| 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 | | |
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