I. Schuppe-Koistinen

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Correlation Network Analysis for Data Integration and Biomarker Selectionw

Johan Lindberg, Paul Stroobant, Raji Balasubramanian, 2007 .

Screening of biomarkers in rat urine using LC/electrospray ionization-MS and two-way data analysis.

Ina Schuppe-Koistinen, O. Kvalheim, I. Schuppe-Koistinen, 2003, Analytical chemistry.

Optimal protocols for sequence-based characterization of the human vaginal microbiome

L. Engstrand, I. Schuppe-Koistinen, L. W. Hugerth, 2020, bioRxiv.

Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome

L. Engstrand, I. Schuppe-Koistinen, L. W. Hugerth, 2020, mSphere.

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling

G. Bergström, F. Edfors, Björn Forsström, 2020, EBioMedicine.

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling

G. Bergström, F. Edfors, Björn Forsström, 2020, bioRxiv.

Second-order peak detection for multicomponent high-resolution LC/MS data.

J. Lindberg, I. Schuppe-Koistinen, S. Jacobsson, 2006, Analytical chemistry.

Peak alignment of NMR signals by means of a genetic algorithm

I. Schuppe-Koistinen, S. Jacobsson, J. Forshed, 2003 .

Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments

Leo L. Cheng, P. Rocca-Serra, J. Griffiths, 2007, Metabolomics.

Metabolic fingerprinting of rat urine by LC/MS Part 2. Data pretreatment methods for handling of complex data.

I. Schuppe-Koistinen, P. Edlund, S. Jacobsson, 2005, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

Metabolic fingerprinting of rat urine by LC/MS Part 1. Analysis by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry.

I. Schuppe-Koistinen, P. Edlund, S. Jacobsson, 2005, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

Identification of S-glutathionylated cellular proteins during oxidative stress and constitutive metabolism by affinity purification and proteomic analysis.

A. Holmgren, I. Schuppe-Koistinen, I. Cotgreave, 2002, Archives of biochemistry and biophysics.

Summary recommendations for standardization and reporting of metabolic analyses

Nigel W. Hardy, Jake T. M. Pearce, Stephen J. Bruce, 2005, Nature Biotechnology.

Reliable profile detection in comparative metabolomics.

Johan Lindberg, Henrik Antti, Pär Jonsson, 2007, Omics : a journal of integrative biology.

Statistical multivariate metabolite profiling for aiding biomarker pattern detection and mechanistic interpretations in GC/MS based metabolomics

Johan Lindberg, Henrik Antti, Pär Jonsson, 2007, Metabolomics.

S-glutathionylation of glyceraldehyde-3-phosphate dehydrogenase: role of thiol oxidation and catalysis by glutaredoxin.

I. Schuppe-Koistinen, I. Cotgreave, C. Lind, 2002, Methods in enzymology.

What are the best reference values for a normal serum alanine transaminase activity (ALT)? Impact on the presumed prevalence of drug induced liver injury (DILI).

Y. Ngo, I. Schuppe-Koistinen, H. Perazzo, 2011, Regulatory toxicology and pharmacology : RTP.

Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data--a potential tool for multi-parametric diagnosis.

Johan Lindberg, Johan Trygg, Henrik Antti, 2006, Journal of proteome research.

The right bug in the right place: opportunities for bacterial vaginosis treatment

I. Schuppe-Koistinen, Shengru Wu, L. W. Hugerth, 2022, NPJ biofilms and microbiomes.

Genome-Wide Association and Replication Study of Hepatotoxicity Induced by Antiretrovirals Alone or with Concomitant Anti-Tuberculosis Drugs.

Michiaki Kubo, Ina Schuppe-Koistinen, Atsushi Takahashi, 2017, Omics : a journal of integrative biology.

Evaluation of Patterns of Liver Toxicity in Patients on Antiretroviral and Anti-Tuberculosis Drugs: A Prospective Four Arm Observational Study in Ethiopian Patients

I. Schuppe-Koistinen, L. Lindquist, W. Amogne, 2014, PloS one.

Keratin‐18 and microRNA‐122 complement alanine aminotransferase as novel safety biomarkers for drug‐induced liver injury in two human cohorts

P. Watkins, C. Mattsson, B. Ekblom, 2014, Liver international : official journal of the International Association for the Study of the Liver.

