Tomasz Kosciolek

Tomasz Kosciolek
Jagiellonian University | UJ · Malopolska Center o Biotechnology

PhD

About

67
Publications
46,379
Reads
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10,264
Citations
Additional affiliations
July 2019 - present
Jagiellonian University
Position
  • Group Leader
January 2016 - present
University of California, San Diego
Position
  • PhD Student
Description
  • * understanding the microbiome and its implications to human health, esp. in the context of the microbiome-gut-brain axis. * predicting protein structures encoded in bacterial genomes and use this to understand the functional potential of the microbiome
September 2011 - December 2015
University College London
Position
  • PhD Student
Education
September 2011 - December 2015
University College London
Field of study
  • Structural, Chemical and Computational Biology
February 2009 - July 2010
University of Warsaw
Field of study
  • MSc thesis under supervision of Prof. Andrzej Kolinski
October 2005 - July 2010
Jagiellonian University
Field of study
  • Chemistry (biological & theoretical chemistry)

Publications

Publications (67)
Article
Full-text available
Understanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the...
Preprint
Comprehensive protein function annotation is key to understanding microbiome-related disease mechanisms in the host organisms. We have developed a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling and deep learning-based functional annotations from DeepFRI. We validate DeepFRI functional annotations by...
Preprint
For the past half-century, structural biologists relied on the notion that similar protein sequences give rise to similar structures and functions. While this assumption has driven research to explore certain parts of the protein universe, it disregards spaces that don't rely on this assumption. Here we explore areas of the protein universe where s...
Article
Full-text available
Probiotics are known to regulate host metabolism. In randomized controlled trial we aimed to assess whether interventions with probiotic containing following strains: Bifidobacterium bifidum W23, Bifidobacterium lactis W51, Bifidobacterium lactis W52, Lactobacillus acidophilus W37, Levilactobacillus brevis W63, Lacticaseibacillus casei W56, Ligilac...
Preprint
Full-text available
Understanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the...
Article
Full-text available
The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated function prediction. Here, we introduce DeepFRI, a Graph Convolutional Network for predicting protein functions by leveraging sequence features extracted from a protein language model and protein s...
Article
Full-text available
Background Substance use disorder emerges from a complex interaction between genetic predisposition, life experiences, exposure, and subsequent adaptation of biological systems to the repeated use of drugs. Recently, investigators have proposed that the human microbiota may play a role in brain health and disease. In particular, the human oral micr...
Article
Emerging evidence has linked the gut microbiome changes to schizophrenia. However, there has been limited research into the functional pathways by which the gut microbiota contributes to the phenotype of persons with chronic schizophrenia. We characterized the composition and functional potential of the gut microbiota in 48 individuals with chronic...
Article
Full-text available
QIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open‐source web‐bas...
Article
Full-text available
Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions1–10, we re-examined whole-genome and whole-transcrip...
Chapter
The human microbiota (the microscopic organisms that inhabit us) and microbiome (their genes) hold considerable potential for improving pharmacological practice. Recent advances in multi-“omics” techniques have dramatically improved our understanding of the constituents of the microbiome and their functions. The implications of this research for hu...
Article
Full-text available
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees i...
Preprint
Recent massive increases in the number of sequences available in public databases challenges current experimental approaches to determining protein function. These methods are limited by both the large scale of these sequences databases and the diversity of protein functions. We present a deep learning Graph Convolutional Network (GCN) trained on s...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Schizophrenia and bipolar disorder (BD) are associated with debilitating psychiatric and cognitive dysfunction, worse health outcomes, and shorter life expectancies. The pathophysiological understanding of and therapeutic resources for these neuropsychiatric disorders are still limited. Humans harbor over 1000 unique bacterial species in our gut, w...
Article
Full-text available
Background: Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a facial lotion, a moisturizer, a foot powder, and a deodorant) on 11 volunteers over 9 weeks. Results: Mass spectrometry and 16S...
Article
Full-text available
Dupilumab is a fully human antibody to interleukin-4 receptor α that improves the signs and symptoms of moderate to severe atopic dermatitis (AD). To determine the effects of dupilumab on Staphylococcus aureus colonization and microbial diversity on the skin, bacterial DNA was analyzed from swabs collected from lesional and nonlesional skin in a do...
Preprint
Full-text available
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visua...
Preprint
Full-text available
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visua...
Preprint
Full-text available
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visua...
Article
Full-text available
Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qi...
Article
Intestinal microbiome and gut-brain axis have been receiving increasing attention for their role in the regulation of brain/behavior and possible biological basis of psychiatric disorders. Several recent clinical studies have linked the microbiome with neuropsychiatric conditions, although the literature on schizophrenia is quite limited. This stud...
Conference Paper
Full-text available
People's lived experiences provide intuitions about health. Can they transform these personal intuitions into testable hypotheses that could inform both science and their lives? This paper introduces an online learning architecture and provides system principles for people to brainstorm causal scientific theories. We describe the Learn-Train-Ask wo...
Article
Background: The microbiota-gut-brain axis and membrane dysfunction in the brain has attracted increasing attention in the field of psychiatric research. However, the possible interactive role of gut microbiota and brain function in the prodromal stage of schizophrenia has not been studied yet. Methods: To explore this, we collected fecal samples...
Article
Full-text available
Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over ea...
Article
Full-text available
We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as...
Preprint
Full-text available
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,00...
Article
Schizophrenia and bipolar disorder are among the leading causes of disability, morbidity, and mortality worldwide. In addition to being serious mental illnesses, these disorders are associated with considerable systemic physiological dysfunction, including chronic inflammation and elevated oxidative stress. The advent of sophisticated sequencing te...
Article
Full-text available
Intrinsically disordaered proteins (IDPs) are a prevalent phenomenon with over 30% of human proteins estimated to have long disordered regions. Computational methods are widely used to study IDPs, however, nearly all treat disorder in a binary fashion, not accounting for the structural heterogeneity present in disordered regions. Here, we present a...
Article
Full-text available
Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about mi...
Conference Paper
Full-text available
Learners worldwide collectively spend millions of hours per week testing their skills on assignments with known answers. Might some of this time fruitfully be spent posing and exploring novel questions? This paper investigates an approach for learners to contribute scientific ideas. The Gut Instinct system embodies this approach, hosting online lea...
Article
Full-text available
Online learners spend millions of hours per year testing their new skills on assignments with known answers. This paper explores whether framing research questions as assignments with unknown answers helps learners generate novel, useful, and difficult-to-find knowledge while increasing their motivation by contributing to a larger goal. Collaborati...
Conference Paper
Intrinsically disordered proteins (IDPs), due to their dynamic nature, play important roles in molecular recognition, signalling, regulation, or binding of nucleic acids. IDPs have been extensively studied computationally in terms of binary disorder/order classification. This approach has proven to be fruitful and enabled researchers to estimate th...
Article
Full-text available
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effective sequences, our server achieved an average top-L/5 long-range contact precision of 27%. MetaPSICOV...
Article
The prospect of identifying contacts in protein structures purely from aligned protein sequences has lured researchers for a long time, but progress has been modest until recently. Here, we reviewed the most successful methods for identifying structural contacts from sequence and how these methods differ and made an initial assessment of the overla...
Article
Full-text available
Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3-D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predict...
Article
Homology modeling is a reliable method of predicting the three-dimensional structures of proteins that lack NMR or X-ray crystallographic data. It employs the assumption, that a structural resemblance exists between closely related proteins. Despite the availability of many crystal structures of possible templates, only the closest ones are chosen...
Article
Full-text available
The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm - FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse...
Article
Full-text available
Over the years, homology modelling has grown into an important tool for biochemistry and pharmacology. It allows prediction of three-dimensional structure of proteins , which have not been resolved with empirical methods. The final outcome of such research is affected by many factors, the choice of template being a crucial one. Current paradigm sta...
Article
Full-text available
Cheminformatic methods, such as Virtual Screening, constitute a vital part of modern drug design process. This technique enables not only viable prediction of physicochemical properties of the molecules, but also effective database mining, being particularly useful tool in search for ligands of desired activity. Successful performance in case of si...
Article
Following "click chemistry" guidelines, a 1,2,3-triazole scaffold was introduced in place of a benzene ring to mimic the non-classical cannabinoid pharmacophore model in a novel class of compounds aimed at CB1 receptor agonism. The design, synthesis and results of receptor affinity tests for the new group of ligands are described. The obtained seri...
Article
Introduction Oesophageal cancer (OAC) arises in Barrettt's oesopahgus (BE) and carries a poor prognosis. Early mucosal neoplasia arising in BE can be treated successfully with minimally invasive endotherapy. Fourier transform infrared spectroscopy (FTIR) can detect specific molecules from their unique vibrational absorption spectra in complex mater...
Article
We introduce a new approach to the known concept of interaction profiles, based on Structural Interaction Fingerprints (SIFt), for precise and rapid binding site description. A set of scripts for batch generation and analysis of SIFt were prepared, and the implementation is computationally efficient and supports parallelization. It is based on a 9-...
Article
Full-text available
Many studies show involvement of metabotropic glutamate receptors (mGluRs) in synaptic excitation transudation. The mGluR family consists of eight proteins divided into three groups corresponding to sequence similarities, pharmacology and physiological role. These groups are: I (mGluR1, -5), II (mGluR2, -3) and III (mGluR4, -6, -7, -8). Group II li...
Article
Full-text available
One of the most troublesome stages of Computer Aided Drug Design (CADD) process is analyzing huge amount of data provided by docking studies. Simple scoring functions alone can provide only shallow information about ligand-receptor interactions, since they do not distinguish neither residues nor single atoms. Very often a visual inspection is the o...
Article
Full-text available
SIFt is a bit string representing interactions between ligand and receptor. It can be divided into chunks expressing contacts for individual amino acids. In this research nine bits were used to describe those associations: any contact, backbone, side chain, polar, aromatic, hydrophobic interaction and hydrogen bond donor/acceptor. Basic algorithm i...
Article
Full-text available
Briggs, J. M. Dynamic receptor-based pharmacophore model development and its application in designing novel HIV-1 integrase inhibitors. Singh, J.; Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. Methods The set of over 700 known, and structurally diversified, 5-HT7R liga...
Article
Full-text available
Briggs, J. M. Dynamic receptor-based pharmacophore model development and its application in designing novel HIV-1 integrase inhibitors. Singh, J.; Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. Methods As a starting point, the set of over 700 known, and structurally div...