Each "Model of the Month" is an article which explores the biological significance of a particular model from BioModels Database. Every article includes elements such as:
- the description of the model itself and its results
- the biological background of the model
- a brief description of the biological processes that are encoded as a mathematical model
- the biological role of each of the model elements
- the diseases that are caused due to the malfunction of these elements
- the presenters' own view on the model
Direct access to the models of the month for a given year: 2024 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 |
2024
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August: BIOMD0000001078
Protein synthesis and post-translational modification
Eva-Maria Geissen -
May: BIOMD0000001077
Deciphering cell fate: a mathematical model of life and death decisions in erythroid progenitors
Lorenz Adlung -
January: BIOMD0000001080, BIOMD0000001079
DeBoeck2021 - Modular approach to modelling the cell cycle
Jan Rombouts
2021
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December: BIOMD0000001029, BIOMD0000001028, BIOMD0000001027, BIOMD0000001039
Zake2021 - PBPK model of metformin in mice and humans
Krishna Kumar Tiwari -
August: BIOMD0000001022
Creemers2021 - Tumor-immune dynamics and implications on immunotherapy responses
Emilia Chen -
March: BIOMD0000000827
Ito2019 - Gefitinib resistance of lung adenocarcinoma caused by MET amplification
Krishna Kumar Tiwari
2020
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September: BIOMD0000000955
SIDARTHE model of COVID-19 transmission in Italy
Kausthubh Ramachandran -
July: BIOMD0000000918
Schwarz et al (2018 ). Cdk Activity Threshold Determines Passage through the Restriction Point
Ahmad Zyoud -
May: BIOMD0000000546
Miao2010 - Quantifying the Early Immune Response and Adaptive Immune Response Kinetics in Mice Infected with Influenza A Virus
Rahuman Sheriff -
March: BIOMD0000000712
Manchanda2014 – Modelling infection course induced by four different influenza strains
Krishna Kumar Tiwari
2019
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December: BIOMD0000000642
Mufudza2012 - Estrogen effect on the dynamics of breast cancer
Mohammad Umer Sharif Shohan -
November: BIOMD0000000636, BIOMD0000000635
Nair2015 - Interaction between neuromodulators via GPCRs - Effect on cAMP/PKA signaling
Johannes Meyer -
October: BIOMD0000000788
Schropp2019 - Target-Mediated Drug Disposition Model for Bispecific Antibodies
Johannes Meyer -
September: BIOMD0000000373
Bertram et al. (2004). Pancreatic Beta Cells
Jinghao Men -
August: BIOMD0000000711
Hancioglu2007 - Human Immune Response to Influenza A virus Infection
Jinghao Men -
June: BIOMD0000000703
A data-entrained computational model for testing the regulatory logic of the vertebrate unfolded pro
Diedrichs DR et al. 2018 -
April: BIOMD0000000335
Hockin_2002: A mathematical model of Blood coagulation pathway
Krishna Kumar Tiwari -
January: BIOMD0000000724
Mathematical modeling identifies Lck as a potential mediator for PD-1 induced inhibition of early TCR signaling
Krishna Kumar Tiwari
2018
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December: BIOMD0000000056
Chen2004 - An integrated yeast cell cycle model
Ashley Xavier -
November: BIOMD0000000612
Proctor2016 - Circadian rhythm of PTH and the dynamics of signalling molecules on bone remodelling
Sarubini Kananathan -
October:
Liebal et al., (2012). Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis
Thawfeek M. Varusai -
August: BIOMD0000000700
Heldt2018 - Proliferation-quiescence decision in response to DNA damage.
Lu Li -
July: BIOMD0000000564
Gould2013 - Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures.
Matthew Roberts -
June:
Rateitschak et al (2012). Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells
Vincent Knight-Schrijver -
May: BIOMD0000000572
Costa et al (2014). An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production
Matthew Roberts -
April: BIOMD0000000641
Jaiswal et al (2017). ATM/Wip1 activities at chromatin control Plk1 re-activation to determine G2 checkpoint duration.
Rahuman Sheriff -
March: BIOMD0000000651
Nguyen LK and Kholodenko BN (2016). Akt/mTOR and RTK/MAPK siganlling model may serve as a valuable tool for therapeutic research
Thawfeek M Varusai -
February: BIOMD0000000432, BIOMD0000000430, BIOMD0000000433, BIOMD0000000431
Sarma U and Ghosh I (2012). Design of kinase-phosphatase interactions and phosphatase sequestration shape MAPK cascade robustness and signal flow.
