Related papers: Pervasive variation of transcription factor orthol…
In this work, we carried out an overlay-aware variation study on Flip FET (FFET) considering the impact on RC parasitics induced by the lithography misalignment in backside processes, and benchmarked it with CFET in terms of the…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
A blood cell lineage consists of several consecutive developmental stages from the pluripotent or multipotent stem cell to a particular stage of terminally differentiated cells. There is considerable interest in identifying the key…
We present a theory of pattern formation in growing domains inspired by biological examples of tissue development. Gradients of signaling molecules regulate growth, while growth changes these graded chemical patterns by dilution and…
Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target…
Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds…
We present schema redescription as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. In our formulation, canalization becomes synonymous with redundancy present in the logic…
Pediatric high grade gliomas are lethal evolutionary disorders with stalled developmental trajectories and disrupted differentiation hierarchies. We integrate transcriptional and algorithmic network complexity based perturbation analysis to…
Zak-transform based orthogonal time frequency space (Zak-OTFS) is a delay-Doppler (DD) domain modulation scheme in which the signal processing is carried out in the DD domain. The channel when viewed in the DD domain is predictable.…
Histone modification is a vital epigenetic mechanism for transcriptional control in eukaryotes. High-throughput techniques have enabled whole-genome analysis of histone modifications in recent years. However, most studies assume one…
A feed-forward loop (FFL) is a common gene-regulatory motif in which usually the upstream regulator is a protein, a transcription factor, that regulates the expression of the target protein in two parallel pathways. Here, we study a…
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the…
Context: L-type ultra-cool dwarfs and brown dwarfs have cloudy atmospheres that could host weather-like phenomena. The detection of photometric or spectral variability would provide insight into unresolved atmospheric heterogeneities, such…
The family of TGFb ligands is large and its members are involved in many different signaling processes. These signaling processes strongly differ in type with TGFb ligands eliciting both sustained or transient responses. Members of the TGFb…
In multicellular organisms, patterns of gene expression are established in response to gradients of signaling molecules. During fly development in early Drosophila embryos, the Bicoid (Bcd) morphogen gradient is established within the first…
We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…
(ABRIDGED) We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were…
A theory for qualitative models of gene regulatory networks has been developed over several decades, generally considering transcription factors to regulate directly the expression of other transcription factors, without any intermediate…
Despite significant progress in structural and functional characterization of human genome, understanding of mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. We report that non-randomly distributed…
A fundamental goal in neuroscience is to understand the relationship between neural activity and behavior. For example, the ability to extract behavioral intentions from neural data, or neural decoding, is critical for developing effective…