Biological interaction networks are often organized into groups or modules of related genes and proteins carrying out specific biological functions. Over the past few years, many methods have been proposed to rationally decompose those networks into functional modules, yet this challenging problem has not been fully satisfactorily solved.
Jmod is an extensible tool implementing state of the art modularity detection methods. Jmod implements three modularity detection methods, Newman’s spectral algorithm , a genetic algorithm-based method that we developed, and a brute force approach. We also developed a refinement technique called global Moving Vertex Method (gMVM) that can be used to further improve the performance of modularity detection methods, and provide an improved version of Newman’s spectral algorithm. The performance of the modularity detection and refinement methods in Jmod have been evaluated using biological and in silico benchmarks.
> Author’s project web page
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Video introduction to GeneNetWeaver (GNW) and in silico benchmark generation and performance profiling of network inference methods.
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In silico benchmark generation and performance profiling of network inference methods
Java library for simulating stochastic differential equations
Observation and interaction in experimental environments
Publications
Journal Articles Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics X. Fernandez Cassi ; T. Kohn
Food and Environmental Virology . 2024. DOI : 10.1007/s12560-024-09594-3. Impact of CO2-rich seawater injection on the flow properties of basalts E. Stavropoulou ; C. Griner ; L. Laloui
International Journal of Greenhouse Gas Control . 2024-04-19. Vol. 134 , p. 104128. DOI : 10.1016/j.ijggc.2024.104128. TSLAM: a tag-based object-centered monocular navigation system for augmented manual woodworking. S. Andrea ; H-B. Yang ; G. Julien ; W. Yves
Construction Robotics . 2024-04-16. Vol. 8 , num. 4 . DOI : 10.1007/s41693-024-00118-w. Water weakening and the compressive brittle strength of carbonates: Influence of fracture toughness and static friction C. Noël ; B. Fryer ; P. Baud ; M. Violay
International Journal of Rock Mechanics and Mining Sciences . 2024. Vol. 177 , p. 105736. DOI : 10.1016/j.ijrmms.2024.105736. An extension of the stochastic sewing lemma and applications to fractional stochastic calculus T. Matsuda ; N. Perkowski
Forum Of Mathematics Sigma . 2024-04-11. Vol. 12 , p. e52. DOI : 10.1017/fms.2024.32. Capsizing due to friction-induced twist in the failure of stopper knots P. Johanns ; P. M. Reis
Extreme Mechanics Letters . 2024-02-19. Vol. 68 , p. 102134. DOI : 10.1016/j.eml.2024.102134. A CTCF-dependent mechanism underlies the Hox timer relation to a segmented body plan H. Rekaik ; D. Duboule
Current Opinion In Genetics & Development . 2024-04-01. Vol. 85 , p. 102160. DOI : 10.1016/j.gde.2024.102160. Gradient High-Q Dielectric Metasurfaces for Broadband Sensing and Control of Vibrational Light-Matter Coupling F. U. Richter ; I. Sinev ; S. Zhou ; A. Leitis ; S-H. Oh et al.
Advanced Materials . 2024-04-09. DOI : 10.1002/adma.202314279. SOMOphilic alkyne vs radical-polar crossover approaches: The full story of the azido-alkynylation of alkenes J. A. Borrel ; J. Waser
Beilstein Journal Of Organic Chemistry . 2024-04-03. Vol. 20 , p. 701-713. DOI : 10.3762/bjoc.20.64. Dielectric elastomer actuator-based valveless pump as Fontan failure assist device: introduction and preliminary study A. Benouhiba ; A. M. Walter ; S. E. Jahren ; T. G. Martinez ; F. Clavica et al.
Interdisciplinary Cardiovascular And Thoracic Surgery . 2024-03-29. Vol. 38 , num. 4 , p. ivae041. DOI : 10.1093/icvts/ivae041. Comprehensive Memory Safety Validation: An Alternative Approach to Memory Safety K. Huang ; M. Payer ; Z. Qian ; J. Sampson ; G. Tan et al.
Ieee Security & Privacy . 2024-04-04. DOI : 10.1109/MSEC.2024.3379947. A Method of Moments Estimator for Interacting Particle Systems and their Mean Field Limit G. A. Pavliotis ; A. Zanoni
Siam-Asa Journal On Uncertainty Quantification . 2024-01-01. Vol. 12 , num. 2 , p. 262-288. DOI : 10.1137/22M153848X. An aircraft assembly process formalism and verification method based on semantic modeling and MBSE X. Zheng ; X. Hu ; J. Lu ; R. Arista ; J. Lentes et al.
