Biology subjects

Mikic, I.

Publications and source records attributed to Mikic, I..

3 recordsLinked to original sources

bioRxiv2025

Unpaired Image-to-Image Translation for Segmentation and Signal Unmixing

This work introduces Ui2i, a novel model for unpaired image-to-image translation, trained on content-wise unpaired datasets to enable style transfer across domains while preserving content. Building on CycleGAN, Ui2i incorporates key modifications to better disentangle content and style features, and preserve content integrity. Specifically, Ui2i employs U-Net-based generators with skip connections to propagate localized shallow features deep into the generator. Ui2i removes feature-based normalization layers from all modules and replaces them with approximate bidirectional spectral normalization--a parameter-based alternative that enhances training stability. To further support content preservation, channel and spatial attention mechanisms are integrated into the generators. Training is facilitated through image scale augmentation. Evaluation on two biomedical tasks--domain adaptation for nuclear segmentation in immunohistochemistry (IHC) images and unmixing of biological structures superimposed in single-channel immunofluorescence (IF) images--demonstrates Ui2is ability to preserve content fidelity in settings that demand more accurate structural preservation than typical translation tasks. To the best of our knowledge, Ui2i is the first approach capable of separating superimposed signals in IF images using real, unpaired training data.

bioinformatics↗

bioRxiv2025

Historic Genomes Uncover Demographic Shifts and Kinship Structures in Post-Roman Central Europe

Many European towns and villages trace their origins to Early Medieval foundations. In former Roman territories, their emergence has traditionally been linked to mass migrations from outside the Roman Empire. However, recent studies have emphasised local continuity with some individual-level mobility. We generated and analysed 248 historic genomes from Late Roman (3rd and 4th century CE) and Early Medieval (5th-8th century CE) burial sites in southern Germany, comparing them to over 2,500 contemporary and Iron Age genomes in addition to 1,344 modern-day genomes from Germany, Italy and Great-Britain. Despite small inferred Early Medieval period community sizes, genetic diversity exceeded that of modern German cities. In the Altheim graveyard, established in the 5th century by a group of Northern European descent, we inferred a demographic shift in the 6th century with the integration of newcomers with ancestry typical of a nearby Roman military camp, likely as a result of the collapse of Roman state structures. We reconstructed multigenerational pedigrees and, using a novel approach to infer ancestry of unsampled relatives, inferred immediate intermarriage between incoming and local groups, with a distinct tendency for men from former Roman background marrying women of northern descent. Burial proximity correlates strongly with kinship, in some cases spanning six generations. These communities were organized around small family units, exhibited loosely patrilineal or bilateral descent patterns, practiced reproductive monogamy, and avoided close-kin marriages. Such practices reflect broader transformations in family structures that began during the Late Roman period, were transferred to small agrarian societies in the Early Medieval period, and continued to shape European societies. By the 7th century, ongoing admixture had shaped genetic diversity patterns into those resembling Central Europe today.

genetics↗

bioRxiv2021

Cosmopolitanism at the Roman Danubian Frontier, Slavic Migrations, and the Genomic Formation of Modern Balkan Peoples

The Roman Empire expanded through the Mediterranean shores and brought human mobility and cosmopolitanism across this inland sea to an unprecedented scale. However, if this was also common at the Empire frontiers remains undetermined. The Balkans and Danube River were of strategic importance for the Romans acting as an East-West connection and as a defense line against "barbarian" tribes. We generated genome-wide data from 70 ancient individuals from present-day Serbia dated to the first millennium CE; including Viminacium, capital of Moesia Superior province. Our analyses reveal large scale-movements from Anatolia during Imperial rule, similar to the pattern observed in Rome, and cases of individual mobility from as far as East Africa. Between [~]250-500 CE, we detect gene-flow from Central/Northern Europe harboring admixtures of Iron Age steppe groups. Tenth-century CE individuals harbored North-Eastern European-related ancestry likely associated to Slavic-speakers, which contributed >20% of the ancestry of todays Balkan people.

evolutionary biology↗