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List of works by Pierre Baldi

A 3-Dimensional Trimeric β-Barrel Model for Chlamydia MOMP Contains Conserved and Novel Elements of Gram-Negative Bacterial Porins ⬇️

scientific article published on July 25, 2013

A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens

scholarly article

A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval.

scientific article

A Genomic Analysis Pipeline and Its Application to Pediatric Cancers

scientific article published on September 2014

A WNT/p21 Circuit Directed by the C-Clamp, a Sequence-Specific DNA Binding Domain in TCFs ⬇️

scientific article published on July 9, 2012

A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi

scientific article published on 12 May 2008

A machine learning information retrieval approach to protein fold recognition.

scientific article

A non-pharmacological therapeutic approach in the gut triggers distal metabolic rewiring capable of ameliorating diet-induced dysfunctions encompassed by metabolic syndrome

scientific article published on 31 July 2020

A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray

scientific article

A scalable and integrative system for pathway bioinformatics and systems biology

scientific article

A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking

scientific article

A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions ⬇️

scientific article published on April 23, 2013

Accurate and efficient target prediction using a potency-sensitive influence-relevance voter

scientific article (publication date: 2015)

An enhanced MITOMAP with a global mtDNA mutational phylogeny

scientific article published on 18 December 2006

Assessment of predictions submitted for the CASP7 domain prediction category.

scientific article

Asymptotic normality of some Graph-Related statistics

scientific article published in 1989

Bayesian Causality

scientific article published on 26 August 2019

Bayesian surprise attracts human attention

scientific article published on 19 October 2008

Biomimetic Design of Protein Nanomaterials for Hydrophobic Molecular Transport

scientific article published on 23 April 2012

COBEpro: a novel system for predicting continuous B-cell epitopes

scientific article published on 10 December 2008

COBRA: a computational brewing application for predicting the molecular composition of organic aerosols

scientific article

ChemDB: a public database of small molecules and related chemoinformatics resources

scientific article

Chemoinformatics, drug design, and systems biology.

scientific article published in January 2005

CircadiOmics: circadian omic web portal.

scientific article published in July 2018

Circadian acetylome reveals regulation of mitochondrial metabolic pathways

scientific article published on 22 January 2013

Circadian clock regulates the host response to Salmonella

scientific article published on 28 May 2013

Circadian control of fatty acid elongation by SIRT1 protein-mediated deacetylation of acetyl-coenzyme A synthetase 1.

scientific article published on 14 January 2014

Classifying shoulder implants in X-ray images using deep learning

scientific article published on 15 April 2020

Cocaine-mediated circadian reprogramming in the striatum through dopamine D2R and PPARγ activation

scientific article published on 07 September 2020

Combining Deep Learning With Optical Coherence Tomography Imaging to Determine Scalp Hair and Follicle Counts

scientific article published on 22 September 2020

Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate

scientific article

Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver

scientific article published on 7 December 2015

Complex-valued autoencoders ⬇️

scientific article published on May 4, 2012

Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability

scientific article

Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors

scientific article

Contrastive Learning and Neural Oscillations

Coordination of the transcriptome and metabolome by the circadian clock ⬇️

scientific article published on March 19, 2012

Correction: Serological Profiling of a Candida albicans Protein Microarray Reveals Permanent Host-Pathogen Interplay and Stage-Specific Responses during Candidemia

scientific article published on 30 September 2010

Cyber-T web server: differential analysis of high-throughput data

scientific article

Cycles in spatial and temporal chromosomal organization driven by the circadian clock

scientific article published on 22 September 2013

Data structures and compression algorithms for genomic sequence data

scientific article

Data structures and compression algorithms for high-throughput sequencing technologies

scientific article

Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress ⬇️

scientific article published on March 18, 2011

Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response to the Letter by the Cambridge Crystallographic Data Centre ⬇️

scientific article published on December 7, 2011

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules ⬇️

scientific article published on July 2, 2013

Deep Learning Analysis of Vibrational Spectra of Bacterial Lysate for Rapid Antimicrobial Susceptibility Testing

scientific article published on 23 October 2020

Deep architectures for protein contact map prediction ⬇️

scientific article published on July 30, 2012

Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas

scientific article published on 10 May 2018

Development and validation of a deep neural network model to predict postoperative mortality, acute kidney injury, and reintubation using a single feature set

scientific article published on 20 April 2020

Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes ⬇️

scientific article published on August 24, 2010

Differential analysis of DNA microarray gene expression data

scientific article

Discovery of power-laws in chemical space.

