Freeman*1
Addr... | 18433497 | TBK1 = ( External_Activator )
IL1R1 = ( External_Activator )
APAF1gene = ( TP53nucleus )
ILIB_IL1R1_MYD88_IRAK1_IRAK4 = ( ILIB_IL1R1 AND ( ( ( IRAK4 AND IRAK1 AND MYD88 ) ) ) )
TNFRSF10B = ( External_Activator )
RELAp65_NFKB1p50cytoplasm = ( NFKBIA_RELAp65_NFKB1p50 AND ( ( ( MAP3K7 OR RPS6KA5 OR IKBKB OR C... |
Network model of survival signaling in large granular
lymphocyte leukemia
Ranran Zhang†, Mithun Vinod Shah†, Jun Yang†, Susan B. Nyland†, Xin Liu†, Jong K. Yun‡, Re´ka Albert§¶,
and Thomas P. Loughran, Jr.†
†Penn State Hershey Cancer Institute and ‡Department of Pharmacology, The Pennsylvania State University College ... | 18852469 | FasT = ( ( NFKB ) AND NOT ( Apoptosis ) )
sFas = ( ( FasT ) AND NOT ( Apoptosis ) )
IL2 = ( ( ( STAT3 ) AND NOT ( Apoptosis ) ) AND NOT ( TBET ) ) OR ( ( ( NFAT ) AND NOT ( Apoptosis ) ) AND NOT ( TBET ) ) OR ( ( ( NFKB ) AND NOT ( Apoptosis ) ) AND NOT ( TBET ) )
NFKB = ( ( PI3K ) AND NOT ( Apopt... |
BioMed Central
Page 1 of 14
(page number not for citation purposes)
BMC Systems Biology
Open Access
Research article
Dynamical modeling of the cholesterol regulatory pathway with
Boolean networks
Gwenael Kervizic* and Laurent Corcos
Address: Inserm U613, Faculté de Médecine, Université de Bretagne Occidentale, 29238 B... | 19025648 | SREBP_SCAP = ( ( Insig_SREBP_SCAP ) AND NOT ( Statins ) )
Mevalonyl_pyrophosphate = ( Mevalonic_Acid )
mSREBP = ( pSREBP )
Farnesyl_pyrophosphate = ( ( Geranyl_pyrophosphate ) AND NOT ( FPP_Synthase ) )
Desmosterol = ( Lanosterol )
Acetyl_CoA_acetyltransferase = ( Acetyl_CoA_acetyltransferase_RNA )
HMG_CoA_Sy... |
BioMed Central
Page 1 of 20
(page number not for citation purposes)
BMC Systems Biology
Open Access
Research article
Modeling ERBB receptor-regulated G1/S transition to find novel
targets for de novo trastuzumab resistance
Özgür Sahin*1, Holger Fröhlich1, Christian Löbke1,2, Ulrike Korf1,
Sara Burmester1, Meher Majet... | 19118495 | ERa = ( MEK1 ) OR ( Akt1 )
p21 = ( ( ( ( ERa ) AND NOT ( Akt1 ) ) AND NOT ( CDK4 ) ) AND NOT ( cMYC ) )
CDK6 = ( CycD1 )
ErbB3 = ( EGF )
ErbB2_3 = ( ErbB2 AND ( ( ( ErbB3 ) ) ) )
pRB = ( CDK2 AND ( ( ( CDK4 AND CDK6 ) ) ) ) OR ( CDK4 AND ( ( ( CDK6 ) ) ) )
CDK2 = ( ( ( CycE1 ) AND NOT ( p21 ) ... |
BMC Systems Biology
Research article
Reconstruction and logical modeling of glucose repression
signaling pathways in Saccharomyces cerevisiae
Tobias S Christensen†1,2, Ana Paula Oliveira†1,3 and Jens Nielsen*1,4
Address: 1Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark... | 19144179 | Gal3p = ( GAL3 AND ( ( ( galactose_int ) ) ) )
MIG3 = NOT ( ( Rgt1p ) )
GAL4 = NOT ( ( Mig1p ) )
SCF_grr1 = ( GRR1 )
Sip4p = ( SIP4 AND ( ( ( Snf1p ) ) ) )
Gal2p = ( GAL2 )
galactose_int = ( galactose_ext AND ( ( ( Gal2p ) ) ) )
MalRp = ( MALR AND ( ( ( maltose_int ) ) ) )
IDP2 = ( Cat8p )
HXT3 = ... |
The Logic of EGFR/ErbB Signaling: Theoretical Properties
and Analysis of High-Throughput Data
Regina Samaga1, Julio Saez-Rodriguez2,3, Leonidas G. Alexopoulos2,3,4, Peter K. Sorger2,3, Steffen
Klamt1*
1 Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany, 2 Department of Systems Biology, ... | 19662154 | mkk4 = ( mlk3 ) OR ( mekk1 ) OR ( mekk4 )
mkk7 = ( mekk1 )
erbb12 = ( ( btc AND ( ( ( erbb1 AND erbb2 ) ) ) ) AND NOT ( shp1d ) ) OR ( ( tgfa AND ( ( ( erbb1 AND erbb2 ) ) ) ) AND NOT ( shp1d ) ) OR ( ( bir AND ( ( ( erbb1 AND erbb2 ) ) ) ) AND NOT ( shp1d ) ) OR ( ( hbegf AND ( ( ( erbb1 AND ... |