Corina Dueñas Roca
2017
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November: BIOMD0000000625
Leber et al (2016). Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection
Vincent Knight-Schrijver -
October: BIOMD0000000574
Lai et al., (2015). Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.
Lu Li -
September:
Padala et al., (2017). Cancerous perturbations within the ERK, PI3K/Akt, and Wnt/β-catenin signaling network constitutively activate inter-pathway positive feedback loops.
Emma Louise Fairbanks -
August:
Mathias Uhlen et al., (2017). A pathology atlas of the human cancer transcriptome
Varun Kothamachu; Rahuman Sheriff -
June: BIOMD0000000640
Dalle Pezze et al. (2016). A systems study reveals concurrent activation of AMPK and mTOR by amino acids.
Thawfeek Mohamed Varusai -
May: BIOMD0000000616
Dunster et al. (2014). The resolution of inflammation: a mathematical model of neutrophil and macrophage interactions.
Corina Dueñas Roca -
April: BIOMD0000000620, BIOMD0000000621
Palmér et al., (2014). Effects of IL-1β-Blocking Therapies in Type 2 Diabetes Mellitus: A Quantitative Systems Pharmacology Modeling Approach to Explore Underlying Mechanisms.
Vincent Knight-Schrijver -
February: BIOMD0000000588
Benson et al. (2013). Systems pharmacology of the nerve growth factor pathway: use of a systems biology model for the identification of key drug targets...
Varun Bhaskar Kothamachu -
January: BIOMD0000000622
Nguyen et al. (2011). Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system.
Thawfeek Mohamed Varusai
2016
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December: BIOMD0000000451
Carbo et al. (2013). Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity.
Corina Dueñas Roca -
November: BIOMD0000000607, BIOMD0000000610, BIOMD0000000604, BIOMD0000000605, BIOMD0000000606, BIOMD0000000603
Petelenz-Kurdzeil et al. (2013). Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress
Nick Juty -
October: BIOMD0000000439
Smith et al. (2009). Dual positive and negative regulation of GPCR signaling by GTP hydrolysis.
Shukanto Das -
September: BIOMD0000000595, BIOMD0000000594
Capuani et al. (2015). Quantitative analysis reveals how EGFR activation and downregulation are coupled in normal but not in cancer cell.
Lu Li -
July: BIOMD0000000613
Peterson and Riggs (2010). A physiologically based mathematical model of integrated calcium homeostasis and bone remodeling.
Vincent Knight-Schrijver -
June: BIOMD0000000611
Nayak et al. (2015). Using a Systems Pharmacology Model of the Blood Coagulation Network to Predict the Effects of Various Therapies on Biomarkers.
Corina Dueñas Roca -
May: BIOMD0000000608
Palsson et al. (2013). The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.
Corina Dueñas Roca -
April: BIOMD0000000313
Raia et al. (2010). Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets.
Thawfeek Mohamed Varusai -
March: BIOMD0000000583
Leber et al. (2015). Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection.
Florent Yvon -
January: BIOMD0000000512
Benson et al. (2014). A Systems Pharmacology Perspective on the Clinical Development of Fatty Acid Amide Hydrolase Inhibitors for Pain
Vincent Knight-Schrijver
2015
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October: BIOMD0000000533
Steckmann et al. (2012). Kinetics of peptide secondary structure conversion during amyloid ?-protein fibrillogenesis.
Lu Li -
August: BIOMD0000000554
Cloutier et al. (2009). An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements.
Felix Winter -
June: BIOMD0000000527
Kaiser et al. (2014). Cecum lymph node dentritic cells harbor slow-growing bacteria phenotypically tolerant to antibiotic treatment.
Nick Juty -
May: BIOMD0000000528, BIOMD0000000529
Fribourg et al. (2014). Dynamics of viral antagonism and innate immune response.
Florent Yvon -
April: BIOMD0000000490
Demin et al. (2013). Systems Pharmacology Models Can Be Used to Understand Complex Pharmacokinetic-Pharmacodynamic Behavior: An Example Using 5-Lipoxygenase Inhibitors
Vincent Knight-Schrijver -
March: BIOMD0000000559
Ouzounoglou et al. (2014). Modeling of alpha-synuclein effects on neuronal homeostasis.
Audald Lloret-Villas -
February: BIOMD0000000294
Restif and Grenfell. (2007). Vaccination and the dynamics of immune evasion.
Massimo Lai -
January: BIOMD0000000379
Dalla Man et al. (2007). Meal simulation model of the glucose-insulin system.
Maciej Swat
2014
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November: BIOMD0000000446
Erguler et al. (2013). A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis.