Elevated levels of circulating CDH5 and FABP1 in association with human drug‐induced liver injury

J. Lindberg, M. Uhlén, C. Kampf, 2016, Liver international : official journal of the International Association for the Study of the Liver.

Isoform-specific alanine aminotransferase measurement can distinguish hepatic from extrahepatic injury in humans.

R. Kim, B. Ekblom, A. Kotronen, 2012, International journal of molecular medicine.

The development of in vitro culture methods to characterize primary T-cell responses to drugs.

B. K. Park, D. Naisbitt, I. Schuppe-Koistinen, 2012, Toxicological sciences : an official journal of the Society of Toxicology.

Serum apolipoprotein A1 and haptoglobin, in patients with suspected drug-induced liver injury (DILI) as biomarkers of recovery

Y. Ngo, R. Andrade, M. Rudler, 2017, PloS one.

S-thiolation of human endothelial cell glyceraldehyde-3-phosphate dehydrogenase after hydrogen peroxide treatment.

T. Bergman, I. Schuppe-Koistinen, P. Moldéus, 1994, European journal of biochemistry.

Adaptation to acetaminophen exposure elicits major changes in expression and distribution of the hepatic proteome

N. Kitteringham, B. K. Park, R. Eakins, 2015, Scientific Reports.

A role for gamma-glutamyl transpeptidase in the transport of cystine into human endothelial cells: relationship to intracellular glutathione.

I. Schuppe-Koistinen, I. Cotgreave, 1994, Biochimica et biophysica acta.

The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle

L. Engstrand, I. Schuppe-Koistinen, L. W. Hugerth, 2021, Human reproduction.

The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis

Justine W. Debelius, I. Schuppe-Koistinen, J. Debelius, 2022, Scientific Reports.

Individual and stable autoantibody repertoires in healthy individuals

G. Bergström, M. Uhlén, L. Fagerberg, 2019, Autoimmunity.

Studies on the reversibility of protein S-thiolation in human endothelial cells.

I. Schuppe-Koistinen, P. Moldéus, I. Cotgreave, 1994, Archives of biochemistry and biophysics.

Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) – assessing the dynamic associations between the microbiome and maternal and neonatal adverse events

L. Engstrand, I. Schuppe-Koistinen, L. W. Hugerth, 2022, BMJ Open.

Reversible S-thiolation of Human Endothelial Cell Actin Accompanies a Structural Reorganisation of the Cytoskeleton

T. Bergman, I. Schuppe-Koistinen, P. Moldéus, 1995 .

Application of Dolichos biflorus in immunoassay detection of kidney collecting duct biomarkers

G. Betton, D. Riccardi, I. Schuppe-Koistinen, 2010, Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals.

A systems biology approach to understanding elevated serum alanine transaminase levels in a clinical trial with ximelagatran

Johan Lindberg, Raji Balasubramanian, Ina Schuppe-Koistinen, 2009, Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals.

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

J. Stender, M. Lindskog, C. Glass, 2015, Cell.

SOT/EUROTOX debate: biomarkers from blood and urine will replace traditional histopathological evaluation to determine adverse responses.

K. Boekelheide, I. Schuppe-Koistinen, 2012, Toxicological sciences : an official journal of the Society of Toxicology.

No evidence for a placental microbiome in human pregnancies at term.

P. Angelidou, L. Engstrand, A. Scheynius, 2020, American journal of obstetrics and gynecology.

Voluntary exploratory data submissions to the US FDA and the EMA: experience and impact

Jiri Aubrecht, Weida Tong, Huixiao Hong, 2010, Nature Reviews Drug Discovery.

Skeletal Muscle PGC-1α1 Modulates Kynurenine Metabolism and Mediates Resilience to Stress-Induced Depression

Ina Schuppe-Koistinen, Juleen R. Zierath, Maria Lindskog, 2014, Cell.

Candidate biomarkers for the diagnosis and prognosis of drug‐induced liver injury: An international collaborative effort

Jiri Aubrecht, John-Michael Sauer, Simon Kirby, 2018, Hepatology.

