TACO: a general-purpose tool for predicting cell-type–specific transcription factor dimers

por Jankowski, Aleksander, Prabhakar, Shyam, Tiuryn, Jerzy
Publicado 2014

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data

por Jankowski, Aleksander, Tiuryn, Jerzy, Prabhakar, Shyam
Publicado 2016

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

por Jankowski, Aleksander, Szczurek, Ewa, Jauch, Ralf, Tiuryn, Jerzy, Prabhakar, Shyam
Publicado 2013

Noncoding origins of anthropoid traits and a new null model of transposon functionalization

por del Rosario, Ricardo C.H., Rayan, Nirmala Arul, Prabhakar, Shyam
Publicado 2014

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

por Huang, Yong-Heng, Jankowski, Aleksander, Cheah, Kathryn S. E., Prabhakar, Shyam, Jauch, Ralf
Publicado 2015

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

por Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M, Boffelli, Dario
Publicado 2007

Gene expression profiles of Bapx1 expressing FACS sorted cells from wildtype and Bapx1-EGFP null mouse embryos

por Chatterjee, Sumantra, Sivakamasundari, V., Kraus, Petra, Yap, Sook Peng, Kumar, Vibhor, Prabhakar, Shyam, Lufkin, Thomas
Publicado 2015

Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro

por Chatterjee, Sumantra, Kraus, Petra, Sivakamasundari, V., Yap, Sook Peng, Kumar, Vibhor, Prabhakar, Shyam, Lufkin, Thomas
Publicado 2016

A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development

por Sivakamasundari, V., Kraus, Petra, Sun, Wenjie, Hu, Xiaoming, Lim, Siew Lan, Prabhakar, Shyam, Lufkin, Thomas
Publicado 2016

Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-β effectors

por BabuRajendran, Nithya, Palasingam, Paaventhan, Narasimhan, Kamesh, Sun, Wenjie, Prabhakar, Shyam, Jauch, Ralf, Kolatkar, Prasanna R.
Publicado 2010

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

por Ng, Calista K. L., Li, Noel X., Chee, Sheena, Prabhakar, Shyam, Kolatkar, Prasanna R., Jauch, Ralf
Publicado 2012

Transposable elements that have recently been mobile in the human genome

por Autio, Matias I., Bin Amin, Talal, Perrin, Arnaud, Wong, Jen Yi, Foo, Roger S.-Y., Prabhakar, Shyam
Publicado 2021

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data

por Ranjan, Bobby, Schmidt, Florian, Sun, Wenjie, Park, Jinyu, Honardoost, Mohammad Amin, Tan, Joanna, Arul Rayan, Nirmala, Prabhakar, Shyam
Publicado 2021

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data

por Hu, Yongli, Hase, Takeshi, Li, Hui Peng, Prabhakar, Shyam, Kitano, Hiroaki, Ng, See Kiong, Ghosh, Samik, Wee, Lawrence Jin Kiat
Publicado 2016

DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1

por Wang, Xuecong, Srivastava, Yogesh, Jankowski, Aleksander, Malik, Vikas, Wei, Yuanjie, del Rosario, Ricardo CH, Cojocaru, Vlad, Prabhakar, Shyam, Jauch, Ralf
Publicado 2018

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in t...

por Chatterjee, Sumantra, Sivakamasundari, V, Yap, Sook Peng, Kraus, Petra, Kumar, Vibhor, Xing, Xing, Lim, Siew Lan, Sng, Joel, Prabhakar, Shyam, Lufkin, Thomas
Publicado 2014

Genome Wide Analysis Reveals Zic3 Interaction with Distal Regulatory Elements of Stage Specific Developmental Genes in Zebrafish

por Winata, Cecilia L., Kondrychyn, Igor, Kumar, Vibhor, Srinivasan, Kandhadayar G., Orlov, Yuriy, Ravishankar, Ashwini, Prabhakar, Shyam, Stanton, Lawrence W., Korzh, Vladimir, Mathavan, Sinnakaruppan
Publicado 2013

Primate-specific evolution of an LDLR enhancer

por Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, Eisen, Michael B, Cheng, Jan-Fang, Rubin, Edward M, Boffelli, Dario
Publicado 2006

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

por Ramaswami, Gokul, Won, Hyejung, Gandal, Michael J., Haney, Jillian, Wang, Jerry C., Wong, Chloe C. Y., Sun, Wenjie, Prabhakar, Shyam, Mill, Jonathan, Geschwind, Daniel H.
Publicado 2020

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

por Kumar, Vibhor, Rayan, Nirmala Arul, Muratani, Masafumi, Lim, Stefan, Elanggovan, Bavani, Xin, Lixia, Lu, Tess, Makhija, Harshyaa, Poschmann, Jeremie, Lufkin, Thomas, Ng, Huck Hui, Prabhakar, Shyam
Publicado 2016