Mathematical Modelling of Cell-Fate Decision in
Response to Death Receptor Engagement
Laurence Calzone1,2,3*, Laurent Tournier1,2,3, Simon Fourquet1,2,3, Denis Thieffry4,5, Boris Zhivotovsky6,
Emmanuel Barillot1,2,3", Andrei Zinovyev1,2,3"
1 Institut Curie, Paris, France, 2 Ecole des Mines ParisTech, Paris, France, 3 I... | 20221256 | RIP1 = ( ( DISC-FAS ) AND NOT ( CASP8 ) ) OR ( ( TNFR ) AND NOT ( CASP8 ) )
NonACD = ( NOT ( ( ATP ) ) ) OR NOT ( ATP )
XIAP = ( ( NFkB ) AND NOT ( SMAC ) )
NFkB = ( ( IKK ) AND NOT ( CASP3 ) )
RIP1ub = ( cIAP AND ( ( ( RIP1 ) ) ) )
cFLIP = ( NFkB )
BCL2 = ( NFkB )
BAX = ( ( CASP8 ) AND NOT ( BCL2... |
A Boolean Model of the Gene Regulatory Network
Underlying Mammalian Cortical Area Development
Clare E. Giacomantonio1, Geoffrey J. Goodhill1,2*
1 Queensland Brain Institute, The University of Queensland, St Lucia, Queensland, Australia, 2 School of Mathematics and Physics, The University of Queensland, St Lucia,
Queens... | 20862356 | Sp8 = ( ( Fgf8 ) AND NOT ( Emx2 ) )
Coup_fti = ( NOT ( ( Fgf8 ) OR ( Sp8 ) ) ) OR NOT ( Fgf8 OR Sp8 )
Pax6 = ( ( ( Sp8 ) AND NOT ( Coup_fti ) ) AND NOT ( Emx2 ) )
Fgf8 = ( ( Fgf8 AND ( ( ( Sp8 ) ) ) ) AND NOT ( Emx2 ) )
Emx2 = ( ( ( ( Coup_fti ) AND NOT ( Fgf8 ) ) AND NOT ( Sp8 ) ) AND NOT ( Pax6... |
Dynamical and Structural Analysis of a T Cell Survival
Network Identifies Novel Candidate Therapeutic Targets
for Large Granular Lymphocyte Leukemia
Assieh Saadatpour1, Rui-Sheng Wang2, Aijun Liao3, Xin Liu3, Thomas P. Loughran3, Istva´n Albert4, Re´ka
Albert2*
1 Department of Mathematics, The Pennsylvania State Univer... | 22102804 | Caspase = ( ( ( BID ) AND NOT ( IAP ) ) AND NOT ( Apoptosis ) ) OR ( ( DISC ) AND NOT ( Apoptosis ) )
Apoptosis = ( Apoptosis ) OR ( Caspase )
sFas = ( ( S1P ) AND NOT ( Apoptosis ) )
MCL1 = NOT ( ( Apoptosis ) OR ( DISC ) )
Ceramide = ( ( ( Fas ) AND NOT ( Apoptosis ) ) AND NOT ( S1P ) )... |
Network Model of Immune Responses Reveals Key
Effectors to Single and Co-infection Dynamics by a
Respiratory Bacterium and a Gastrointestinal Helminth
Juilee Thakar1,2, Ashutosh K. Pathak1,3, Lisa Murphy4¤, Re´ka Albert1,5, Isabella M. Cattadori1,3*
1 Center for Infectious Disease Dynamics, The Pennsylvania State Unive... | 22253585 | MPI_Bacterium = ( IFNg_Bacterium AND ( ( ( Bb ) ) ) ) OR ( PIC AND ( ( ( Bb ) ) ) )
Th2I_Bacterium = ( Th2II_Bacterium )
Oag = ( Bb )
Th1II_TRetortaeformis = ( DCII_TRetortaeformis AND ( ( ( T0 ) ) AND ( ( DCII_TRetortaeformis ) ) AND ( ( IL12II ) ) ) )
Bb = ( ( Bb ) AND NOT ( PH ) )
PIC = ( ( ( EC_T... |
Helikar et al. BMC Systems Biology 2012, 6:96
http://www.biomedcentral.com/1752-0509/6/96
SOFTWARE
Open Access
The Cell Collective: Toward an open and
collaborative approach to systems biology
Tom´aˇs Helikar1*, Bryan Kowal2, Sean McClenathan2, Mitchell Bruckner1, Thaine Rowley1,
Alex Madrahimov1, Ben Wicks2, Manish Sh... | 22871178 | STAT1 = ( Jak1 ) OR ( IL27 AND ( ( ( NFAT ) ) ) )
IL23R = ( ( IL23 AND ( ( ( STAT3 ) ) ) ) AND NOT ( Tbet ) ) OR ( STAT3 )
Foxp3 = ( ( ( ( TGFbR ) AND NOT ( GATA3 ) ) AND NOT ( IL6R AND ( ( ( STAT3 ) ) ) ) ) AND NOT ( IL21R ) ) OR ( ( ( ( STAT5 ) AND NOT ( GATA3 ) ) AND NOT ( IL6R AND ( ( ( STA... |
BIOINFORMATICS
Vol. 28 ECCB 2012, pages i495–i501
doi:10.1093/bioinformatics/bts410
Boolean approach to signalling pathway modelling in
HGF-induced keratinocyte migration