scientific article

Distinct Circadian Signatures in Liver and Gut Clocks Revealed by Ketogenic Diet.

scientific article

Distribution patterns of over-represented k-mers in non-coding yeast DNA.

scientific article

Editorial: Charting Chemical Space: Challenges and Opportunities for Artificial Intelligence and Machine Learning.

scientific article published in September 2011

Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory

scientific article published in Nature Communications

Erratum to "Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock" [Mol Metab 3 (2014) 29-41].

scientific article published on 16 September 2014

Fold recognition by scoring protein maps using the congruence coefficient

scientific article published on 25 September 2020

From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis

scientific article

Function and Regulation of Cph2 in Candida albicans

scientific article

GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program

scientific article

Genome-Wide Identification of Bcl11b Gene Targets Reveals Role in Brain-Derived Neurotrophic Factor Signaling ⬇️

scientific article published on January 1, 2011

Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein

scientific article

Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR.

scientific article published on 15 May 2003

Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA.

scientific article

Global landscape of recent inferred Darwinian selection for Homo sapiens

scientific article

Graph kernels for chemical informatics

scientific article

Guidelines for Genome-Scale Analysis of Biological Rhythms

scientific article published on November 2017

Gut microbiota directs PPARγ-driven reprogramming of the liver circadian clock by nutritional challenge

scientific article published on 14 July 2016

Hashing algorithms and data structures for rapid searches of fingerprint vectors

scientific article

High-throughput prediction of protein antigenicity using protein microarray data ⬇️

scientific article published on October 7, 2010

Hippocampal gene expression patterns linked to late-life physical activity oppose age and AD-related transcriptional decline

scientific article published on 20 February 2019

How noisy and replicable are DNA microarry data?

scientific article

Identification of Immunodominant Antigens by Probing a Whole Chlamydia trachomatis Open Reading Frame Proteome Microarray Using Sera from Immunized Mice ⬇️

scientific article published on October 18, 2010

Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques

scientific article

Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarrays

scientific article

Immunodominant Francisella tularensis antigens identified using proteome microarray

scientific article published in June 2007

Improved residue contact prediction using support vector machines and a large feature set.

scientific article

Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles.

scientific article

Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures.

scientific article

Influence relevance voting: an accurate and interpretable virtual high throughput screening method

scientific article published on April 2009

Inner and Outer Recursive Neural Networks for Chemoinformatics Applications

scientific article published on 10 January 2018

Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms

scientific article published on 22 September 2021

Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens

scientific article

Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching

scientific article

Learning in the Machine: Random Backpropagation and the Deep Learning Channel

scholarly article by Pierre Baldi et al published July 2018 in Artificial Intelligence

Learning to play Go using recursive neural networks

scientific article

Leptin engages a hypothalamic neurocircuitry to permit survival in the absence of insulin

scientific article published on September 2013

LineUp: statistical detection of chromosomal homology with application to plant comparative genomics

scientific article

Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites

scientific article published on 27 June 2019

Longitudinal Monitoring of Biofilm Formation via Robust Surface-Enhanced Raman Scattering Quantification of Pseudomonas aeruginosa-Produced Metabolites

scientific article published on 28 March 2018

Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis

scientific article published on May 2016

MITOMAP: a human mitochondrial genome database--2004 update

scientific article

MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences

scientific article published on January 2009

Machine learning methods for protein structure prediction

scientific article

Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy

scientific article

Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling

scientific article

Mathematical correction for fingerprint similarity measures to improve chemical retrieval

scientific article

Metabolic changes associated with methionine stress sensitivity in MDA-MB-468 breast cancer cells

scientific article published on 2 May 2016

Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis

scientific article published on 30 July 2020

Methyl Anion Affinities of the Canonical Organic Functional Groups

scientific article published on 04 March 2020

MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex

scientific article published on 07 October 2020

Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling.

scientific article

Mir-132/212 is required for maturation of binocular matching of orientation preference and depth perception

scientific article

Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells

scientific article published on 09 July 2019

Mitochondrial mutations and polymorphisms in psychiatric disorders

scientific article

Mitochondrial mutations in subjects with psychiatric disorders

scientific article published on 26 May 2015

Modeling of Mitochondria Bioenergetics Using a Composable Chemiosmotic Energy Transduction Rate Law: Theory and Experimental Validation ⬇️

scientific article published on September 8, 2011

Modular DAG-RNN architectures for assembling coarse protein structures.

