Andrzej Kudlicki - Publications (selected)

Genomics and Development:
  • The precise timeline of transcriptional regulation reveals causation in mouse somitogenesis network B. Fongang, A. Kudlicki BMC developmental biology 13 (1), 42, 2013
  • G-Quadruplexes Involving Both Strands of Genomic DNA Are Highly Abundant and Colocalize with Functional Sites in the Human Genome A. Kudlicki PLoS ONE 11 (1), e0146174, 2016
  • Comparison of pattern detection methods in microarray time series of the segmentation clock Mary-Lee Dequeant, Sebastian Ahnert, Herbert Edelsbrunner, Thomas MA Fink, Earl F Glynn, Gaye Hattem, Andrzej Kudlicki, Yuriy Mileyko, Jason Morton, Arcady R Mushegian, Lior Pachter, Maga Rowicka, Anne Shiu, Bernd Sturmfels, Olivier Pourquié PLoS ONE 3 (8), e2856, 2008
  • The 3D organization of the yeast genome correlates with co-expression and reflects functional relations between genes Dirar Homouz, Andrzej S Kudlicki PloS ONE 8 (1), 2013
  • Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition Bing Tian, Xueling Li, Mridul Kalita, Steven G Widen, Jun Yang, Suresh K Bhavnani, Bryant Dang, Andrzej Kudlicki, Mala Sinha, Fanping Kong, Thomas G Wood, Bruce A Luxon, Allan R Brasier BMC Genomics 16:529, 2015
Transcriptomics:
  • High-resolution timing of cell cycle-regulated gene expression
  • Modulation of gene expression regulated by the transcription factor NF-κB/RelA
  • Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes
  • Inferring Genome-Wide Functional Modulatory Network: A Case Study on NF-κB/RelA Transcription Factor
  • Correcting positional correlations in Affymetrix [reg] Genome Chips
  • Differential WBC Gene Expression Is Associated with Pneumonia Development after Burn Injury
  • Let the data speakBenjamin P Tu, Andrzej Kudlicki, Maga Rowicka, Steven L McKnightNature Reviews Molecular Cell Biology 7, 12, 2006
  • SCEPTRANS: an online tool for analyzing periodic transcription in yeast
  • Robust Weighted Kernel Logistic Regression To Predict Gene-Gene Regulatory Association
  • Bayesian modeling of protein interaction networks
Molecular Biology:
  • Probabilistic approach to predicting substrate specificity of methyltransferases
  • Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome
  • Valosin-containing protein (p97) is a regulator of endoplasmic reticulum stress and of the degradation of N-end rule and ubiquitin-fusion degradation pathway substrates in mammalian cells
  • Results from the pharmasat nanosatellite mission: Dose dependence of growth and metabolic parameters for S. cerevisiae grown in microgravity and challenged by voriconazole
  • PharmaSat: Drug dose response in microgravity from a free-flying integrated biofluidic/optical culture-and-analysis satellite
Proteomics:
  • Systematic determination of human cyclin dependent kinase (CDK)-9 interactome identifies novel functions in RNA splicing mediated by the DEAD Box (DDX)-5/17 RNA helicases
  • The optimal exponent base for emPAI is 6.5
Crystallography:
  • The crystallographic fast Fourier transform. I. p3 symmetry
  • The crystallographic fast Fourier transform. II. One-step symmetry reduction
  • The crystallographic fast Fourier transform. III. Centred lattices
  • The crystallographic fast Fourier transform. IV. FFT-asymmetric units in the reciprocal space
  • Coordinate transformations in modern crystallographic computing
  • Stereochemical rules for connecting disjoint protein fragments
  • An efficient routine for computing symmetric real spherical harmonics for high orders of expansion
  • The crystallographic Fast Fourier Transform. Recursive symmetry reduction
Astrophysics:
  • Local Group Velocity Versus Gravity: Nonlinear Effects
  • Gaussianity of Cosmic Velocity Fields and Linearity of the Gravity--Velocity Relation
  • The cosmic gravity-velocity relation
  • Reconstructing cosmic peculiar velocities from the mildly non-linear density field
  • Peculiar Velocities from the Nonlinear Density Field
  • Non-linearity and stochasticity in the density-velocity relation
  • Structure formation in cosmology
  • CPPA--a New Hydrodynamical Code for Cosmological Large-Scale Structure Simulations
  • Nonuniform Distribution of Galaxies in Very Large Scale