A longitudinal assessment of miR-122 and GLDH as biomarkers of drug-induced liver injury in the rat

B. K. Park, C. Goldring, I. Schuppe-Koistinen, 2017, Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals.

Studies on the mechanism of oxidative modification of human glyceraldehyde-3-phosphate dehydrogenase by glutathione: catalysis by glutaredoxin.

I. Schuppe-Koistinen, I. Cotgreave, C. Lind, 1998, Biochemical and biophysical research communications.

A MicroRNA Gene Panel Predicts the Vaginal Microbiota Composition

L. Engstrand, M. Olovsson, I. Schuppe-Koistinen, 2021, mSystems.

High-fat diet and estrogen modulate the gut microbiota in a sex-dependent manner in mice

L. Engstrand, I. Schuppe-Koistinen, N. Brusselaers, 2023, Communications Biology.

The reproductive microbiome - clinical practice recommendations for fertility specialists.

C. Santjohanser, S. Vieira-Silva, J. Laven, 2020, Reproductive biomedicine online.

Biomarkers of drug-induced vascular injury.

S. Gould, G. Betton, K. Kenne, 2005, Toxicology and applied pharmacology.

The impact of CYP2E1 on the development of alcoholic liver disease as studied in a transgenic mouse model.

M. Ingelman-Sundberg, K. Nilsson, I. Schuppe-Koistinen, 2009, Journal of hepatology.

A note on normalization of biofluid 1D 1H-NMR data

R. J. O. Torgrip, I. Schuppe-Koistinen, J. Lindberg, 2008, Metabolomics.

A generic operational strategy to qualify translational safety biomarkers.

Hannes Planatscher, Michael Merz, Jean-Marc Vidal, 2011, Drug discovery today.

A strategy for modelling dynamic responses in metabolic samples characterized by GC/MS

Johan Lindberg, Johan Trygg, Henrik Antti, 2006, Metabolomics.

Skeletal Muscle PGC-1α1 Modulates Kynurenine Metabolism and Mediates Resilience to Stress-Induced Depression

M. Lindskog, M. Goiny, J. Zierath, 2015, Cell.

A comprehensive automated pipeline for human microbiome sampling, 16S rRNA gene sequencing and bioinformatics processing

L. Engstrand, I. Schuppe-Koistinen, L. W. Hugerth, 2018, bioRxiv.

Vaginal microbiota and human papillomavirus infection among young Swedish women

P. Angelidou, L. Engstrand, M. Olovsson, 2020, npj Biofilms and Microbiomes.

Molecular Profiling and Prediction of Toxicity

I. Schuppe-Koistinen, 2001 .

Molecular profiling of hepatotoxicity induced by a aminoguanidine carboxylate in the rat: gene expression profiling.

I. Schuppe-Koistinen, L. Janzon, A. Frisk, 2002, Toxicology.

Electroconvulsive therapy suppresses the neurotoxic branch of the kynurenine pathway in treatment-resistant depressed patients

M. Frye, M. Landén, I. Schuppe-Koistinen, 2016, Journal of Neuroinflammation.

Feature detection and alignment of hyphenated chromatographic-mass spectrometric data. Extraction of pure ion chromatograms using Kalman tracking.

Johan Lindberg, K Magnus Aberg, Ina Schuppe-Koistinen, 2008, Journal of chromatography. A.

Pre-pregnancy complications - associated factors and wellbeing in early pregnancy: a Swedish cohort study

L. Engstrand, I. Schuppe-Koistinen, L. W. Hugerth, 2023, BMC Pregnancy and Childbirth.

Imbalanced Kynurenine Pathway in Schizophrenia

I. Schuppe-Koistinen, S. Erhardt, M. Samuelsson, 2014, International journal of tryptophan research : IJTR.

Gene and protein expression profiling of human cerebral endothelial cells activated with tumor necrosis factor-alpha.

B. Engelhardt, I. Schuppe-Koistinen, B. Franzén, 2003, Brain research. Molecular brain research.

Genome-wide association and replication study of anti-tuberculosis drugs-induced liver toxicity

M. Lee, T. Mushiroda, M. Kubo, 2016, BMC Genomics.

Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar

L. Engstrand, I. Schuppe-Koistinen, N. Bostanci, 2021, Frontiers in Cellular and Infection Microbiology.

Increased levels of IL-6 in the cerebrospinal fluid of patients with chronic schizophrenia--significance for activation of the kynurenine pathway.

