Nvidia, Harvard researchers use AI to find active areas in cell DNA – ZDNet
By daniellenierenberg
Researchers from Nvidia and Harvard are publishing research this week on a new way they've applied deep learning to epigenomics -- the study of modifications on the genetic material of a cell.
Using a neural network originally developed for computer vision, the researchers have developed a deep learning toolkit that can help scientists study rare cell types -- and possibly identify mutations that make people more vulnerable to diseases.
The new deep learning toolkit, called AtacWorks, "allows us to study how diseases and genomic variation influence very specific types of cells of the human body," Nvidia researcher Avantika Lal, lead author on the paper, told reporters last week. "And this will enable previously impossible biological discovery, and we hope would also contribute to the discovery of new drug targets."
AtacWorks, featured in Nature Communications, works with ATAC-seq -- a popular method for finding the parts of the human genome that are accessible in cells.
Just about every cell in your body carries a copy of your genome sequence -- a sequence of your DNA about 3 billion bases long. However, only certain parts of the genome sequence are accessible to certain cells. Every cell type -- whether it's liver, blood or skin cells -- can only access the regions of DNA they need for their respective function.
"That allows us to understand what makes every type of cell different from each other, or how every type of cell is affected in disease, or in other biological changes," Lal said.
ATAC-seq finds those accessible parts by producing a signal for every base in the genome. Peaks in the signal denote accessible regions of DNA. This method typically requires tens of thousands of certain kinds of cells to get a clean signal. This makes it challenging to study rare cell types, like the stem cells that produce blood cells and platelets.
However, by applying AtacWorks to ATAC-seq data, the researchers found they could rely on just tens of cells, rather than tens of thousands. In the research described in their new paper, the Nvidia and Harvard scientists applied AtacWorks to a dataset of stem cells that produce red and white blood cells. They used a sample set of just 50 cells to identify distinct regions of DNA associated with cells that develop into white blood cells, as well as separate sequences that correlate with red blood cells.
AtacWorks is a PyTorch-based convolutional neural network that was trained on labeled pairs of matching ATAC-seq datasets -- one high quality and one "noisy." The model learned to predict an accurate, high-quality version of a dataset and identify peaks in the signal.
Running on Nvidia Tensor Core GPUs, the model took under 30 minutes for inference on a whole genome, a process that normally takes 15 hours on a system with 32 CPU cores.
Lal noted that the researchers were able to train the model on any type of cell and then apply it to any different type.
"That's a really wonderful thing because it means that we can train models using whatever data we have available and then apply it to entirely new biological samples," she said.
The model could help deliver insights into a range of diseases, including cardiovascular disease, Alzheimer's disease, diabetes or neurological disorders. It's available on the NGC Software Hub, Nvidia's hub of GPU-optimized software, where any researcher can access it.
"We are hoping that once our paper comes out, other scientists working with different diseases would also pick up this technique and be interested in using it," Lal said. "And we are excited to see what new research and new developments that can enable."
Continue reading here:
Nvidia, Harvard researchers use AI to find active areas in cell DNA - ZDNet
- 001 Elaine Fuchs discusses research on skin and adult stem cells [Last Updated On: June 25th, 2011] [Originally Added On: June 25th, 2011]
- 002 Skin Stem Cells: Their Biology [Last Updated On: June 25th, 2011] [Originally Added On: June 25th, 2011]
- 003 Come Back Kid [Last Updated On: June 26th, 2011] [Originally Added On: June 26th, 2011]
- 004 Emerge Labs New Anti Aging Swiss Apple Stem Cell Skin Care [Last Updated On: June 26th, 2011] [Originally Added On: June 26th, 2011]
- 005 PhytoCell.mp4 [Last Updated On: June 26th, 2011] [Originally Added On: June 26th, 2011]