Vijayalakshmi Chelliah -
October: BIOMD0000000501, BIOMD0000000500
Begitt et al.(2014). STAT1-cooperative DNA binding distinguishes type 1 from type 2 interferon signaling.
Nick Juty -
September: BIOMD0000000536, BIOMD0000000537, BIOMD0000000534, BIOMD0000000535
Dwivedi et al. (2014). A multiscale model of interleukin-6-mediated immune regulation in Crohn's disease and its application in drug discovery and development.
Vincent Knight-Schrijver -
August: BIOMD0000000488
Proctor et al. (2013). Investigating interventions in Alzheimer's disease with computer simulation models.
Audald Lloret-Villas -
July: BIOMD0000000530
Schmitz et al. (2014). Cooperative gene regulation by microRNA pairs and identification using a computational workflow.
Florent Yvon -
June: BIOMD0000000498
Mitchell and Mendes (2013). A computational model of liver iron metabolism.
Martina Fröhlich -
May: BIOMD0000000462
Proctor et al. (2012). Aggregation, impaired degradation and immunization targeting of amyloid-beta dimers in Alzheimer's disease: a stochastic modelling approach.
Massimo Lai -
March: BIOMD0000000521
Ribba et al., (2012). A tumor growth inhibition model for low-grade glioma treated with chemotherapy or radiotherapy.
Maciej Swat -
January: BIOMD0000000075
Xu et al. (2003). Kinetic analysis of receptor-activated phosphoinositide turnover.
Christine Seeliger
2013
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November: BIOMD0000000288
Wang et al. (2009). PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk.
Lu Li -
October: BIOMD0000000434
McAuley et al. (2012). A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation.
Nick Juty -
September: BIOMD0000000233
Wilhelm T. (2009). The smallest chemical reaction system with bistability.
Vladimir Kiselev -
August: BIOMD0000000149
Kim et al. (2007). A hidden oncogenic positive feedback loop caused by crosstalk between Wnt and ERK pathways.
Vijayalakshmi Chelliah -
July: BIOMD0000000286
Proctor and Gray. (2010). GSK3 and p53 - is there a link in Alzheimer's disease?
Martina Fröhlich -
June: BIOMD0000000252
Hunziker et al. (2010). Stress-specific response of the p53-Mdm2 feedback loop.
Massimo Lai -
May: BIOMD0000000321, BIOMD0000000320
Grange et al. (2001). A pharmacokinetic model to predict the PK interaction of L-dopa and benserazide in rats.
Stuart Moodie -
April: BIOMD0000000008
Gardner et al., (1998). A theory for controlling cell cycle dynamics using a reversibly binding inhibitor.
Maciej Swat -
February: BIOMD0000000253
Teusink et al. (1998). The danger of metabolic pathways with turbo design.
Benedetta Frida Baldi -
January: BIOMD0000000414, BIOMD0000000413
Band et al. (2010). Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Vladimir Kiselev
2012
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December: BIOMD0000000415
Mellor et al. (2010). Reduction of off-flavor generation in soybean homogenates: a mathematical model.
Christine Seeliger -
November: BIOMD0000000410
Wegner et al. (2012). Dynamics and feedback loops in the transforming growth factor ? signaling pathway.
Martina Fröhlich -
October: BIOMD0000000291
Nikolaev et al. (2005). Mathematical model of binding of albumin-bilirubin complex to the surface of carbon pyropolymer.
Vijayalakshmi Chelliah -
September: BIOMD0000000337
Pfeiffer et al. (2001). Cooperation and competition in the evolution of ATP-producing pathways.
Massimo Lai -
August: BIOMD0000000424
Faratian et al. (2009). Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab.
Stuart Moodie -
July: BIOMD0000000407
Schliemann et al. (2011). Heterogeneity Reduces Sensitivity of Cell Death for TNF-Stimuli.
Nick Juty -
June: BIOMD0000000318
Yao et al., (2008). A bistable Rb-E2F switch underlies the restriction point.
Maciej Swat -
May: BIOMD0000000180, BIOMD0000000179
Kim et al. (2007). Interlinked mutual inhibitory positive feedbacks induce robust cellular memory effects.
Vladimir Kiselev -
April: BIOMD0000000405
Cookson et al. (2011). Queueing up for enzymatic processing: correlated signaling through coupled degradation.
Benedetta Frida Baldi -
March: BIOMD0000000118, BIOMD0000000119
Golomb et al. (2006). Contribution of persistent Na+ current and M-type K+ current to somatic bursting in CA1 pyramidal cells: combined experimental and modeling study.
