Publications

Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing

Tim Van Den Bossche et al.

Proteomics. 2025 Jan 31:e202400321. doi: 10.1002/pmic.202400321. Online ahead of print.

Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing proteins, metaproteomics offers insights into community phenotypes and the roles individual members play in diverse ecosystems. Although database-dependent search engines are commonly used for peptide identification, they rely on pre-existing protein databases,...

Adaptive sequence alignment for metagenomic data analysis

Sami Pietilä et al.

Comput Biol Med. 2025 Mar;186:109743. doi: 10.1016/j.compbiomed.2025.109743. Epub 2025 Jan 26.

With advances in sequencing technologies, the use of high-throughput sequencing to characterize microbial communities is becoming increasingly feasible. However, metagenomic assembly poses computational challenges in reconstructing genes and organisms from complex samples. To address this issue, we introduce a new concept called Adaptive Sequence Alignment (ASA) for analyzing metagenomic DNA sequence data. By iteratively adapting a set of partial alignments of reference sequences to match the...

Dual physiological responsive structural color hydrogel particles for wound repair

Li Wang et al.

Bioact Mater. 2025 Jan 7;46:494-502. doi: 10.1016/j.bioactmat.2025.01.002. eCollection 2025 Apr.

Hydrogel-based patches have demonstrated their values in diabetic wounds repair, particularly those intelligent dressings with continuous repair promoting and monitoring capabilities. Here, we propose a type of dual physiological responsive structural color particles for wound repair. The particles are composed of a hyaluronic acid methacryloyl (HAMA)-sodium alginate (Alg) inverse opal scaffold, filled with oxidized dextran (ODex)/quaternized chitosan (QCS) hydrogel. The photo-polymerized HAMA...

Mechanically regulated microcarriers with stem cell loading for skin photoaging therapy

Xiang Lin et al.

Bioact Mater. 2025 Jan 3;46:448-456. doi: 10.1016/j.bioactmat.2024.12.024. eCollection 2025 Apr.

Long-term exposure to ultraviolet radiation compromises skin structural integrity and results in disruption of normal physiological functions. Stem cells have gained attention in anti-photoaging, while controlling the tissue mechanical microenvironment of cell delivery sites is crucial for regulating cell fate and achieving optimal therapeutic performances. Here, we introduce a mechanically regulated human recombinant collagen (RHC) microcarrier generated through microfluidics, which is capable...

Early precursor-derived pituitary gland tissue-resident macrophages play a pivotal role in modulating hormonal balance

Henna Lehtonen et al.

Cell Rep. 2025 Feb 25;44(2):115227. doi: 10.1016/j.celrep.2024.115227. Epub 2025 Jan 21.

The pituitary gland is the central endocrine regulatory organ producing and releasing hormones that coordinate major body functions. The physical location of the pituitary gland at the base of the brain, though outside the protective blood-brain barrier, leads to an unexplored special immune environment. Using single-cell transcriptomics, fate mapping, and imaging, we characterize pituitary-resident macrophages (pitMØs), revealing their heterogeneity and spatial specialization. Microglia-like...

Microfluidics-enabled core/shell nanostructure assembly: Understanding encapsulation processes via particle characterization and molecular dynamics

Wali Inam et al.

Adv Colloid Interface Sci. 2025 Apr;338:103400. doi: 10.1016/j.cis.2025.103400. Epub 2025 Jan 12.

In the realm of hybrid nanomaterials, the construction of core/shell nanoparticles offer an effective strategy for encompassing a particle by a polymeric or other suitable material, leading to a nanocomposite with distinct features within its structure. The polymer shell can be formed via nanoprecipitation, optimized by manipulating fluid flow, fluid mixing, modulating device features in microfluidics. In addition to the process optimization, success of polymer assembly in encapsulation strongly...