C. Svensson, I. Schuppe-Koistinen, S. Erhardt, 2015, Journal of psychiatry & neuroscience : JPN.

Kynurenic acid and psychotic symptoms and personality traits in twins with psychiatric morbidity

Tyrone D. Cannon, C. Hultman, L. Wetterberg, 2017, Psychiatry Research.

Prediction of Clinically Relevant Safety Signals of Nephrotoxicity through Plasma Metabolite Profiling

I. Schuppe-Koistinen, W. Mattes, H. Kamp, 2013, BioMed research international.

Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.

P. Dönnes, M. Uhlén, P. Nilsson, 2011, Journal of proteome research.

The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design

L. Engstrand, I. Schuppe-Koistinen, L. W. Hugerth, 2022, Human reproduction open.

New modes of data partitioning based on PARS peak alignment for improved multivariate biomarker/biopattern detection in 1H-NMR spectroscopic metabolic profiling of urine

B. Karlberg, R. J. O. Torgrip, J. Lindberg, 2006, Metabolomics.

Analysis of time-related metabolic fluctuations induced by ethionine in the rat.

Johan Lindberg, Elaine Holmes, Jeremy K Nicholson, 2007, Journal of proteome research.

Proof of principle of a generalized fuzzy Hough transform approach to peak alignment of one-dimensional 1H NMR data

Ralf J. O. Torgrip, Erik Alm, K. Magnus Åberg, 2007, Analytical and bioanalytical chemistry.

Time-resolved biomarker discovery in 1H-NMR data using generalized fuzzy Hough transform alignment and parallel factor analysis

Erik Alm, K. Magnus Åberg, Johan Lindberg, 2010, Analytical and bioanalytical chemistry.

Effects of Consuming Fermented Fish (Surströmming) on the Fecal Microflora in Healthy Individuals.

Justine W. Debelius, L. Engstrand, I. Schuppe-Koistinen, 2023, Journal of medicinal food.

A solution to the 1D NMR alignment problem using an extended generalized fuzzy Hough transform and mode support

Ralf J. O. Torgrip, Erik Alm, K. Magnus Åberg, 2009, Analytical and bioanalytical chemistry.

Real Time Identification of Drug-Induced Liver Injury (DILI) through Daily Screening of ALT Results: A Prospective Pilot Cohort Study

Y. Ngo, P. Coriat, D. Khayat, 2012, PloS one.

Differentiation of human hepatoma cells during confluence as revealed by gene expression profiling.

M. Ingelman-Sundberg, K. Nilsson, I. Schuppe-Koistinen, 2004, Biochemical pharmacology.

Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages and bacterial genes

Henrik Nielsen, L. Engstrand, I. Schuppe-Koistinen, 2023, bioRxiv.

Prevalence of the human papillomavirus (HPV) types among cervical dysplasia women attending a gynaecological clinic in Sweden

L. Engstrand, M. Olovsson, I. Schuppe-Koistinen, 2023, BJC Reports.

A Systematic Approach to Preclinical and Clinical Safety Biomarker Qualification Incorporating Bradford Hill's Principles of Causality Association

F. Sistare, I. Schuppe-Koistinen, F. Dieterle, 2010, Clinical pharmacology and therapeutics.

Vaginal microbiota and human papillomavirus infection among young Swedish women

P. Angelidou, L. Engstrand, M. Olovsson, 2020, npj Biofilms and Microbiomes.

Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.

M. Uhlén, P. Nilsson, J. Schwenk, 2011, Journal of proteome research.

The impact of CYP2E1 on the development of alcoholic liver disease as studied in a transgenic mouse model.

M. Ingelman-Sundberg, K. Nilsson, I. Schuppe-Koistinen, 2009, Journal of hepatology.

Evaluation of plasma Short chain fatty acid levels as markers for Inflammatory bowel disease

L. Engstrand, A. Kiasat, I. Schuppe-Koistinen, 2023, Scandinavian journal of gastroenterology.

Erratum for Hugerth et al., “Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome”

L. Engstrand, I. Schuppe-Koistinen, L. W. Hugerth, 2020, mSphere.