Amit Singh1,2,†, Juliana M. Nascimento1,2,†, Silke Kowar1,2, Hauke Busch1,2,‡,∗
and Melanie Boerries1,2,‡,∗
1Freiburg Institute for Advanced Studies,... | 22962472 | EGFR = ( HBEGF ) OR ( EGF )
CDKN2A = ( Elk1 ) OR ( ETS )
DAG = ( PLC_g )
PAK3 = ( Cdc42_Rac1 )
uPA = ( uPAR )
Mkk4 = ( Mekk4 ) OR ( Mekk1 ) OR ( MLK3 )
p38 = ( ( Mkk3 AND ( ( ( Mkk6 ) ) ) ) AND NOT ( DUSP1 ) ) OR ( PAK1 )
PTGS2 = ( ATF2 ) OR ( cFOS AND ( ( ( cJUN ) ) ) )
JNK = ( Mekk7 AND ( ( ( Mk... |
Ergodic Sets as Cell Phenotype of Budding Yeast Cell
Cycle
Robert G. Todd*, Toma´sˇ Helikar
Department of Mathematics, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
Abstract
It has been suggested that irreducible sets of states in Probabilistic Boolean Networks correspond to cellular phenot... | 23049686 | Cdc14 = ( MEN AND ( ( ( FEAR ) ) ) )
Whi5 = ( NOT ( ( Cln3 AND ( ( ( Start ) ) ) ) OR ( Cln2 AND ( ( ( Start ) ) ) ) ) ) OR NOT ( Start OR Cln2 OR Cln3 )
Swi5 = ( ( Cdc14 AND ( ( ( NOT Swi5 ) ) AND ( ( SFF ) ) ) ) AND NOT ( Clb2 ) )
Cdh1 = ( ( Cdc14 ) ) OR NOT ( Cdc14 OR Clb2 OR Cln2 OR Clb5 )
S... |
A Boolean Model of the Cardiac Gene Regulatory
Network Determining First and Second Heart Field
Identity
Franziska Herrmann1,2,3., Alexander Groß1,3., Dao Zhou1, Hans A. Kestler1*, Michael Ku¨ hl2*
1 Research Group Bioinformatics and Systems Biology, Institute for Neural Information Processing, Ulm University, Ulm, Ger... | 23056457 | Bmp2 = ( ( exogen_BMP2_II ) AND NOT ( canWnt ) )
GATAs = ( Nkx2_5 ) OR ( Tbx5 ) OR ( Mesp1 )
Isl1 = ( Mesp1 ) OR ( Tbx1 ) OR ( Fgf8 ) OR ( canWnt AND ( ( ( exogen_canWnt_II ) ) ) )
exogen_canWnt_II = ( exogen_CanWnt_I )
canWnt = ( exogen_canWnt_II )
Nkx2_5 = ( Tbx1 ) OR ( Mesp1 AND ( ( ( Dkk1 ) ) ) )... |
RESEARCH
Open Access
Boolean modeling and fault diagnosis in
oxidative stress response
Sriram Sridharan1, Ritwik Layek1, Aniruddha Datta1*, Jijayanagaram Venkatraj2
From IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2011
San Antonio, TX, USA. 4-6 December 2011
Abstract
Background: Ox... | 23134720 | ARE = ( ( ( ( Nrf2 ) AND NOT ( GSK3b ) ) AND NOT ( Bach1 ) ) AND NOT ( ARE ) )
Ras = ( ROS )
PTEN = NOT ( ( ROS ) )
Akt = ( PIP3 )
p53 = ( ( ATM ) AND NOT ( Mdm2 ) )
Bad = NOT ( ( Akt ) )
PI3K = ( Ras )
Nrf2 = ( ( Akt ) OR ( PKC ) ) OR NOT ( Akt OR Keap1 OR PKC )
Keap1 = ( ( Keap1 ) AND NOT ( Bach1 ... |
ORIGINAL RESEARCH ARTICLE
published: 10 December 2012
doi: 10.3389/fphys.2012.00446
Boolean model of yeast apoptosis as a tool to study yeast
and human apoptotic regulations
Laleh Kazemzadeh1,2, Marija Cvijovic 1,3* and Dina Petranovic 1*
1 Department of Chemical and Biological Engineering, Chalmers University of Techn... | 23233838 | SDP1 = ( MSN2-4 )
CDC48 = ( HK )
NDI1 = ( HK )
MT-ALT = ( MMI1 ) OR ( RAS2 ) OR ( MT-Frag ) OR ( PKA )
MEC1 = ( AbnormalTelomer )
YCA1 = ( ( Salt ) AND NOT ( SRO7 ) ) OR ( MEC1 ) OR ( MT-Frag ) OR ( RedActinDyn ) OR ( ROS-CYT ) OR ( CytC-CYT )
DesCyclinCCDK8 = NOT ( ( SLT2 ) )
Apoptosis = ( ( POR1-2 AN... |
Canalization and Control in Automata Networks: Body
Segmentation in Drosophila melanogaster
Manuel Marques-Pita1,2*, Luis M. Rocha1,2*
1 Instituto Gulbenkian de Cieˆncia, Oeiras, Portugal, 2 Indiana University, Bloomington, Indiana, United States of America
Abstract
We present schema redescription as a methodology to c... | 23520449 | HH_protein = ( hh )
EN_protein = ( en )
WG_protein = ( wg )
CIR = ( ( CI_protein AND ( ( ( PTC_protein ) ) ) ) AND NOT ( hh_external ) )