scientific article

MotifMap-RNA: a genome-wide map of RBP binding sites

scientific article published on 22 February 2017

MotifMap: a human genome-wide map of candidate regulatory motif sites

scientific article

MotifMap: integrative genome-wide maps of regulatory motif sites for model species

scientific article

Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock

scientific article published on 23 October 2013

Neural Networks and Principal Component Analysis: Learning from Examples Without Local Minima

article

No electron left behind: a rule-based expert system to predict chemical reactions and reaction mechanisms

scientific article

On the relationship between deterministic and probabilistic directed Graphical models: from Bayesian networks to recursive neural networks.

scientific article

One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties.

scientific article

PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure

scientific article

Partitioning circadian transcription by SIRT6 leads to segregated control of cellular metabolism

scientific article

Prediction of coordination number and relative solvent accessibility in proteins.

scientific article

Prediction of protein stability changes for single-site mutations using support vector machines

scientific article published in March 2006

Profiling humoral immune responses to P. falciparum infection with protein microarrays

scientific article

Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery

scientific article

Protein profiles: Biases and protocols

scientific article published on 27 August 2020

Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity

scientific article published in 2022

Rationally selected single‐site mutants of the Thermoascus aurantiacus endoglucanase increase hydrolytic activity on cellulosic substrates ⬇️

scientific article published on January 2, 2012

Reprogramming of the circadian clock by nutritional challenge.

scientific article

Reshaping circadian metabolism in the suprachiasmatic nucleus and prefrontal cortex by nutritional challenge

scientific article published on 10 November 2020

Retrotransposon profiling of RNA polymerase III initiation sites

scientific article published on 27 January 2012

S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling

scientific article published on 16 December 2020

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs

scientific article published on 3 December 2008

SIDEpro: A novel machine learning approach for the fast and accurate prediction of side‐chain conformations ⬇️

scientific article published on November 9, 2011

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity.

scientific article

Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity

scientific article

Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during candidemia

scientific article

Small-molecule 3D structure prediction using open crystallography data

scientific article (publication date: 23 December 2013)

Speeding up chemical searches using the inverted index: the convergence of chemoinformatics and text search methods

scientific article published on 10 April 2012

Sterile protective immunity to malaria is associated with a panel of novel P. falciparum antigens

scientific article

Structural proteomics of the poxvirus family

scientific article published on June 2004

Structure, self-assembly, and properties of a truncated reflectin variant

scientific article published on 15 December 2020

Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis

scholarly article

TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins

scientific article published on 15 November 2007

Temporal Evolution of Generalization during Learning in Linear Networks

article published in 1991

The Dropout Learning Algorithm

scientific article

The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition

scientific article

The TY3 Gag3 Spacer Controls Intracellular Condensation and Uncoating ⬇️

scientific article published on January 26, 2011

The absence of favorable aromatic interactions between beta-sheet peptides.

scientific article

The central clock suffices to drive the majority of circulatory metabolic rhythms

scientific article published in 2022

The fixed-size Luria-Delbruck model with a nonzero death rate

scientific article published on 3 May 2007

The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory

scientific article published on 24 March 2013

The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework

scientific article

The stability and complexity of antibody responses to the major surface antigen of Plasmodium falciparum are associated with age in a malaria endemic area

scientific article published on 8 August 2011

Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms.

scientific article

Towards a systems view of IBS

scientific article (publication date: October 2015)

Training and Validation of Deep Neural Networks for the Prediction of 90-Day Post-Liver Transplant Mortality Using UNOS Registry Data

scientific article published on 08 January 2020

Tree and Hashing Data Structures to Speed up Chemical Searches: Analysis and Experiments

scientific article

Ty3 capsid mutations reveal early and late functions of the amino-terminal domain

scientific article

User contribution and trust in Wikipedia

scientific article published on 04 March 2012

VIRALpro: a tool to identify viral capsid and tail sequences

scientific article published on 5 January 2016

Weakly Supervised Polyp Segmentation in Colonoscopy Images Using Deep Neural Networks

scientific article published on 22 April 2022

What time is it? Deep learning approaches for circadian rhythms

scientific article published on June 2016

What time is it? Deep learning approaches for circadian rhythms

scientific article published on 19 August 2016

When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values

scientific article

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