You are here : Home > Research Centers and Units > Genoscope > UMR8030 > Publications

Systems & Synthetic Biology (LISSB)


Controlled E. coli aggregation mediated by DNA and XNA hybridization
Gasse C, Srivastava P, Shepers G, Jose J, Hollenstein M, Marliere P and Herdewijn P
Chembiochem (), e202300191, 2023
The Replicative DnaE Polymerase of Bacillus subtilis Recruits the Glycolytic Pyruvate Kinase (PykA) When Bound to Primed DNA Templates
Holland A, Pitoulias M, Soultanas P and Janniere L
Life (Basel) 13 (4), , 2023
Synergistic activation of RARbeta and RARgamma nuclear receptors restores cell specialization during stem cell differentiation by hijacking RARalpha-controlled programs
Koshy A, Mathieux E, Studer F, Bramoulle A, Lieb M, Colombo BM, Gronemeyer H and Mendoza-Parra MA
Editorial: Cancer and nutrients: new chemicals, signals, and biomarker-based therapy
Qin XY, Mendoza-Parra MA and Shirakami Y
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering
Herisson J, Duigou T, du Lac M, Bazi-Kabbaj K, Sabeti Azad M, Buldum G, Telle O, El Moubayed Y, Carbonell P, Swainston N, Zulkower V, Kushwaha M, Baldwin GS and Faulon JL
Pyruvate kinase, a metabolic sensor powering glycolysis, drives the metabolic control of DNA replication
Horemans S, Pitoulias M, Holland A, Pateau E, Lechaplais C, Ekaterina D, Perret A, Soultanas P and Janniere L
A versatile active learning workflow for optimization of genetic and metabolic networks
Pandi A, Diehl C, Kharrazi AY, Scholz SA, Bobkova E, Faure L, Nattermann M, Adam D, Chapin N, Foroughijabbari Y, Moritz C, Paczia N, Cortina NS, Faulon JL and Erb TJ
Cell-Free Biosensors and AI Integration
Soudier P, Faure L, Kushwaha M and Faulon JL
Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima
Soudier P, Pinzon DR, Reif-Trauttmansdorff T, Hijazi H, Cherriere M, Pereira CG, Blaise D, Pispisa M, Saint-Julien A, Hamlet W, Nguevo M, Gomes E, Belkhelfa S, Niarakis A, Kushwaha M and Grigoras I
A Core Transcription Regulatory Circuitry Defining Microglia Cell Identity Inferred from the Reanalysis of Multiple Human Microglia Differentiation Protocols
Aubert A, Studer F, Colombo BM and Mendoza-Parra MA
Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery
Baladi T, Nilsson JR, Gallud A, Celauro E, Gasse C, Levi-Acobas F, Sarac I, Hollenstein MR, Dahlen A, Esbjorner EK and Wilhelmsson LM
The NANOTUMOR consortium - Towards the Tumor Cell Atlas
Colin F, Schauer K, Hamiche A, Martineau P, Borg JP, Bednar J, Bertolin G, Camoin L, Collette Y, Dimitrov S, Fournier I, Hyenne V, Mendoza-Parra MA, Morelli X, Ronde P, Sumara I, Tramier M, Schultz P and Goetz JG
Patient-matched analysis identifies deregulated networks in prostate cancer to guide personalized therapeutic intervention
Kumar A, Kasikci Y, Badredine A, Azzag K, Ranty MLQ, Zaidi F, Aragou N, Mazerolles C, Malavaud ENR, Mendoza M, Vandel LRC and Gronemeyer R
Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer
Moehlin J, Mollet B, Colombo BM and Mendoza-Parra MA
Noncanonical DNA polymerization by aminoadenine-based siphoviruses
Pezo V, Jaziri F, Bourguignon PY, Louis D, Jacobs-Sera D, Rozenski J, Pochet S, Herdewijn P, Hatfull GF, Kaminski PA and Marliere P
A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes
Sleiman D, Garcia PS, Lagune M, Loc'h J, Haouz A, Taib N, Rothlisberger P, Gribaldo S, Marliere P and Kaminski PA
Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
Studer F, Petit JL, Engelen S and Mendoza-Parra MA
A comprehensive resource for retrieving, visualizing, and integrating functional genomics data
Blum M, Cholley PE, Malysheva V, Nicaise S, Moehlin J, Gronemeyer H and Mendoza-Parra MA