PTC_protein = ( ptc ) OR ( ( PTC_protein ) AND NOT ( hh_external ) )
ci = NOT ( ( EN_protein ) )
en = ( ( WG_external ) AND NOT ( SLP ) )
PH = ( PTC_protein AND ( ( (... |
A Comprehensive, Multi-Scale Dynamical Model of ErbB
Receptor Signal Transduction in Human Mammary
Epithelial Cells
Toma´sˇ Helikar1, Naomi Kochi1, Bryan Kowal2, Manjari Dimri3, Mayumi Naramura4,5,6, Srikumar M. Raja4,5,
Vimla Band4,5,6, Hamid Band4,5,6,7, Jim A. Rogers1,6*
1 Department of Mathematics, University of Ne... | 23637902 | Grb2 = ( EGFR_Y1068 ) OR ( EGFR_Y1086 ) OR ( ErbB2_Y1139 ) OR ( Src AND ( ( ( Fak ) ) ) ) OR ( Shc )
ILK = ( PIP3_345 )
PIP2_45 = ( PTEN AND ( ( ( PIP3_345 ) ) ) ) OR ( PI4K AND ( ( ( PI5K ) ) ) ) OR ( ( PIP2_45 ) AND NOT ( PI3K AND ( ( ( PIP2_45 ) ) ) ) )
PKC = ( ( AA AND ( ( ( PKC_primed ) ) A... |
Integrative Modelling of the Influence of MAPK Network
on Cancer Cell Fate Decision
Luca Grieco1,2,3,4,5,6*, Laurence Calzone6,7,8, Isabelle Bernard-Pierrot6,9, Franc¸ois Radvanyi6,9,
Brigitte Kahn-Perle`s2, Denis Thieffry2,3,4,5,10*
1 Aix-Marseille Universite´, Marseille, France, 2 TAGC – Inserm U1090, Marseille, Fran... | 24250280 | PDK1 = ( PI3K )
FRS2 = ( ( ( FGFR3 ) AND NOT ( SPRY ) ) AND NOT ( GRB2 ) )
MAX = ( p38 )
GAB1 = ( GRB2 ) OR ( PI3K )
PI3K = ( GAB1 ) OR ( RAS AND ( ( ( SOS ) ) ) )
AKT = ( ( PDK1 ) AND NOT ( PTEN ) )
p70 = ( PDK1 AND ( ( ( ERK ) ) ) )
ERK = ( MEK1_2 )
SOS = ( ( GRB2 ) AND NOT ( RSK ) )
JNK = ( ... |
Boolean ErbB network reconstructions and
perturbation simulations reveal individual drug
response in different breast cancer cell lines
von der Heyde et al.
von der Heyde et al. BMC Systems Biology 2014, 8:75
http://www.biomedcentral.com/1752-0509/8/75
von der Heyde et al. BMC Systems Biology 2014, 8:75
http://www.bio... | 24970389 | p70S6K = ( ( ( ( ERK1_2 ) AND NOT ( TSC2 ) ) AND NOT ( Nfkb ) ) AND NOT ( PRAS ) ) OR ( ( ( ( p70S6K ) AND NOT ( TSC2 ) ) AND NOT ( Nfkb ) ) AND NOT ( PRAS ) )
Nfkb = ( Nfkb )
FoxO1_3a = ( ( FoxO1_3a ) AND NOT ( AKT ) )
AKT = ( ( ERBB3 ) AND NOT ( PTEN ) ) OR ( ( AKT ) AND NOT ( PTEN ) ) OR ( ( ... |
ORIGINAL RESEARCH ARTICLE
published: 05 December 2014
doi: 10.3389/fimmu.2014.00599
Design, assessment, and in vivo evaluation of a
computational model illustrating the role of CAV1 in CD4+
T-lymphocytes
Brittany D. Conroy 1†,Tyler A. Herek 1†,Timothy D. Shew 1†, Matthew Latner 1, Joshua J. Larson1,
Laura Allen1, Paul H... | 25538703 | FYN = ( CAV1_scaffold ) OR ( CD3 AND ( ( ( TCR ) ) ) )
PKA = ( cAMP )
MEK3 = ( MEKK4 )
FOXP3 = ( ( ( SMAD3 AND ( ( ( STAT5 AND NFAT ) ) ) ) AND NOT ( STAT1 ) ) AND NOT ( STAT3 AND ( ( ( RORGT ) ) ) ) ) OR ( NFAT AND ( ( ( FOXP3 AND STAT5 ) ) ) )
IL17 = ( ( ( ( NFAT AND ( ( ( proliferation AND S... |
EDUCATION
Integrating Interactive Computational
Modeling in Biology Curricula
Tomáš Helikar1*, Christine E. Cutucache2, Lauren M. Dahlquist2, Tyler A. Herek2, Joshua
J. Larson2, Jim A. Rogers3
1 Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, Nebraska, United States of America,
2 Department of Biol... | 25790483 | lac_mRNA = ( lac_operon )
lactose_breakdown = ( ( lac_enzymes ) AND NOT ( betaGal_LOF_mutation ) )
lac_repressor = NOT ( ( allolactose ) )
allolactose = ( lactose )
CAP = ( cAMP )
lac_operon = ( ( CAP ) AND NOT ( lac_repressor ) )
cAMP = NOT ( ( glucose ) OR ( lactose_breakdown ) )
lac_enzymes = ( lac_mRNA ... |
Iron acquisition and oxidative stress response
in aspergillus fumigatus
Brandon et al.