Youwei Zheng -
February: BIOMD0000000328
Bucher et al. 2011. A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes.
Christine Seeliger -
January: BIOMD0000000401, BIOMD0000000402, BIOMD0000000403
Ayati et al. (2010). A mathematical model of bone remodeling dynamics for normal bone cell populations and myeloma bone disease.
Vijayalakshmi Chelliah
2011
-
December: BIOMD0000000364
Lee et al. (2010). A revisit to the one form kinetic model of prothrombinase.
Massimo Lai -
November: BIOMD0000000356
Nyman et al. (2011). A Hierarchical Whole-body Modeling Approach Elucidates the Link between in Vitro Insulin Signaling and in Vivo Glucose Homeostasis.
Ishan Ajmera -
October: BIOMD0000000271, BIOMD0000000272
Becker et al. (2010). Covering a broad dynamic range: information processing at the erythropoietin receptor.
Nick Juty -
September: BIOMD0000000069
Fuss et al. (2006). Bistable switching and excitable behaviour in the activation of Src at mitosis.
Denis Brun -
August: BIOMD0000000239
Jiang et al. (2007). A kinetics core model of the Glucose-simulated insulin secretion network of pancreatic beta cells.
Ishan Ajmera -
July: BIOMD0000000338, BIOMD0000000339, BIOMD0000000340
Wajima et al. (2009), A comprehensive model for the humoral coagulation network in human.
Michael Schubert -
June: BIOMD0000000301
Friedland et al., (2009). Synthetic gene networks that count.
Gael Jalowicki -
May: BIOMD0000000296
Balagaddé et al., (2008). A synthetic Escherichia coli predator-prey ecosystem.
Michele Mattioni -
April: BIOMD0000000306, BIOMD0000000310, BIOMD0000000311, BIOMD0000000307, BIOMD0000000308, BIOMD0000000312, BIOMD0000000309
Tyson et al., (2003). Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.
Lukas Endler -
March: BIOMD0000000129, BIOMD0000000133, BIOMD0000000142, BIOMD0000000131, BIOMD0000000130, BIOMD0000000134, BIOMD0000000132, BIOMD0000000141, BIOMD0000000136, BIOMD0000000135
Izhikevich EM (2004), Which model to use for cortical spiking neurons?
Junmei Zhu -
February: BIOMD0000000270
Schilling et al. (2009), Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions.
Benedetta Frida Baldi -
January: BIOMD0000000215
Schulz et al., (2009), Sequential polarization and imprinting of type 1 T helper lymphocytes by interferon-gamma and interleukin-12.
Christine Seeliger
2010
-
December: BIOMD0000000258
Ortega et al. (2006), Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements.
Massimo Lai -
November: BIOMD0000000249
Restif and Grenfell (2006), Integrating life history and cross-immunity into the evolutionary dynamics of pathogens.
Lukas Endler -
August: BIOMD0000000267, BIOMD0000000178
Lebeda et. al. (2008), Onset dynamics of type A botulinum neurotoxin-induced paralysis.
Vijayalakshmi Chelliah -
July: BIOMD0000000139, BIOMD0000000140
Hoffmann et. al. (2002), The IkB-NF-kB Signaling Module: Temporal Control and Selective Gene Activation.