Advanced Engineering Informatics . 2024-02-20. Vol. 60 , p. 102412. DOI : 10.1016/j.aei.2024.102412. Twisted pair transmission line coil – a flexible, self-decoupled and robust element for 7 T MRI J. Vliem ; Y. Xiao ; D. Wenz ; L. Xin ; W. Teeuwise et al.
Magnetic Resonance Imaging . 2024-02-19. Vol. 108 , p. 146-160. DOI : 10.1016/j.mri.2024.02.007. 3D Printing of Double Network Granular Elastomers with Locally Varying Mechanical Properties E. J. Baur ; B. Tiberghien ; E. Amstad
Advanced Materials . 2024-04-04. DOI : 10.1002/adma.202313189. Proliferation-driven mechanical compression induces signalling centre formation during mammalian organ development N. P. Shroff ; P. Xu ; S. Kim ; E. R. Shelton ; B. J. Gross et al.
Nature Cell Biology . 2024-04-03. DOI : 10.1038/s41556-024-01380-4. Spin-Reorientation-Driven Linear Magnetoelectric Effect in Topological Antiferromagnet Cu3TeO6 V. Kisicek ; D. Dominko ; M. Culo ; Z. Rapljenovic ; M. Kuvezdic et al.
Physical Review Letters . 2024-02-26. Vol. 132 , num. 9 , p. 096701. DOI : 10.1103/PhysRevLett.132.096701. Stick-slip-to-stick transition of liquid oscillations in a U-shaped tube A. Bongarzone ; F. Gallaire
Physical Review Fluids . 2024-03-19. Vol. 9 , num. 3 , p. 034401. DOI : 10.1103/PhysRevFluids.9.034401. Impact of beam-coupling impedance on the Schottky spectrum of bunched beam C. Lannoy ; K. Lasocha ; T. Pieloni ; D. Alves ; N. Mounet
Journal Of Instrumentation . 2024-03-01. Vol. 19 , num. 3 , p. P03017. DOI : 10.1088/1748-0221/19/03/P03017. Diffusion of brain metabolites highlights altered brain microstructure in type C hepatic encephalopathy: a 9.4 T preliminary study J. Mosso ; G. Briand ; K. Pierzchala ; D. Simicic ; A. Sierra et al.
Frontiers In Neuroscience . 2024-03-20. Vol. 18 , p. 1344076. DOI : 10.3389/fnins.2024.1344076. Teaching about non-deterministic physics: an almost forgotten fundamental contribution of Marie Curie G. Margaritondo
European Journal Of Physics . 2024-05-01. Vol. 45 , num. 3 , p. 035803. DOI : 10.1088/1361-6404/ad312e. Learning Weakly Convex Regularizers for Convergent Image-Reconstruction Algorithms A. Goujon ; S. J. Neumayer ; M. Unser
Siam Journal On Imaging Sciences . 2024-01-01. Vol. 17 , num. 1 , p. 91-115. DOI : 10.1137/23M1565243. An interior penalty coupling strategy for isogeometric non-conformal Kirchhoff-Love shell patches G. Guarino ; P. Antolin ; A. Milazzo ; A. Buffa
Engineering With Computers . 2024-03-27. DOI : 10.1007/s00366-024-01965-5. On the Arithmetic and Geometric Fusion of Beliefs for Distributed Inference M. Kayaalp ; Y. Inan ; E. Telatar ; A. H. Sayed
Ieee Transactions On Automatic Control . 2024-04-01. Vol. 69 , num. 4 , p. 2265-2280. DOI : 10.1109/TAC.2023.3330405. Alpha1-antitrypsin improves survival in murine abdominal sepsis model by decreasing inflammation and sequestration of free heme J. D. Zemtsovski ; S. Tumpara ; S. Schmidt ; V. Vijayan ; A. Klos et al.
Frontiers In Immunology . 2024-03-18. Vol. 15 , p. 1368040. DOI : 10.3389/fimmu.2024.1368040. Quantitative prediction of crystallization in laser powder bed fusion of a Zr-based bulk metallic glass with high oxygen content N. Sohrabi ; T. Ivas ; J. Jhabvala ; J. E. K. Schawe ; J. F. Loffler et al.
