A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data

Autor: Devin O’Kelly, James Campbell, Jeni L. Gerberich, Paniz Karbasi, Venkat Malladi, Andrew Jamieson, Liqiang Wang, Ralph P. Mason

Publikováno v: Scientific Reports, Vol 11, Iss 1, Pp 1-18 (2021)

Abstract Multispectral photoacoustic tomography enables the resolution of spectral components of a tissue or sample at high spatiotemporal resolution. With the availability of commercial instruments, the acquisition of data using this modality has be

Externí odkaz: https://doaj.org/article/947aff8483c8407089fb51ce97ce6eb4

Acute interstitial nephritis, a potential predictor of response to immune checkpoint inhibitors in renal cell carcinoma

Autor: Raquibul Hannan, Alana Christie, Payal Kapur, James Brugarolas, Hans Hammers, Viral Patel, Roy Elias, Joseph Formella, William Schwartzman, Qi Cai, Venkat Malladi, Miguel Vazquez, Renee McKay, Ivan Pedrosa

Publikováno v: Journal for ImmunoTherapy of Cancer, Vol 8, Iss 2 (2020)

Immune checkpoint inhibitors (ICIs) such as nivolumab and ipilimumab have improved outcomes in metastatic renal cell carcinoma (mRCC) patients, but they are also associated with immune-related adverse events (irAEs). As observed in melanoma, we hypot

Externí odkaz: https://doaj.org/article/d537c5164f5e4142be6b5b1d2952a0ff

SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers

Autor: Christopher Bennett, Micah Thornton, Chanhee Park, Gervaise Henry, Yun Zhang, Venkat Malladi, Daehwan Kim

Publikováno v: Bioinformatics

Motivation With the vast improvements in sequencing technologies and increased number of protocols, sequencing is being used to answer complex biological problems. Subsequently, analysis pipelines have become more time consuming and complicated, usua

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c4651c90fae52bd20dbce5e219f95e4
https://doi.org/10.1093/bioinformatics/btac050

An integrated encyclopedia of DNA elements in the human genome

Autor: Robert Altshuler, Laura Elnitski, Michael Anaya, Alec Victorsen, Deborah Winter, Javier Herrero, Katherine Varley, Andrea Sboner, Oscar Junhong Luo, Marco Mariotti, Cristina Sisu, Mike Kay, Timothy Dreszer, Jane Loveland, Alexandra Bignell, Ewan Birney, Tim @timjph Hubbard, Kuljeet Sandhu, Eric Haugen, Chris Gunter, Alexej Abyzov, Lucas Ward, Georgi Marinov, Michael Pazin, Thomas Gingeras, Alexander Dobin, Kimberly Foss, Xianjun Dong, Benoit Miotto, Piotr Mieczkowski, Cedric Notredame, Andrew Berry, Shawn Gillespie, Axel Visel, Shawn Levy, Richard Sandstrom, Jose M Gonzalez, Melissa Fullwood, Timo Lassmann, Michael Tress, Julien Lagarde, Kevin Yip, Leslie Adams, Sylvain Foissac, Bronwen Aken, Piero Carninci, Suganthi Balasubramanian, Andrea Tanzer, Sarah Djebali, Michael Hoffman, Gloria Despacio-Reyes, Peter Park, Felix Kokocinski, Katherine Fisher-Aylor, Juan M Vaquerizas, Peggy Farnham, Patrick Collins, Amonida Zadissa, Pedro Ferreira, Philippe Batut, Michael Snyder, Electra Tapanari, Adam Frankish, Paul Flicek, AMARTYA SANYAL, Tyler Alioto, Giovanni Bussotti, Laurence Meyer, Jingyi Jessica Li, Matthew Blow, Tristan FRUM, Roger Alexander, Rory Johnson, Charles Steward, Meizhen Zheng, Margus Lukk, Ross Hardison, Claire Davidson, Gary Saunders, Alan Boyle, Luiz Penalva, Rajinder Kaul, Lazaro Centanin, Florencia Pauli Behn, Thomas Derrien, Nathan Sheffield, Toby Hunt, Eric Nguyen, Jeff Vierstra, Konrad Karczewski, Kimberly Bell, Yanbao Yu, Hagen U Tilgner, James Taylor, Balázs Bánfai, Catherine Snow, Benjamin Vernot, Stephan Kirchmaier, Michael Sammeth, Steven Wilder, Angelika Merkel, Joanna Mieczkowska, Guoliang Li, Wei Lin, Jennifer Harrow, Thomas Oliver Auer, Daniel Barrell, Eddie Park, Alvis Brazma, Hazuki Takahashi, Nathan Johnson, Daniel Sobral, Terry Furey, Alexandre Reymond, Jonathan Mudge, Anshul Kundaje, Jose Rodriguez, Akshay Bhinge, James Gilbert, Jakub Karczewski, Venkat Malladi, Troy Whitfield, Orion Buske, Ian Dunham, Jennifer Moran, Joachim Wittbrodt, Charles B. Epstein, Laurens Wilming, Jason Gertz, Joshua Akey, Joel Rozowsky

Publikováno v: Nature
Nature, Nature Publishing Group, 2012, 489 (7414), pp.57-74. ⟨10.1038/nature11247⟩
NATURE
Nature, Vol. 489, No 7414 (2012) pp. 57-74
PMC
Recercat. Dipósit de la Recerca de Catalunya
instname

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription fa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2b208801384684d0028cc28316677b0d
https://hal.archives-ouvertes.fr/hal-01217624

Analysis of Forensic SNPs in the Canine mtDNA HV1 Mutational Hotspot Region*

Autor: David Glenn Smith, S B S Venkat Malladi, Melody R. Dayton, Sreetharan Kanthaswamy, Jessica Satkoski, L B S Jennifer Kinaga, B S Alexander Kou, B S Vivek Goyal, Danielle T. Baute, Theresa F. Spear

Publikováno v: Journal of Forensic Sciences.

A 60 bp sequence variation hotspot in the canine mitochondrial DNA hypervariable region 1 was evaluated for its use in forensic investigations. Nineteen haplotypes containing 18 single nucleotide polymorphisms were observed among laboratory-generated

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2cd01ac1c9c31b04d4baacc522da53e0
https://doi.org/10.1111/j.1556-4029.2008.00880.x