Large scale active-learning-guided exploration for in vitro protein production optimization
Borkowski O, Koch M, Zettor A, Pandi A, Batista AC, Soudier P and Faulon JL
Reinforcement Learning for Bioretrosynthesis
Koch M, Duigou T and Faulon JL
Use of beta(3)-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase
Nigro G, Bourcier S, Lazennec-Schurdevin C, Schmitt E, Marliere P and Mechulam Y
Vitamin-guanosine monophosphate conjugates for in vitro transcription priming
Papastavrou N, Bande O, Marliere P, Groaz E and Herdewijn P
CDYL2 Epigenetically Regulates MIR124 to Control NF-kappa B/STAT3-Dependent Breast Cancer Cell Plasticity
Siouda M, Dujardin AD, Barbollat-Boutrand L, Mendoza-Parra MA, Gibert B, Ouzounova M, Bouaoud J, Tonon L, Robert M, Foy JP, Lavergne V, Manie SN, Viari A, Puisieux A, Ichim G, Gronemeyer H, Saintigny P and Mulligan P
Biosensor-based enzyme engineering approach applied to psicose biosynthesis
Armetta J, Berthome R, Cros A, Pophillat C, Colombo BM, Pandi A and Grigoras I
The Synthetic Microbiology Caucus: a fresh channel for exploring new ideas, challenging conventional wisdom and fostering community projects
de Lorenzo V and Marliere P
RetroRules: a database of reaction rules for engineering biology
Duigou T, du Lac M, Carbonell P and Faulon JL
RAR beta Agonist Drug (C286) Demonstrates Efficacy in a Pre-clinical Neuropathic Pain Model Restoring Multiple Pathways via DNA Repair Mechanisms
Goncalves MB, Moehlin J, Clarke E, Grist J, Hobbs C, Carr AM, Jack J, Mendoza-Parra MA and Corcoran JPT
Custom-made transcriptional biosensors for metabolic engineering
Koch M, Pandi A, Borkowski O, Batista AC and Faulon JL
On the Enzymatic Formation of Metal Base Pairs with Thiolated and pK(a)-Perturbed Nucleotides
Levi-Acobas F, Rothlisberger P, Sarac I, Marliere P, Herdewijn P and Hollenstein M
Invading Escherichia coli Genetics with a Xenobiotic Nucleic Acid Carrying an Acyclic Phosphonate Backbone (ZNA)
Luo M, Groaz E, Froeyen M, Pezo V, Jaziri F, Leonczak P, Schepers G, Rozenski J, Marliere P and Herdewijn P
Optimizing Cell-Free Biosensors to Monitor Enzymatic Production
Pandi A, Grigoras I, Borkowski O and Faulon JL
Metabolic perceptrons for neural computing in biological systems
Pandi A, Koch M, Voyvodic PL, Soudier P, Bonnet J, Kushwaha M and Faulon JL
Kinetic analysis of N-alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases
Renders M, Dumbre S, Abramov M, Kestemont D, Margamuljana L, Largy E, Cozens C, Vandenameele J, Pinheiro VB, Toye D, Frere JM and Herdewijn P
Towards the enzymatic formation of artificial metal base pairs with a carboxy-imidazole-modified nucleotide
Rothlisberger P, Levi-Acobas F, Sarac I, Marliere P, Herdewijn P and Hollenstein M
Microbial Genes for a Circular and Sustainable Bio-PET Economy
Salvador M, Abdulmutalib U, Gonzalez J, Kim J, Smith AA, Faulon JL, Wei R, Zimmermann W and Jimenez JI
CiliaCarta: An integrated and validated compendium of ciliary genes
van Dam TJP, Kennedy J, van der Lee R, de Vrieze E, Wunderlich KA, Rix S, Dougherty GW, Lambacher NJ, Li CM, Jensen VL, Leroux MR, Hjeij R, Horn N, Texier Y, Wissinger Y, van Reeuwijk J, Wheway G, Knapp B, Scheel JF, Franco B, Mans DA, van Wijk E, Kepes F, Slaats GG, Toedt G, Kremer H, Omran H, Szymanska K, Koutroumpas K, Ueffing M, Nguyen TMT, Letteboer SJF, Oud MM, van Beersum SEC, Schmidts M, Beales PL, Lu QH, Giles RH, Szklarczyk R, Russell RB, Gibson TJ, Johnson CA, Blacque OE, Wolfrum U, Boldt K, Roepman R, Hernandez-Hernandez V and Huynen MA
Extended Metabolic Space Modeling
Carbonell P, Delepine B and Faulon J-L
Modeling gene-regulatory networks to describe cell fate transitions and predict master regulators
Cholley PE, Moehlin J, Rohmer A, Zilliox V, Nicaise S, Gronemeyer H and Mendoza-Parra MA