- 006 Elaine Fuchs Part 2: Tapping the Potential of Adult Stem Cells, and Summary [Last Updated On: June 28th, 2011] [Originally Added On: June 28th, 2011]
- 007 Elaine Fuchs Part 1: Introduction to Stem Cells [Last Updated On: July 1st, 2011] [Originally Added On: July 1st, 2011]
- 008 Stem Cell Facial At Metamorphosis Day Spa Using Emerge Labs Skin Care [Last Updated On: July 1st, 2011] [Originally Added On: July 1st, 2011]
- 009 A Major Breakthrough in Skin Care and Nutrition [Last Updated On: July 7th, 2011] [Originally Added On: July 7th, 2011]
- 010 The Skin Gun stem cell research [Last Updated On: July 7th, 2011] [Originally Added On: July 7th, 2011]
- 011 The Skin Gun [Last Updated On: July 7th, 2011] [Originally Added On: July 7th, 2011]
- 012 E'shee HBA Global Expo 2011, NYC. Skin Care Anti-Aging Symposium [Last Updated On: July 8th, 2011] [Originally Added On: July 8th, 2011]
- 013 World's 1st Nutricosmetic with Stem Cell Nutrients [Last Updated On: July 15th, 2011] [Originally Added On: July 15th, 2011]
- 014 Stem cells acquired from human skin [Last Updated On: August 22nd, 2011] [Originally Added On: August 22nd, 2011]
- 015 DermaStem Renewal Serum - Stem Cells for Your Skin from STEMTech - New Paradigm in Beauty! [Last Updated On: August 30th, 2011] [Originally Added On: August 30th, 2011]
- 016 Stem Cells Made From Human Skin [Last Updated On: September 4th, 2011] [Originally Added On: September 4th, 2011]
- 017 ReLuma-stemcells- skin rejuvenation [Last Updated On: September 5th, 2011] [Originally Added On: September 5th, 2011]
- 018 Jeunesse Global Business Opportunity with Stem Cell Skin Care Developed by Dr Nathan Newman [Last Updated On: September 5th, 2011] [Originally Added On: September 5th, 2011]
- 019 Dr Nathan Newman- Formulator of Stem Cell Skin Care Line LUMINESCE [Last Updated On: September 6th, 2011] [Originally Added On: September 6th, 2011]
- 020 Luminesce Stem Cell Skin Care - Leaders in Jeunesse [Last Updated On: September 7th, 2011] [Originally Added On: September 7th, 2011]
- 021 Stem Cell Therapy - BioLogic Anti-Aging Skin Cream [Last Updated On: September 7th, 2011] [Originally Added On: September 7th, 2011]
- 022 Isolation and Culture of Adult Epithelial Stem Cells from Human Skin [Last Updated On: September 8th, 2011] [Originally Added On: September 8th, 2011]
- 023 Stem Cell Skin Care- What is the role of stem cells in Luminesce Featuring Dr Nathan Newman [Last Updated On: September 9th, 2011] [Originally Added On: September 9th, 2011]
- 024 Genetic Skin Disease (EB): Spotlight on Stem Cell Research - Patient Advocate [Last Updated On: September 11th, 2011] [Originally Added On: September 11th, 2011]
- 025 Genetic Skin Disease (EB): Optimizing Embryonic Stem Cell Differentiation Protocols [Last Updated On: September 12th, 2011] [Originally Added On: September 12th, 2011]
- 026 Genetic Skin Disease (EB): Spotlight on Stem Cell Research - Introduction [Last Updated On: September 13th, 2011] [Originally Added On: September 13th, 2011]
- 027 The Skin Gun (Stem Cell research to replace burnt off skin. Done in 3 days!) [Last Updated On: September 15th, 2011] [Originally Added On: September 15th, 2011]
- 028 Best natural skin care serum using stem cell technology [Last Updated On: September 22nd, 2011] [Originally Added On: September 22nd, 2011]
- 029 Stem Cells: Fulfilling the Promise - 2011 CIRM Grantee Meeting [Last Updated On: September 24th, 2011] [Originally Added On: September 24th, 2011]
- 030 Jeunesse Global Opportunity- Stem Cell Skin Care [Last Updated On: September 25th, 2011] [Originally Added On: September 25th, 2011]
- 031 Research on skin cancer: ERC funds studies on stem cells [Last Updated On: September 26th, 2011] [Originally Added On: September 26th, 2011]
- 032 Stem Cell Therapy Skin Repair and Anti-Wrinkle Cream [Last Updated On: September 29th, 2011] [Originally Added On: September 29th, 2011]
- 033 Skin engineering [Last Updated On: September 30th, 2011] [Originally Added On: September 30th, 2011]
- 034 Stem Cell Face Treatment - What People Are Saying | Beverly Hills | Los Angeles [Last Updated On: October 1st, 2011] [Originally Added On: October 1st, 2011]
- 035 How To Use Your Stem Cells For Facial Skin Rejuvenation [Last Updated On: October 5th, 2011] [Originally Added On: October 5th, 2011]
- 036 AMAZING - Stem Cell Skin Cream And Liquid Face Lift Revealed [Last Updated On: October 5th, 2011] [Originally Added On: October 5th, 2011]