Lu Li -
June: BIOMD0000000209, BIOMD0000000210
Chickarmane and Peterson (2008), A computational model for understanding stem cell, trophectoderm and endoderm lineage determination
Nick Juty -
May: BIOMD0000000127
Izhikevich EM (2003), Simple model of spiking neurons
Michele Mattioni -
April: BIOMD0000000166
Zhu et al. (2007), A theoretical study on activation of transcription factor modulated by intracellular Ca2+ oscillations
Benedetta Frida Baldi -
March: BIOMD0000000223
Borisov et al. (2009), Systems-level interactions between insulin-EGF networks amplify mitogenic signaling
Christine Seeliger -
February: BIOMD0000000228
Swat et al. (2004), Bifurcation analysis of the regulatory modules of the mammalian G1/S transition
Lukas Endler -
January: BIOMD0000000234
Tham et al. (2008), A Pharmacodynamic Model for the Time Course of Tumour Shrinkage by Gemcitabine + Carboplatin in Non-Small Cell Lung Cancer Patients
Vijayalakshmi Chelliah
2009
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September: BIOMD0000000200
Bray and Bourret (1995), Bacterial Chemotaxis
Melanie I. Stefan -
August: BIOMD0000000098, BIOMD0000000224
Goldbeter et al. (1990), Meyer and Stryer (1991), Two Models of Calcium Spiking
Vijayalakshmi Chelliah -
July: BIOMD0000000184
Lavrentovich and Hemkin (2008), Calcium Oscillations in Astrocytes
Michele Mattioni -
June: BIOMD0000000018
Morrison and Allegra (1989), Folate Cycle
Lukas Endler -
May: BIOMD0000000023
Rohwer and Botha (2001), Sucrose accumulation in sugar cane
Nick Juty -
April: BIOMD0000000201
Goldbeter and Pourquie (2008), Somite Segmentation Clock
Melanie I. Stefan -
March: BIOMD0000000183
Stefan et al. (2008), Allosteric Model of Calmodulin
Lu Li -
February: BIOMD0000000188, BIOMD0000000189
Proctor and Gray (2008), The p53-Mdm2 System
Vijayalakshmi Chelliah -
January: BIOMD0000000152
Fernandez et al. (2006), Integration of glutamate and dopamine signals
Michele Mattioni
2008
-
December: BIOMD0000000105
Proctor et al. (2007), Ubiquitin-Proteasome System
Ranjita Dutta Roy -
November: BIOMD0000000071
Bakker et al. (2001), Glycolysis in Trypanosoma
Lukas Endler -
October: BIOMD0000000067
Fung et al. (2005), Metabolator
Nick Juty -
September: BIOMD0000000101
Vilar et al. (2006), TGF-β
Noriko Hiroi -
August: BIOMD0000000106
Yang et al. (2007), Arachidonic Acid
Dominic P. Tolle -
July: BIOMD0000000039
Marhl et al. (2000), Calcium Oscillations
Lu Li -
June: BIOMD0000000102
Legewie et al. (2006), Apoptosis
Melanie I. Stefan -
May: BIOMD0000000085
Maurya et al. (2005), GTPase-Cycle Module
Michele Mattioni -
April: BIOMD0000000003, BIOMD0000000004
Goldbeter (1991), Minimal Mitotic Oscillator
Anika Oellrich -
March: BIOMD0000000107
Novak and Tyson (1993), M-phase Control
Michele Mattioni and Judith Zaugg -
February: BIOMD0000000147
O'Dea et al. (2007), IΚB Metabolism
Dominic P. Tolle -
January: BIOMD0000000032
Kofahl and Klipp (2004), Yeast Pheromone Pathway
Melanie I. Stefan
2007
-
December: BIOMD0000000138
Tabak et al. (2007), Dopamine
Lu Li -
November: BIOMD0000000125
Komarova et al. (2005), Specificity in Cell Signaling
Dominic P. Tolle -
October: BIOMD0000000148
Komarova et al. (2003), Bone Remodeling
Anika Oellrich -
September: BIOMD0000000040
Fields and Noyes (1974), The Oregonator
Christian Knüpfer -
August: BIOMD0000000079
Goldbeter (2006), Human Weight Cycling
Melanie I. Stefan -
July: BIOMD0000000062
Bhartiya et al. (2004), Tryptophan Operon
Antonia Mayer -
June: BIOMD0000000026, BIOMD0000000031
Markevich et al. (2004), MAPK
Lu Li -
May: BIOMD0000000017
Hoefnagel et al. (2002), Metabolic Control Analysis
Dominic P. Tolle -
April: BIOMD0000000058
Bindschadler and Sneyd (2001), Coupled Calcium Oscillators
Melanie I. Stefan -
March: BIOMD0000000001
Edelstein (1996), Nicotinic Receptor
Nicolas Le Novère -
February: BIOMD0000000049
Sasagawa (2005), MAPK
Lu Li -
January: BIOMD0000000064
Teusink (2000), Glycolysis
Dominic P. Tolle
2006
-
December: BIOMD0000000065
Yildirim (2003), lac Operon
Melanie I. Stefan -
November: BIOMD0000000025
Smolen (2002), Circadian Oscillator
Enuo He -
October: BIOMD0000000005
Tyson (1991), Modelling Cell Division
Nicolas Le Novère -
September: BIOMD0000000020
Hodgkin and Huxley (1952), Membrane Current in the Giant Squid Axon
Melanie I. Stefan -
August: BIOMD0000000048
Kholodenko (1999), Epidermal Growth Factor Receptor signalling
Renaud Schiappa -
July: BIOMD0000000012
Elowitz and Leibler (2000), The Repressilator
Dominic P. Tolle -
June: BIOMD0000000009
Huang and Ferrell (1996), MAPK ultrasensitivity
Nicolas Le Novère