bioRxiv

ISSN	2692-8205
ISSN-L	-
IUID	bac7a86aa80746f5b569f8c4a1b0d273
Modified	2024-11-18T14:26:23.861Z
Created	2024-11-18T14:26:23.861Z

Template-based RNA structure prediction advanced through a blind code competition.

bioRxiv - (-) - [2025-12-30; online 2025-12-30]

Insight into Malt1 activation mechanism through synergetic approach of AlphaFold, MD Simulation and NMR dynamic analyses.

Lesovoy D, Agback T, Roshchin K, ..., Orekhov V, Agback P

bioRxiv - (-) - [2025-12-19; online 2025-12-19]

PubMed DOI Crossref

Inter- and intra-individual differences in brain sex map to neuroendocrine profiles.

Bon GM, Kimmig AS, Comasco E, Derntl B, Kaufmann T

bioRxiv - (-) - [2025-12-11; online 2025-12-11]

PubMed DOI Crossref

Blind prediction of complex water and ion ensembles around RNA in CASP16.

Kretsch RC, Posani E, Baulin EF, ..., Case DA, Das R

bioRxiv - (-) - [2025-11-03; online 2025-11-03]

PubMed DOI Crossref

Structure-guided allosteric modulation of the delta opioid receptor.

Mobbs JI, Nguyen MD, Deo O, ..., Valant C, Thal DM

bioRxiv - (-) - [2025-10-17; online 2025-10-17]

PubMed DOI Crossref

Cotranslational folding and maturation of HIV-1 protease.

Westerfield J, Nicolaus F, Swanstrom R, von Heijne G

bioRxiv - (-) - [2025-08-27; online 2025-08-27]

PubMed DOI Crossref

Nonlinear transcriptional responses to gradual modulation of transcription factor dosage.

Domingo J, Minaeva M, Morris JA, ..., Sanjana NE, Lappalainen T

bioRxiv - (-) - [2025-08-07; online 2025-08-07]

PubMed DOI Crossref

Charting structural brain asymmetry across the human lifespan.

Dorfschmidt L, White S, Gardner M, ..., Seidlitz J, Alexander-Bloch A

bioRxiv - (-) - [2025-07-24; online 2025-07-24]

PubMed DOI Crossref

A novel mechanism for bacterial sporulation based on programmed peptidoglycan degradation.

Ramírez Carbó CA, Irazoki O, Venkatesan S, ..., Cava F, Nan B

bioRxiv - (-) - [2025-06-26; online 2025-06-26]

PubMed DOI Crossref

Age and Alzheimer's disease affect functional connectivity along separate axes of functional brain organization.

Rittmo J, Franzmeier N, Strandberg O, ..., Hansson O, Vogel JW

bioRxiv - (-) - [2025-05-25; online 2025-05-25]

PubMed DOI Crossref

Cell shapes decode molecular phenotypes in image-based spatial proteomics.

Le T, Leineweber WD, Viana MP, ..., Rafelski SM, Lundberg E

bioRxiv - (-) - [2025-05-16; online 2025-05-16]

DDLS Fellow Wei Ouyang

PubMed DOI Crossref

The effectiveness of selection in a species affects the direction of amino acid frequency evolution.

McShea H, Wheeler AL, Goodman P, ..., Huttley G, Masel J

bioRxiv - (-) - [2025-05-10; online 2025-05-10]

PubMed DOI Crossref

INLAomics for Scalable and Interpretable Spatial Multiomic Data Integration.

Arnroth L, Vickovic S

bioRxiv - (-) - [2025-05-08; online 2025-05-08]

PubMed DOI Crossref

Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.

Kretsch RC, Albrecht R, Andersen ES, ..., Moult J, Kryshtafovych A

bioRxiv - (-) - [2025-04-18; online 2025-04-18]

PubMed DOI Crossref

Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells

Kang W, Yip WH, Li-Wang X, ..., Carninci P, Bienko M

bioRxiv - (-) - [2025-03-14; online 2025-03-14]

PubMed DOI Crossref

Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells.

Schaepe JM, Fries T, Doughty BR, ..., Marklund E, Greenleaf WJ

bioRxiv - (-) - [2025-01-30; online 2025-01-30]

PubMed DOI Crossref

Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome.

Zgadzay Y, Mirabello C, Wanes G, ..., Gahura O, Amunts A

bioRxiv - (-) - [2025-01-24; online 2025-01-24]

PubMed DOI Crossref

Flexible and robust cell type annotation for highly multiplexed tissue images.