Modulation of BACE1 Activity by Chemically Modified Aptamers
Gasse C, Zaarour M, Noppen S, Abramov M, Marliere P, Liekens S, De Strooper B and Herdewijn P
Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo
Jabgunde AM, Jaziri F, Bande O, Froeyen M, Abramov M, Nguyen H, Schepers G, Lescrinier E, Pinheiro VB, Pezo V, Marliere P and Herdewijn P
XNA ligation using T4 DNA ligase in crowding conditions
Kestemont D, Renders M, Leonczak P, Abramov M, Schepers G, Pinheiro VB, Rozenski J and Herdewijn P
Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster
Koch M, Faulon JL and Borkowski O
A dataset of small molecules triggering transcriptional and translational cellular responses
Koch M, Pandi A, Delepine B and Faulon J-L
A Polymer Model for the Quantitative Reconstruction of Chromosome Architecture from HiC and GAM Data
Le Treut G, Kepes F and Orland H
Phosphonomethyl Oligonucleotides as Backbone-Modified Artificial Genetic Polymers
Liu C, Cozens C, Jaziri F, Rozenski J, Marechal A, Dumbre S, Pezo V, Marliere P, Pinheiro VB, Groaz E and Herdewijn P
Division-Based, Growth Rate Diversity in Bacteria
Nana GYG, Ripoll C, Cabin-Flaman A, Gibouin D, Delaune A, Janniere L, Grancher G, Chagny G, Loutelier-Bourhis C, Lentzen E, Grysan P, Audinot JN and Norris V
Multiple links connect central carbon metabolism to DNA replication initiation and elongation in Bacillus subtilis
Nouri H, Monnier AF, Fossum-Raunehaug S, Maciag-Dorszynska M, Cabin-Flaman A, Kepes F, Wegrzyn G, Szalewska-Palasz A, Norris V, Skarstad K and Janniere L
Metabolic Recruitment and Directed Evolution of Nucleoside Triphosphate Uptake in Escherichia coli
Pezo V, Hassan C, Louis D, Sargueil B, Herdewijn P and Marliere P
Incorporation of a minimal nucleotide into DNA
Rothlisberger P, Levi-Acobas F, Sarac I, Ricoux R, Mahy JP, Herdewijn P, Marliere P and Hollenstein M
Integrating transcriptional activity in genome-scale models of metabolism
Banos DT, Trebulle P and Elati M
Golden Gate Assembly system dedicated to complex pathway manipulation in Yarrowia lipolytica
Celinska E, Ledesma-Amaro R, Larroude M, Rossignol T, Pauthenier C and Nicaud JM
Base-Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology
Eremeeva E, Abramov M, Margamuljana L and Herdewijn P
The 5-chlorouracil:7-deazaadenine base pair as an alternative to the dT:dA base pair
Eremeeva E, Abramov M, Marliere P and Herdewijn P
Biotin-independent strains of Escherichia coli for enhanced streptavidin production
Jeschek M, Bahls MO, Schneider V, Marliere P, Ward TR and Panke S
Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0
Koch M, Duigou T, Carbonell P and Faulon JL
Overcoming the membrane barrier: Recruitment of gamma-glutamyl transferase for intracellular release of metabolic cargo from peptide vectors
Kuenzl T, Sroka M, Srivastava P, Herdewijn P, Marliere P and Panke S
Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity
Paschalis V, Le Chatelier E, Green M, Kepes F, Soultanas P and Janniere L
Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery
Rothlisberger P, Gasse C and Hollenstein M
Facile immobilization of DNA using an enzymatic his-tag mimic
Rothlisberger P, Levi-Acobas F, Sarac I, Baron B, England P, Marliere P, Herdewijn P and Hollenstein M
On the enzymatic incorporation of an imidazole nucleotide into DNA
Rothlisberger P, Levi-Acobas F, Sarac I, Marliere P, Herdewijn P and Hollenstein M
Exploring the potential of genome editing CRISPR-Cas9 technology
Singh V, Braddick D and Dhar PK
biochem4j: Integrated and extensible biochemical knowledge through graph databases
Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS and Breitling R

Published on 1 October 2020