Amy H.Y. Tong, Marie Evangelista, Ainslie B. Parsons, Hong Xu et al.
In Saccharomyces cerevisiae, more than 80% of the approximately 6200 predicted genes are nonessential, implying that the genome is buffered from the phenotypic consequences of genetic perturbation. To evaluate function, we developed a method for systematic construction of double mutants, termed synt...
Zheng Fan, Yuan Tao, Piao Liu, Lu-Yu Wang et al.
BACKGROUND: The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it h...
Lorenzo de la Rica, Javier Rodríguez‐Ubreva, Mireia García, Abul Bashar Mir Md. Khademul Islam et al.
BACKGROUND: DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. Local deposition and removal of DNA methylation are tightly coupled with transcription factor binding, although the relationship varies with the specific differentiation process. Conversion of ...
Rafsanjani Muhammod, Sajid Ahmed, Dewan Md. Farid, Swakkhar Shatabda et al.
MOTIVATION: Extracting useful feature set which contains significant discriminatory information is a critical step in effectively presenting sequence data to predict structural, functional, interaction and expression of proteins, DNAs and RNAs. Also, being able to filter features with significant in...
Kunio Kitada, Anthony L. Johnson, Leland H. Johnston, Akio Sugino
We have isolated a multicopy suppressor of the temperature-sensitive growth phenotype of organisms carrying mutations of DBF4, a gene that is required for the initiation of chromosomal DNA replication in Saccharomyces cerevisiae and that interacts with the CDC7 protein kinase. Nucleotide sequence an...
Chenghao Guo, Zhuanzhuan Che, Junjie Yue, Peng Xie et al.
Release of paused RNA polymerase II (Pol II) requires incorporation of the positive transcription elongation factor b (P-TEFb) into the super elongation complex (SEC), thus resulting in rapid yet synchronous transcriptional activation. However, the mechanism underlying dynamic transition of P-TEFb f...
Lohith Madireddy, Nikolaos A. Patsopoulos, Chris Cotsapas, Steffan D. Bos et al.
Genome-wide association studies (GWAS) have identified more than 50,000 unique associations with common human traits. While this represents a substantial step forward, establishing the biology underlying these associations has proven extremely difficult. Even determining which cell types and which p...
Zubair Ahmed Ratan, Sojib Bin Zaman, Varshil Mehta, Mohammad Faisal Haidere et al.
Fluorescence in situ hybridization (FISH) is a macromolecule recognition technique, which is considered as a new advent in the field of cytology. Initially, it was developed as a physical mapping tool to delineate genes within chromosomes. The accuracy and versatility of FISH were subsequently capit...
Ruhul Amin, Chowdhury Rafeed Rahman, Sajid Ahmed, Md. Habibur Rahman Sifat et al.
MOTIVATION: Promoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions, promoters can be of different types. Promoters ...
Farzana Jasmine, Ronald Rahaman, Charlotte Dodsworth, Shantanu Roy et al.
In colorectal cancer (CRC), chromosomal instability (CIN) is typically studied using comparative-genomic hybridization (CGH) arrays. We studied paired (tumor and surrounding healthy) fresh frozen tissue from 86 CRC patients using Illumina's Infinium-based SNP array. This method allowed us to study C...
Firoz Anwar, Syed Murtuza Baker, Taskeed Jabid, Md Mehedi Hasan et al.
BACKGROUND: Eukaryotic promoter prediction using computational analysis techniques is one of the most difficult jobs in computational genomics that is essential for constructing and understanding genetic regulatory networks. The increased availability of sequence data for various eukaryotic organism...
Jeremy H. Toyn, Anthony L. Johnson, Leland H. Johnston
Saccharomyces cerevisiae dbf4 and cdc7 cell cycle mutants block initiation of DNA synthesis (i.e., are iDS mutants) at 37 degrees C and arrest the cell cycle with a 1C DNA content. Surprisingly, certain dbf4 and cdc7 strains divide their chromatin at 37 degrees C. We found that the activation of the...
Nuzhat N. Kabir, Lars Rönnstrand, Julhash U. Kazi
Breast cancer expression profiling has been used for determining biomarkers. Using gene expression profiles of 2,400 patients we identified keratin 19 (KRT19) as a highly deregulated gene in breast cancer. KRT19 expression is independent of patient race but correlates with disease grade, and ER, PR ...
María Paula Zappia, Alice Rogers, Abul Bashar Mir Md. Khademul Islam, Maxim V. Frolov
The importance of the retinoblastoma tumor suppressor protein pRB in cell cycle control is well established. However, less is known about its role in differentiation during animal development. Here, we investigated the role of Rbf, the Drosophila pRB homolog, in adult skeletal muscles. We found that...
Richard Bayly, Takayuki Murase, Brandy D. Hyndman, Rachel Savage et al.
In roughly 5% of cases of acute lymphoblastic leukemia, a chromosomal translocation leads to expression of the oncogenic protein E2A-PBX1. The N-terminal portion of E2A-PBX1, encoded by the E2A gene, is identical in sequence to the corresponding portion of the E proteins E12/E47 and includes transcr...