Sun H, Yu S, Casals AM, ..., Lundberg E, Murphy RF

bioRxiv - (-) - [2024-12-17; online 2024-12-17]

PubMed DOI Crossref

Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis.

Salgueiro V, Bertol J, Gutierrez C, ..., Sanz J, Prados-Rosales R

bioRxiv - (-) - [2024-11-27; online 2024-11-27]

PubMed DOI Crossref

A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS.

Nourreddine S, Doctor Y, Dailamy A, ..., Krogan N, Mali P

bioRxiv - (-) - [2024-11-04; online 2024-11-04]

PubMed DOI Crossref

Isotope Encoded chemical Imaging Identifies Amyloid Plaque Age Dependent Structural Maturation, Synaptic Loss, and Increased Toxicity.

Wood JI, Dulewicz M, Ge J, ..., Edwards FA, Hanrieder J

bioRxiv - (-) - [2024-10-11; online 2024-10-11]

PubMed DOI Crossref

Syngap1 Promotes Cognitive Function through Regulation of Cortical Sensorimotor Dynamics.

Vaissiere T, Michaelson SD, Creson T, ..., Fontolan L, Rumbaugh G

bioRxiv - (-) - [2024-09-27; online 2024-09-27]

PubMed DOI Crossref

Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.

Doktorova M, Daum S, Ebenhan J, ..., Kenworthy AK, Levental I

bioRxiv - (-) - [2024-09-04; online 2024-09-04]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Mechanistic modeling of cell viability assays with in silico lineage tracing.

Mutsuddy A, Huggins JR, Amrit A, ..., Calhoun JC, Birtwistle MR

bioRxiv - (-) - [2024-08-26; online 2024-08-26]

Cemal Erdem DDLS Fellow

PubMed DOI Crossref

Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel.

Pardo-Avila F, Kudva R, Levitt M, von Heijne G

bioRxiv - (-) - [2024-08-20; online 2024-08-20]

PubMed DOI Crossref

Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database.

Gudmundsson S, Singer-Berk M, Stenton SL, ..., MacArthur DG, O'Donnell-Luria A

bioRxiv - (-) - [2024-06-13; online 2024-06-13]

PubMed DOI Crossref

Improved Detection of Drug-Induced Liver Injury by Integrating Predicted in vivo and in vitro Data.

Seal S, Williams DP, Hosseini-Gerami L, ..., Spjuth O, Bender A

bioRxiv - (-) - [2024-06-08; online 2024-06-08]

PubMed DOI Crossref

Chemical signatures delineate heterogeneous amyloid plaque populations across the Alzheimer's disease spectrum.

Koutarapu S, Ge J, Dulewicz M, ..., Schöll M, Hanrieder J

bioRxiv - (-) - [2024-06-03; online 2024-06-03]

SciLifeLab Fellow Wojciech Michno

PubMed DOI Crossref

The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site.

Turnbull K, Paternoga H, von der Weth E, ..., Wilson DN, Hauryliuk V

bioRxiv - (-) - [2024-05-29; online 2024-05-29]

PubMed DOI Crossref

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.

Seal S, Trapotsi MA, Spjuth O, ..., Bender A, Carpenter AE

bioRxiv - (-) - [2024-05-07; online 2024-05-07]

PubMed DOI Crossref

MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations.

Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P

bioRxiv - (-) - [2024-05-03; online 2024-05-03]

PubMed DOI Crossref

Tissue and cellular spatiotemporal dynamics in colon aging.

Daly AC, Cambuli F, Äijö T, ..., Regev A, Vickovic S

bioRxiv - (-) - [2024-04-26; online 2024-04-26]

PubMed DOI Crossref

Efficient calculation of orientation-dependent lipid dynamics from membrane simulations.

Doktorova M, Khelashvili G, Brown MF

bioRxiv - (-) - [2024-04-15; online 2024-04-15]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes.

Rentzsch P, Kollotzek A, Mohammadi P, Lappalainen T

bioRxiv - (-) - [2024-04-10; online 2024-04-10]

PubMed DOI Crossref

Most axonal mitochondria in cortical pyramidal neurons lack mitochondrial DNA and consume ATP.

Hirabayashi Y, Lewis TL, Du Y, ..., Testa I, Polleux F

bioRxiv - (-) - [2024-02-13; online 2024-02-13]

PubMed DOI Crossref

Single-molecule chromatin configurations link transcription factor binding to expression in human cells.

Doughty BR, Hinks MM, Schaepe JM, ..., Bintu L, Greenleaf WJ

bioRxiv - (-) - [2024-02-04; online 2024-02-04]

PubMed DOI Crossref

Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids.