Materials & Design . 2024-03-01. Vol. 239 , p. 112744. DOI : 10.1016/j.matdes.2024.112744. A cut-cell method for the numerical simulation of 3D multiphase flows with strong interfacial effects A. Caboussat ; J. Hess ; A. Masserey ; M. Picasso
Journal Of Computational Physics . 2024-02-26. Vol. 504 , p. 112846. DOI : 10.1016/j.jcp.2024.112846. Can Gas Consumption Data Improve the Performance of Electricity Theft Detection? W. Liao ; R. Zhu ; T. Ishizaki ; Y. Li ; Y. Jia et al.
Ieee Transactions On Industrial Informatics . 2024-03-18. DOI : 10.1109/TII.2024.3371991. Design and in vitro Characterization of a Wearable Multisensing System for Hydration Monitoring S. Tonello ; A. Zacchini ; A. Galli ; A. Golparvar ; A. Meimandi et al.
Ieee Transactions On Instrumentation And Measurement . 2024-01-01. Vol. 73 , p. 1-11. DOI : 10.1109/TIM.2024.3369161. Multi-Ported GC-eDRAM Bitcell with Dynamic Port Configuration and Refresh Mechanism R. Golman ; R. Giterman ; A. Teman
Journal Of Low Power Electronics And Applications . 2024-03-01. Vol. 14 , num. 1 , p. 2. DOI : 10.3390/jlpea14010002. On the Sums over Inverse Powers of Zeros of the Hurwitz Zeta Function and Some Related Properties of These Zeros S. Sekatskii
Symmetry-Basel . 2024-03-01. Vol. 16 , num. 3 , p. 326. DOI : 10.3390/sym16030326. Realization of Organocerium-Based Fullerene Molecular Materials Showing Mott Insulator-Type Behavior P. Pandey ; X. Wang ; H. Gupta ; P. W. Smith ; E. Lapsheva et al.
Acs Applied Materials & Interfaces . 2024-03-27. Vol. 16 , num. 14 , p. 17857-17869. DOI : 10.1021/acsami.3c18766. Mean-field transport equations and energy theorem for plasma edge turbulent transport R. A. J. Coosemans ; W. Dekeyser ; M. Baelmans
Journal Of Plasma Physics . 2024-03-15. Vol. 90 , num. 2 , p. 905900202. DOI : 10.1017/S0022377824000163. Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures J. S. Saini ; A. Adler ; L. Cardona ; P. N. R. Ramirez ; R. Pei et al.
Microbiology Resource Announcements . 2024-03-27. DOI : 10.1128/mra.00102-24. The multimodality cell segmentation challenge: toward universal solutions J. Ma ; R. Xie ; S. Ayyadhury ; C. Ge ; A. Gupta et al.
Nature Methods . 2024-03-26. DOI : 10.1038/s41592-024-02233-6. Search for Inelastic Dark Matter in Events with Two Displaced Muons and Missing Transverse Momentum in Proton-Proton Collisions at p s=13 TeV A. Hayrapetyan ; A. Tumasyan ; W. Adam ; J. W. Andrejkovic ; T. Bergauer et al.
Physical Review Letters . 2024-01-23. Vol. 132 , num. 4 , p. 041802. DOI : 10.1103/PhysRevLett.132.041802. Tumor-educated Gr1+CD11b+cells drive breast cancer metastasis via OSM/IL-6/JAK-induced cancer cell plasticity S. Peyvandi ; M. Bulliard ; A. Yilmaz ; A. Kauzlaric ; R. Marcone et al.
Journal Of Clinical Investigation . 2024-03-15. Vol. 134 , num. 6 , p. e166847. DOI : 10.1172/JCI166847. Dynamics of the charge transfer to solvent process in aqueous iodide J. Lan ; M. Chergui ; A. Pasquarello
Nature Communications . 2024-03-21. Vol. 15 , num. 1 , p. 2544. DOI : 10.1038/s41467-024-46772-0. Evaluation of controllers for augmentative hip exoskeletons and their effects on metabolic cost of walking: explicit versus implicit synchronization A. R. Manzoori ; D. Malatesta ; J. Primavesi ; A. Ijspeert ; M. Bouri
Frontiers In Bioengineering And Biotechnology . 2024-03-12. Vol. 12 , p. 1324587. DOI : 10.3389/fbioe.2024.1324587. Boosting likelihood learning with event reweighting S. Chen ; A. Glioti ; G. Panico ; A. Wulzer
Journal Of High Energy Physics . 2024-03-20. num. 3 , p. 117. DOI : 10.1007/JHEP03(2024)117. Conference Papers Resource-Efficient Continual Learning for Personalized Online Seizure Detection A. Shahbazinia ; F. Ponzina ; J. A. Miranda Calero ; J. Dan ; G. Ansaloni et al.
