bioRxiv

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

PubMed DOI Crossref

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.

Hunt M, Torres MDT, Alikhan NF, ..., Lees JA, Iqbal Z

bioRxiv - (-) - [2026-07-07; online 2026-07-07]

DDLS Fellow Laura Carroll

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 - (-) - [2026-05-27; online 2026-05-27]

Magda Bienko SciLifeLab Fellow

PubMed DOI Crossref

Nanodomain formation in lipid bilayers I: Quantifying the nanoscopic miscibility transition with FRET.

Chaisson EH, Mehta D, Heberle FA

bioRxiv - (-) - [2026-01-09; online 2026-01-09]

PubMed DOI Crossref

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

Lee Y, He S, Oda T, ..., Zhang S, Das R

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

PubMed DOI Crossref

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

Mapping the circulating proteome across neurodegeneration: A harmonized, consortium-scale framework for uncovering molecular pathophysiology.

Finney CA, An L, Winchester LM, ..., Saloner R, Shvetcov A

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

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]

Erika Comasco SciLifeLab Fellow

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

Chromogranin A and catestatin regulate pancreatic islet homeostasis, endocrine function, and neurotransmitter signaling.

Muntjewerff EM, Epremidze D, Nezhyva M, ..., Mahata SK, Christoffersson G

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

Gustaf Christoffersson SciLifeLab Fellow

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

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species.

Ruiz-Ruano FJ, Schlebusch SA, Vontzou N, ..., Whibley A, Suh A

bioRxiv - (-) - [2025-07-18; online 2025-07-18]

PubMed DOI Crossref

Cell atlas of the developing human meninges reveals a dura origin of meningioma.

Vinsland E, Salas SM, Kapustová I, ..., Lönnerberg P, Linnarsson S

bioRxiv - (-) - [2025-07-13; online 2025-07-13]

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]

DDLS Fellow Jennifer James

PubMed DOI Crossref

Streamlining Multiplexed Tissue Image Analysis with PIPΣX: An Integrated Automated Pipeline for Image Processing and EXploration for Diverse Tissue Types.

Mardamshina M, Navarro FB, Casals AM, ..., Wählby C, Lundberg E

bioRxiv - (-) - [2025-05-09; online 2025-05-09]

PubMed DOI Crossref

INLAomics for Scalable and Interpretable Spatial Multiomic Data Integration.

Arnroth L, Vickovic S

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

Sanja Vickovic SciLifeLab Fellow

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

Longer scans boost prediction and cut costs in brain-wide association studies.

Ooi LQR, Orban C, Zhang S, ..., Yeo BTT, Alzheimer’s Disease Neuroimaging Initiative

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

PubMed DOI Crossref

Analysis-ready VCF at Biobank scale using Zarr.

Czech E, Millar TR, Tyler W, ..., Hammerbacher J, Kelleher J

bioRxiv - (-) - [2025-02-06; online 2025-02-06]

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]

Emil Marklund SciLifeLab Fellow

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]

Alexey Amunts SciLifeLab Fellow

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

Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.

Doktorova M, Symons JL, Zhang X, ..., Levental KR, Levental I

bioRxiv - (-) - [2024-12-09; online 2024-12-09]

DDLS Fellow Erdinc Sezgin Milka Doktorova SciLifeLab Fellow

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 genome resource for the marine annelid Platynereis dumerilii.

Mutemi KN, Simakov O, Pan L, ..., Özpolat BD, Arendt D

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

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]

Daniel Fürth SciLifeLab Fellow

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

Bacterial ecology and evolution converge on seasonal and decadal scales.

Rohwer RR, Kirkpatrick M, Garcia SL, ..., McMahon KD, Baker BJ

bioRxiv - (-) - [2024-08-12; online 2024-08-12]

Sarahi Garcia SciLifeLab Fellow

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]

SciLifeLab Fellow

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]

Lucie Delemotte SciLifeLab Fellow

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]

Sanja Vickovic SciLifeLab Fellow

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]

Ilaria Testa SciLifeLab Fellow

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]

Emil Marklund SciLifeLab Fellow

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]

Erdinc Sezgin SciLifeLab Fellow

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

Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis.

Yu H, Khanshour AM, Ushiki A, ..., Ahituv N, Wise CA

bioRxiv - (-) - [2023-11-22; online 2023-11-22]

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

Hippo-deficient cardiac fibroblasts differentiate into osteochondroprogenitors.

Tsai CR, Kim J, Li X, ..., Samee MAH, Martin J

bioRxiv - (-) - [2023-09-08; online 2023-09-08]

PubMed DOI Crossref

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.

Yee SW, Ferrández-Peral L, Alentorn P, ..., Marques-Bonet T, Giacomini KM

bioRxiv - (-) - [2023-08-12; online 2023-08-12]

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]

Lucie Delemotte SciLifeLab Fellow

PubMed DOI Crossref

Helicobacter pylori attachment-blocking antibodies protect against duodenal ulcer disease.

Bugaytsova JA, Moonens K, Piddubnyi A, ..., Hammarström L, Borén T

bioRxiv - (-) - [2023-05-24; online 2023-05-24]

PubMed DOI Crossref

Development of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic strategy for Alzheimer's disease.

Du Y, Bradshaw WJ, Leisner TM, ..., Fu H, Katis VL

bioRxiv - (-) - [2023-05-22; online 2023-05-22]

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]

DDLS Fellow Wei Ouyang

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]

Kristoffer Sahlin SciLifeLab Fellow

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]

Anniina Vihervaara SciLifeLab Fellow

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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