Brandon et al. BMC Systems Biology (2015) 9:19
DOI 10.1186/s12918-015-0163-1
Brandon et al. BMC Systems Biology (2015) 9:19
DOI 10.1186/s12918-015-0163-1
RESEARCH ARTICLE
Open Access
Iron acquisition and oxidative stress respons... | 25908096 | ThP = ( Yap1 )
Cat1/2 = ( ( Yap1 ) AND NOT ( HapX ) )
ROS = ( ( Superoxide ) AND NOT ( SOD2/3 AND ( ( ( ThP AND Cat1/2 ) ) ) ) ) OR ( LIP ) OR ( ( ROS ) AND NOT ( SOD2/3 AND ( ( ( ThP AND Cat1/2 ) ) ) ) )
ICP = ( ( VAC ) AND NOT ( HapX ) ) OR ( ( FCplusFe ) AND NOT ( HapX ) )
FCminusFe = ( SidA... |
RESEARCH
Open Access
Proteins interaction network and modeling
of IGVH mutational status in chronic
lymphocytic leukemia
María Camila Álvarez-Silva1†, Sally Yepes2†, Maria Mercedes Torres2 and Andrés Fernando González Barrios1*
* Correspondence:
andgonza@uniandes.edu.co
†Equal contributors
1Grupo de Diseño de Productos... | 26088082 | MAP2K6 = ( CCL5 )
ILK = NOT ( ( FOS ) )
RUNX3 = NOT ( ( EZH2 ) )
HSP90AA1 = ( HSP90AA1 )
CCND2 = ( ( ANXA2 ) AND NOT ( PTEN ) )
CD81 = ( CD81 )
PTEN = ( ( ( ( ( ( FRK AND ( ( ( INPP5D AND BMI1 AND ILK AND IFNGR2 AND RRM1 AND EGR1 AND TNF ) ) ) ) AND NOT ( ADM ) ) AND NOT ( BMI1 ) ) AND NOT ( TGFBR... |
RESEARCH ARTICLE
A Minimal Regulatory Network of Extrinsic
and Intrinsic Factors Recovers Observed
Patterns of CD4+ T Cell Differentiation and
Plasticity
Mariana Esther Martinez-Sanchez1,2, Luis Mendoza3, Carlos Villarreal2,4, Elena R. Alvarez-
Buylla1,2*
1 Departamento de Ecología Funcional, Instituto de Ecología, Uni... | 26090929 | TGFB = ( ( TGFB ) AND NOT ( IL21 ) ) OR ( ( FOXP3 ) AND NOT ( IL21 ) ) OR ( TGFBe )
IL4 = ( ( ( IL4e ) AND NOT ( IL21 ) ) AND NOT ( IFNG ) ) OR ( ( ( ( GATA3 AND ( ( ( IL4 OR IL2 ) ) ) ) AND NOT ( IL21 ) ) AND NOT ( IFNG ) ) AND NOT ( TBET ) )
IL2 = ( ( ( ( IL2e ) AND NOT ( IL21 ) ) AND NOT ( ... |
RESEARCH ARTICLE
Inference of Network Dynamics and
Metabolic Interactions in the Gut
Microbiome
Steven N. Steinway1,2☯, Matthew B. Biggs3☯, Thomas P. Loughran Jr2, Jason A. Papin3*,
Reka Albert4*
1 College of Medicine, Pennsylvania State University, Hershey, Pennsylvania, United States of America,
2 University of Virgi... | 26102287 | Lachnospiraceae = ( ( Lachnospiraceae ) AND NOT ( Clindamycin ) ) OR ( ( Lachnospiraceae_other ) AND NOT ( Clindamycin ) ) OR ( ( Other ) AND NOT ( Clindamycin ) )
Clindamycin = ( Clindamycin )
Akkermansia = ( Coprobacillus )
Enterobacteriaceae = ( Enterobacteriaceae )
Mollicutes = ( Mollicutes )
Ba... |
1521-0103/354/3/448–458$25.00
http://dx.doi.org/10.1124/jpet.115.224766
THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS
J Pharmacol Exp Ther 354:448–458, September 2015
U.S. Government work not protected by U.S. copyright
Logic-Based and Cellular Pharmacodynamic Modeling of
Bortezomib Responses in U266 Human ... | 26163548 | FLIP = ( pNFKB )
Apo = ( Cl_PARP )
cJun = ( JNK )
Prot = NOT ( ( Bort ) )
MEK1 = ( RAF )
XIAP = ( ( ( pSTAT3 ) AND NOT ( p53 ) ) AND NOT ( Smac ) ) OR ( ( ( pNFKB ) AND NOT ( p53 ) ) AND NOT ( Smac ) )
CYCE = ( MYC )
DNAdam = ( STRESS ) OR ( Cas3 )
BCL2 = ( ( ( pSTAT3 ) AND NOT ( p53 ) ) AND NOT ( ... |
RESEARCH ARTICLE
Predicting Variabilities in Cardiac Gene