2024-04-15. 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Orlando, Florida, USA, July 15-19, 2024. Reviews Is There a Special Role for Ovarian Hormones in the Pathogenesis of Lobular Carcinoma? R. L. Flaherty ; G. Sflomos ; C. Brisken
Endocrinology . 2024-03-29. Vol. 165 , num. 5 , p. bqae031. DOI : 10.1210/endocr/bqae031. Books Field Guide to Northern Tree-related Microhabitats: Descriptions and size limits for their inventory in boreal and hemiboreal forests of Europe and North America R. Bütler Sauvain ; L. Larrieu ; L. F. Lunde ; M. Maxence ; B. Nordén et al.
Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Switzerland , 2024. Radio-Activities: Architecture and Broadcasting in Cold War Berlin A. Thiermann
Cambridge, MA; London : MIT Press , 2024. Theses Studies of crystal collimation for heavy ion operation at the LHC R. Cai / M. Seidel ; R. Bruce (Dir.)
Lausanne , EPFL , 2024. Querying the Digital Archive of Science: Distant Reading, Semantic Modelling and Representation of Knowledge A. Volynskaya / J. Baudry ; J-F. Bert (Dir.)
Lausanne , EPFL , 2024. Hybrid organic/metal-oxide shells on semiconductor nanocrystals via colloidal atomic layer deposition O. Segura Lecina / R. Buonsanti (Dir.)
Lausanne , EPFL , 2024. Electrical and Optical Manifestations of Flat Band Physics in Van der Waals Materials G. Pasquale / A. Kis (Dir.)
Lausanne , EPFL , 2024. Plasmonically enhanced molecular junctions for investigation of atomic-scale fluctuations in self-assembled monolayers S. P. Amirtharaj / C. M. G. Galland (Dir.)
Lausanne , EPFL , 2024. Exact Obstacle Avoidance for Robots in Complex and Dynamic Environments Using Local Modulation L. Huber / A. Billard (Dir.)
Lausanne , EPFL , 2024. Book Chapters How to Support Students to Develop Skills that Promote Sustainability S. R. Isaac ; J. de Lima
Teaching Transversal Skills for Engineering Studens: A Practical Handbook of Activities with Tangibles ; EPFL , 2024. How to Support Students Giving Each Other Constructive Feedback, Especially When It Is Difficult to Hear S. R. Isaac ; J. de Lima
Teaching Transversal Skills for Engineering Studens: A Practical Handbook of Activities with Tangibles ; EPFL , 2024. How teachers can use the 3T PLAY trident framework to design an activity that develops transversal skills S. R. Isaac ; J. de Lima
Teaching Transversal Skills for Engineering Studens: A Practical Handbook of Activities with Tangibles ; EPFL , 2024. All That is Solid A. Thiermann
Transcalar Prospects in Climate Crisis ; Zurich : Lars Müller , 2024. Posters Integration of the Pilatus3 detector for soft X-ray diagnostics on TCV S. Masillo
25th Topical Conference on High Temperature Plasma Diagnostics HTPD 2024, Asheville, North Carolina, 21 – 25 April 2024. Talks Il contributo delle company towns per l’identità produttiva dell’Italia di Mezzo A. K. De Almeida Santos
La Città Lago. Prossimità e trasizione ecologica in un territorio dell’Italia di Mezzo. Laboratorio di Urbanistica 2, Milan, Italy, 2024-03-22. Quantifying the effects of rainfall temporal variability on landscape evolution processes T. Lian ; N. Peleg ; S. Bonetti
EGU 2024, Viena, April 14–19, 2024. Towards a metabolic theory of catchments: scaling of water and carbon fluxes with size F. Bassani ; S. Fatichi ; S. Bonetti
EGU General Assembly 2024, Vienna, Austria, April 14-19, 2024. Media BSL Circular Economy 2024 Conference – BSL Blog S. Nick
2024-04-19. Datasets