WACS: improving ChIP-seq peak calling by optimally weighting controls.

Background: Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), initially introduced more than a decade ago, is widely used by the scientific community to detect protein/DNA binding and histone modifications across the genome. Every experiment is prone to noise and bias, and ChIP-seq experiments are no exception. To alleviate bias, the incorporation of control datasets in ChIP-seq analysis is an essential step.

An Intra-Operatively Diagnosed Case of Hemorrhagic Cholecystitis in a 43-year-old Patient: Case Report.

BACKGROUND Hemorrhagic cholecystitis is an uncommon occurrence in the setting of gallbladder pathology. It is a rare complication of acute cholecystitis that may have a misleading presentation and workup, making it challenging to diagnose pre-operatively. CASE REPORT We report the case of a 43-year-old female who presented for severe epigastric pain with nausea and vomiting and whose imaging was in favor of acute cholecystitis.

An Unusual Case of Left Spigelian Hernia Containing Part of a Fibroid Uterus and the Left Adnexa in a 66-Year-Old Woman.

BACKGROUND Spigelian hernia, or lateral ventral hernia, is rare and represents between 0.1-2% of all hernias of the abdominal wall. The presentation is variable, and the diagnosis may be challenging.

RECAP reveals the true statistical significance of ChIP-seq peak calls.

Motivation: Chromatin Immunopreciptation (ChIP)-seq is used extensively to identify sites of transcription factor binding or regions of epigenetic modifications to the genome. A key step in ChIP-seq analysis is peak calling, where genomic regions enriched for ChIP versus control reads are identified. Many programs have been designed to solve this task, but nearly all fall into the statistical trap of using the data twice-once to determine candidate enriched regions, and again to assess enrichment by classical statistical hypothesis testing.