Expression with a Boolean Network
Incorporating Uncertainty
Melanie Grieb2,5☯, Andre Burkovski2,3,5☯, J. Eric Sträng2☯, Johann M. Kraus2,
Alexander Groß1, Günther Palm3, Michael Kühl4*, Hans A. Kestler1,2,3*
1 Leibniz Institute for Age Research, Fritz-Lipmann In... | 26207376 | Tbx1 = ( Foxc1.2 )
Fgf8 = ( ( Tbx1 ) AND NOT ( Mesp1 ) ) OR ( ( Foxc1.2 ) AND NOT ( Mesp1 ) )
Tbx5 = ( ( ( ( Tbx5 ) AND NOT ( Tbx1 ) ) AND NOT ( Dkk1 AND ( ( ( NOT Mesp1 AND NOT Tbx5 ) ) ) ) ) AND NOT ( canWnt ) ) OR ( ( ( ( Nkx2.5 ) AND NOT ( Tbx1 ) ) AND NOT ( Dkk1 AND ( ( ( NOT Mesp1 AND N... |
RESEARCH ARTICLE
An Extended, Boolean Model of the Septation
Initiation Network in S. pombe Provides
Insights into Its Regulation
Anastasia Chasapi1☯, Paulina Wachowicz2☯, Anne Niknejad1, Philippe Collin2¤,
Andrea Krapp2, Elena Cano2, Viesturs Simanis2*, Ioannis Xenarios1,3*
1 Vital-IT Group, Swiss Institute of Bioinfo... | 26244885 | dma1 = ( sid4 AND ( ( ( CK1 ) ) ) )
plo1 = ( ( ( cdk-H ) AND NOT ( sid4 AND ( ( ( dma1 ) ) ) ) ) AND NOT ( cdk-L ) ) OR ( ( sid4 ) AND NOT ( sid4 AND ( ( ( dma1 ) ) ) ) )
pom1 = ( pak1 )
sid2 = ( cdc11 AND ( ( ( cdc7 AND SIP ) ) ) ) OR ( cdc7 )
Rga4 = NOT ( ( pom1 ) )
fin1 = ( cdk-H )
SIP = (... |
RESEARCH ARTICLE
A Dynamic Gene Regulatory Network Model
That Recovers the Cyclic Behavior of
Arabidopsis thaliana Cell Cycle
Elizabeth Ortiz-Gutiérrez1,2, Karla García-Cruz1, Eugenio Azpeitia1,2¤, Aaron Castillo1,2,
María de la Paz Sánchez1, Elena R. Álvarez-Buylla1,2*
1 Instituto de Ecología, Universidad Nacional Aut... | 26340681 | MYB77 = ( E2Fb AND ( ( ( NOT RBR ) ) OR ( ( CYCD3;1 ) AND ( ( ( NOT KRP1 ) ) ) ) ) )
E2Fe = ( ( CYCD3;1 AND ( ( ( KRP1 ) AND ( ( ( NOT E2Fc AND NOT RBR AND NOT MYB77 AND NOT E2Fb ) ) ) ) ) ) OR ( RBR AND ( ( ( KRP1 ) AND ( ( ( NOT E2Fc AND NOT MYB77 AND NOT CYCD3;1 AND NOT E2Fb ) ) ) ) ) ) OR (... |
Rodríguez et al. Theoretical Biology and Medical Modelling (2015) 12:19
DOI 10.1186/s12976-015-0011-4
RESEARCH ARTICLE
Open Access
Fanconi anemia cells with unrepaired DNA
damage activate components of the
checkpoint recovery process
Alfredo Rodríguez1,2, Leda Torres1, Ulises Juárez1, David Sosa1, Eugenio Azpeitia3,4... | 26385365 | ATR = ( ( ATM ) AND NOT ( CHKREC ) ) OR ( ( ICL ) AND NOT ( CHKREC ) )
FAHRR = ( ( FANCD2I AND ( ( ( DSB ) ) ) ) AND NOT ( NHEJ AND ( ( ( CHKREC ) ) ) ) )
ICL = ( ( ICL ) AND NOT ( DSB ) )
p53 = ( ( ATM ) AND NOT ( CHKREC ) ) OR ( ( NHEJ ) AND NOT ( CHKREC ) ) OR ( ( ATR ) AND NOT ( CHKREC )... |
1
Scientific Reports | 5:14739 | DOI: 10.1038/srep14739
www.nature.com/scientificreports
Network modelling reveals the
mechanism underlying colitis-
associated colon cancer and
identifies novel combinatorial
anti-cancer targets
Junyan Lu1,*, Hanlin Zeng1,*, Zhongjie Liang2,*, Limin Chen1, Liyi Zhang1, Hao Zhang1,
... | 26446703 | ROS = ( ( TNFR ) AND NOT ( SOD ) )
MEK = ( RAF ) OR ( ROS )
Proliferation = ( ( ( CYCLIND1 AND ( ( ( FOS ) ) ) ) AND NOT ( P21 ) ) AND NOT ( CASP3 ) )
SMAD7 = ( NFKB ) OR ( SMAD )
SMAD = ( ( TGFR ) AND NOT ( JUN ) )
CFLIP = ( NFKB )
PP2A = ( ( CERAMIDE ) AND NOT ( AKT ) )
TH1 = ( ( ( ( IFNG ) AND... |
RESEARCH ARTICLE
Mathematical Modelling of Molecular