Haloi N, Huang S, Nichols AL, ..., Mayo SL, Lester HA

bioRxiv - (-) - [2024-01-18; online 2024-01-18]

PubMed DOI Crossref

Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection.

Burman N, Belukhina S, Depardieu F, ..., Wiedenheft B, Isaev A

bioRxiv - (-) - [2024-01-09; online 2024-01-09]

PubMed DOI Crossref

A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors.

Menon I, Sych T, Son Y, ..., Levitz J, Menon AK

bioRxiv - (-) - [2024-01-05; online 2024-01-05]

PubMed DOI Crossref

Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs.

Minaeva M, Domingo J, Rentzsch P, Lappalainen T

bioRxiv - (-) - [2024-01-01; online 2024-01-01]

PubMed DOI Crossref

Expanding the GPCR-RAMP interactome.

Kotliar IB, Bendes A, Dahl L, ..., Schwenk JM, Sakmar TP

bioRxiv - (-) - [2023-11-23; online 2023-11-23]

PubMed DOI Crossref

Large-scale causal discovery using interventional data sheds light on the regulatory network architecture of blood traits.

Brown BC, Morris JA, Lappalainen T, Knowles DA

bioRxiv - (-) - [2023-10-17; online 2023-10-17]

PubMed DOI Crossref

Automated model building and protein identification in cryo-EM maps.

Jamali K, Käll L, Zhang R, ..., Kimanius D, Scheres SHW

bioRxiv - (-) - [2023-10-17; online 2023-10-17]

PubMed DOI Crossref

Genetic ablation of adhesion ligands averts rejection of allogeneic immune cells.

Hammer Q, Perica K, van Ooijen H, ..., Sadelain M, Malmberg KJ

bioRxiv - (-) - [2023-10-09; online 2023-10-09]

PubMed DOI Crossref

Bacterial cell surface nanoenvironment requires a specialized chaperone to activate a peptidoglycan biosynthetic enzyme.

Delerue T, Chareyre S, Anantharaman V, ..., Aravind L, Ramamurthi KS

bioRxiv - (-) - [2023-10-06; online 2023-10-06]

PubMed DOI Crossref

A Molecular Basis of Human Brain Connectivity.

Ng B, Tasaki S, Greathouse KM, ..., Gaiteri C, Herskowitz JH

bioRxiv - (-) - [2023-07-24; online 2023-07-24]

PubMed DOI Crossref

Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.

Kasela S, Aguet F, Kim-Hellmuth S, ..., Graham Barr R, Lappalainen T

bioRxiv - (-) - [2023-06-29; online 2023-06-29]

PubMed DOI Crossref

Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration.

Correia JC, Jannig PR, Gosztyla ML, ..., Yeo GW, Ruas JL

bioRxiv - (-) - [2023-06-13; online 2023-06-13]

PubMed DOI Crossref

The full spectrum of OCT1 (SLC22A1) mutations bridges transporter biophysics to drug pharmacogenomics.

Yee SW, Macdonald C, Mitrovic D, ..., Giacomini KM, Coyote-Maestas W

bioRxiv - (-) - [2023-06-07; online 2023-06-07]

PubMed DOI Crossref

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

Moore J, Basurto-Lozada D, Besson S, ..., Theis FJ, Swedlow JR

bioRxiv - (-) - [2023-05-07; online 2023-05-07]

PubMed DOI Crossref

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.

Tomaszkiewicz M, Sahlin K, Medvedev P, Makova KD

bioRxiv - (-) - [2023-03-18; online 2023-03-18]

PubMed DOI Crossref

Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease.

Sullivan PF, Meadows JRS, Gazal S, ..., Karlsson EK, Lindblad-Toh K

bioRxiv - (-) - [2023-03-10; online 2023-03-10]

PubMed DOI Crossref

PRO-IP-seq Tracks Molecular Modifications of Engaged Pol II Complexes at Nucleotide Resolution.

Vihervaara A, Versluis P, Lis JT

bioRxiv - (-) - [2023-02-04; online 2023-02-04]

PubMed DOI Crossref

Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms.

Jain Y, Godwin LL, Joshi S, ..., Lundberg E, Börner K

bioRxiv - (-) - [2023-01-06; online 2023-01-06]

PubMed DOI Crossref

Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq.

Vazquez SE, Mann SA, Bodansky A, ..., Anderson MS, DeRisi JL

bioRxiv - (-) - [2022-03-24; online 2022-03-24]

PubMed DOI Crossref

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates.

Damas J, Hughes GM, Keough KC, ..., Karlsson EK, Lewin HA

bioRxiv - (-) - [2020-04-18; online 2020-04-18]

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