Pathways Enabling Tumour Cell Invasion and
Migration
David P. A. Cohen1,2,3, Loredana Martignetti1,2,3, Sylvie Robine1,4, Emmanuel Barillot1,2,3,
Andrei Zinovyev1,2,3‡, Laurence Calzone1,2,3‡*
1 Institut Curie, Paris, France, 2 INSERM, U900, Paris, France, 3 Mines Pa... | 26528548 | EMT = ( ( CDH2 ) AND NOT ( CDH1 ) )
p21 = ( ( ( SMAD AND ( ( ( NICD ) ) ) ) AND NOT ( ERK ) ) AND NOT ( AKT1 ) ) OR ( ( ( p63 ) AND NOT ( ERK ) ) AND NOT ( AKT1 ) ) OR ( ( ( p73 ) AND NOT ( ERK ) ) AND NOT ( AKT1 ) ) OR ( ( ( AKT2 ) AND NOT ( ERK ) ) AND NOT ( AKT1 ) ) OR ( ( ( p53 ) AND NOT ... |
Ríos et al. Theoretical Biology and Medical Modelling (2015) 12:26
DOI 10.1186/s12976-015-0023-0
RESEARCH
Open Access
A Boolean network model of human
gonadal sex determination
Osiris Ríos1,2, Sara Frias1,3, Alfredo Rodríguez1,4, Susana Kofman5, Horacio Merchant3, Leda Torres1*
and Luis Mendoza3,6*
*Correspondence:
l... | 26573569 | WT1mKTS = ( GATA4 ) OR ( UGR )
CTNNB1 = ( ( ( RSPO1 ) AND NOT ( SRY ) ) AND NOT ( SOX9 AND ( ( ( AMH ) ) ) ) ) OR ( ( ( WNT4 ) AND NOT ( SRY ) ) AND NOT ( SOX9 AND ( ( ( AMH ) ) ) ) )
AMH = ( ( SOX9 AND ( ( ( GATA4 AND NR5A1 ) ) OR ( ( WT1mKTS AND GATA4 AND NR5A1 ) ) ) ) AND NOT ( NR0B1 AND ( ... |
RESEARCH ARTICLE
A Network Model to Describe the Terminal
Differentiation of B Cells
Akram Méndez1,2, Luis Mendoza2,3*
1 Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad de
México, México, 2 Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México,
C... | 26751566 | XBP1 = ( Blimp1 AND ( ( ( NOT Pax5 ) ) ) )
Blimp1 = ( ( ( ( Irf4 AND ( ( ( NOT Bcl6 OR NOT Bach2 OR NOT Pax5 ) ) ) ) AND NOT ( Bach2 ) ) AND NOT ( Pax5 ) ) AND NOT ( Bcl6 ) ) OR ( ( ( ( ERK ) AND NOT ( Bach2 ) ) AND NOT ( Pax5 ) ) AND NOT ( Bcl6 ) ) OR ( ( ( ( STAT3 ) AND NOT ( Bach2 ) ) AND N... |
ORIGINAL RESEARCH
published: 14 April 2016
doi: 10.3389/fgene.2016.00044
Frontiers in Genetics | www.frontiersin.org
1
April 2016 | Volume 7 | Article 44
Edited by:
Ekaterina Shelest,
Hans-Knöll-Institute, Germany
Reviewed by:
Julio Vera González,
University Hospital Erlangen, Germany
Nils Blüthgen,
Charité-Universität... | 27148350 | ERK = ( MEK )
Dusp6 = ( ETS1 )
ECM = ( Mmp3/10 )
BTG2 = ( AKT ) OR ( JNK )
Fosl1 = ( JNK ) OR ( AKT ) OR ( ERK )
MKK7 = ( MEKK1 )
Mmp3/10 = ( Plasmin )
Plasmin = ( uPA/PLAT )
PI3K = ( TrkA )
Npy = ( AP1 )
RAS = ( SOS )
MSK1/2 = ( P38 ) OR ( ERK )
KLF2 = ( AKT ) OR ( JNK ) OR ( ERK )
AKT = ( PI3K )
u... |
RESEARCH ARTICLE
Open Access
Analysis of a dynamic model of guard cell
signaling reveals the stability of signal
propagation
Xiao Gan and Réka Albert*
Abstract
Background: Analyzing the long-term behaviors (attractors) of dynamic models of biological systems can provide
valuable insight into biological phenotypes and t... | 27542373 | PP1cc_2 = ( ( ( PLD AND ( ( ( NOT phot1_complex AND NOT BL ) ) ) ) AND NOT ( PLD_high ) ) OR ( ( phot1_complex AND ( ( ( NOT PLD ) ) ) ) AND NOT ( PLD_high ) ) OR ( ( BL AND ( ( ( NOT PLD ) ) ) ) AND NOT ( PLD_high ) ) ) OR NOT ( PLD OR phot1_complex OR BL OR PLD_high )
Kv = ( Kc )
carbfix_high = ... |
ORIGINAL RESEARCH
published: 19 August 2016
doi: 10.3389/fphys.2016.00349
Frontiers in Physiology | www.frontiersin.org
1
August 2016 | Volume 7 | Article 349
Edited by:
Christian Diener,
National Institute of Genomic
Medicine, Mexico
Reviewed by:
Oksana Sorokina,
University of Edinburgh, UK
Marcio Luis Acencio,
Norweg... | 27594840 | PI3KAkt_H = ( ( TLR_H ) AND NOT ( FoxO3a_H ) ) OR ( ( CXCR4_H AND ( ( ( CXCR7_H ) ) ) ) AND NOT ( FoxO3a_H ) ) OR ( ( VLA4_H ) AND NOT ( FoxO3a_H ) ) OR ( ( GCSF ) AND NOT ( FoxO3a_H ) ) OR ( ( ROS_H ) AND NOT ( FoxO3a_H ) )
CXCR4_H = ( ( ( ( CXCL12_M ) AND NOT ( CXCR7_H ) ) AND NOT ( GCSF ) ) AN... |
The Author(s) BMC Bioinformatics 2017, 18(Suppl 4):134
DOI 10.1186/s12859-017-1522-2
RESEARCH
Open Access
Towards targeted combinatorial therapy
design for the treatment of castration-resistant
prostate cancer
Osama Ali Arshad1,2 and Aniruddha Datta1,2*
From Third International Workshop on Computational Network Biology... | 28361666 | IGFR1A/B = ( IGF )
RP6SKB1 = ( mTOR AND ( ( ( NOT Temsirolimus ) ) ) ) OR ( PDPK1 ) OR ( ERK1/2 )
p21 = NOT ( ( AKT ) )
mTOR = ( RHEB )
Ras = ( GRB2/SOS )
TMPRSS2 = ( AR/AR AND ( ( ( NOT Enzalutamide ) ) ) )
CDK2-CyclinE = NOT ( ( p21 ) )
Raf = ( PIK3CA AND ( ( ( NOT BKM120 ) ) ) ) OR ( Ras )
AR/AR ... |
Logical modeling of lymphoid and myeloid cell
specification and transdifferentiation
Samuel Collombeta,1, Chris van Oevelenb,2, Jose Luis Sardina Ortegab,2, Wassim Abou-Jaoudéa, Bruno Di Stefanob,3,
Morgane Thomas-Cholliera, Thomas Grafb,c,1, and Denis Thieffrya,1
aComputational Systems Biology Team, Institut de Biolog... | 28584084 | Runx1 = ( Spi1 )
Ebf1 = ( Ebf1_gene )
E2A_gene = ( Ikzf1 AND ( ( ( Spi1 ) ) ) )
Egr1 = ( Spi1_2 ) OR ( Spi1 AND ( ( ( NOT Gfi1 ) ) ) ) OR ( Pax5_protein_active )
Cd19 = ( CD19_gene )
IL7r_activated = ( IL7 AND ( ( ( IL7r ) ) ) )
CD19_gene = ( Pax5_protein_active AND ( ( ( NOT Cebpa ) ) ) )
Spi1 = (... |
RESEARCH ARTICLE
A model of the onset of the senescence
associated secretory phenotype after DNA
damage induced senescence
Patrick Meyer1,2☯, Pallab Maity1,2☯, Andre Burkovski3,4☯, Julian Schwab3,4,
Christoph Mu¨ssel3, Karmveer Singh1,2, Filipa F. Ferreira1, Linda Krug1,2, Harald J. Maier2,
Meinhard Wlaschek1,2, Thomas... | 29206223 | Oncogene = ( IL8 ) OR ( IL6 )
p53 = ( ( CHK1 ) AND NOT ( MDM2 ) ) OR ( ( ATM ) AND NOT ( MDM2 ) ) OR ( ( CHK2 ) AND NOT ( MDM2 ) )
ATR = ( DNAD )
CHK1 = ( ATR )
IkB = ( ( NFkB ) AND NOT ( IKK AND ( ( ( NEMO ) ) ) ) ) OR ( ( IkB ) AND NOT ( IKK AND ( ( ( NEMO ) ) ) ) )
p21 = ( p53 ) OR ( HIF1 )... |
RESEARCH ARTICLE
A systems pharmacology model for
inflammatory bowel disease
Violeta Balbas-Martinez1,2, Leire Ruiz-Cerda´1,2, Itziar Irurzun-Arana1,2, Ignacio Gonza´lez-
Garcı´a1¤a, An Vermeulen3,4, Jose´ David Go´mez-Mantilla1¤b, Iñaki F. Troco´niz1,2*
1 Pharmacometrics & Systems Pharmacology, Department of Pharmacy ... | 29513758 | PERFOR = ( NK_NKG2D ) OR ( NK )
Th2upregulation = ( Th2 AND ( ( ( IL4 ) ) ) )
IL15 = ( MACR AND ( ( ( LPS OR IFNg ) ) ) ) OR ( FIBROBLAST AND ( ( ( PGN OR LPS OR MDP ) ) ) )
IL23 = ( MACR AND ( ( ( IL1b ) ) ) ) OR ( DC )
CD8_NKG2D = ( ( MDP ) AND NOT ( CD8_NKG2D AND ( ( ( IL2 AND IL21 ) ) OR ( ... |
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