- 037 Dr Nathan Newman MD Stem Cell Face lift on Channel 7 KABC.flv [Last Updated On: October 5th, 2011] [Originally Added On: October 5th, 2011]
- 038 Genetic Skin Disease (EB): Spotlight on Stem Cell Research - Welcome [Last Updated On: October 5th, 2011] [Originally Added On: October 5th, 2011]
- 039 Dr.Thomas Barnes' PRP Hair Growth and Skin Rejuvenation [Last Updated On: October 5th, 2011] [Originally Added On: October 5th, 2011]
- 040 For Damaged Skin - Rejuvenate Your Own Stem Cells [Last Updated On: October 5th, 2011] [Originally Added On: October 5th, 2011]
- 041 real food real life - Stemulance stem cell face products [Last Updated On: October 5th, 2011] [Originally Added On: October 5th, 2011]
- 042 Dr Amiya Prasad discusses ACell for Hair Regrowth and Skin Rejuvenation with EYES IN Magazine [Last Updated On: October 5th, 2011] [Originally Added On: October 5th, 2011]
- 043 Stem Cell Face Lift - English (Part 5) [Last Updated On: October 6th, 2011] [Originally Added On: October 6th, 2011]
- 044 Cell Reprogramming Transformed [Last Updated On: October 6th, 2011] [Originally Added On: October 6th, 2011]
- 045 Care for Your Skin with Lifeline Skin Care [Last Updated On: October 6th, 2011] [Originally Added On: October 6th, 2011]
- 046 Dr Nathan Newman Repairs Laugh Lines With Stem Cell Face Lift [Last Updated On: October 6th, 2011] [Originally Added On: October 6th, 2011]
- 047 Ellis Martin Report with International Stem Cell Corp [Last Updated On: October 6th, 2011] [Originally Added On: October 6th, 2011]
- 048 Stem Cell Banking: The Perspective of an iPS Donor Family [Last Updated On: October 6th, 2011] [Originally Added On: October 6th, 2011]
- 049 Dr Nathan Newman Stem Cell Face Lift on Entertainment Tonight [Last Updated On: October 8th, 2011] [Originally Added On: October 8th, 2011]
- 050 Elaine Fuchs Part 1: Introduction to Stem Cells English Subtitle [Last Updated On: October 12th, 2011] [Originally Added On: October 12th, 2011]
- 051 Signals Stem Cell Skin Care Anti Aging Skin Care - Video [Last Updated On: October 14th, 2011] [Originally Added On: October 14th, 2011]
- 052 Stem Cell Skin Care - Born Different.mp4 - Video [Last Updated On: October 18th, 2011] [Originally Added On: October 18th, 2011]
- 053 APPLE STEMCELL by SEMCELL - Video [Last Updated On: October 21st, 2011] [Originally Added On: October 21st, 2011]
- 054 Jeunesse Luminesce Stem Cell Skin care Before and After Pictures - Video [Last Updated On: October 23rd, 2011] [Originally Added On: October 23rd, 2011]
- 055 Stem Cell Therapy -- Reduce Wrinkles,Promote Younger, Healthier Looking Skin - Video [Last Updated On: October 25th, 2011] [Originally Added On: October 25th, 2011]
- 056 Scientists Create Liver from Reprogrammed Human Skin Cells No Stem Cells Needed - Video [Last Updated On: October 25th, 2011] [Originally Added On: October 25th, 2011]
- 057 Vitiligo and Stem Cells: Narrowband UVB Phototherapy in Nonsegmental Vitiligo - Video [Last Updated On: October 25th, 2011] [Originally Added On: October 25th, 2011]
- 058 Dr Nathan Newman MD Stem Cell Face lift on Entertainment Tonight - NewHopeForAging.com - Video [Last Updated On: October 25th, 2011] [Originally Added On: October 25th, 2011]
- 059 Skin Healing And Anti-Aging - Rejuvenate Aging Skin Cells - Video [Last Updated On: October 25th, 2011] [Originally Added On: October 25th, 2011]
- 060 Stem Cell Face Lift - Video [Last Updated On: October 27th, 2011] [Originally Added On: October 27th, 2011]
- 061 Stem Cell Therapy Face Cream - Video [Last Updated On: October 27th, 2011] [Originally Added On: October 27th, 2011]
- 062 Growing skin in lab with stem cells Video Reuters - Video [Last Updated On: October 27th, 2011] [Originally Added On: October 27th, 2011]
- 063 Stem Cells and Their Lineages in Skin - Video [Last Updated On: October 27th, 2011] [Originally Added On: October 27th, 2011]
- 064 Stem Cells Rock - Video [Last Updated On: October 27th, 2011] [Originally Added On: October 27th, 2011]
- 065 Stem Cell Therapy: Healing Force of the future - Video [Last Updated On: October 29th, 2011] [Originally Added On: October 29th, 2011]
- 066 Alex Cosmeceuticals - Phyto Stem Cell Technology - Video [Last Updated On: October 29th, 2011] [Originally Added On: October 29th, 2011]
- 067 Reprogramming skin cells into embryonic stem cells - Video [Last Updated On: October 29th, 2011] [Originally Added On: October 29th, 2011]
- 068 Ellis Martin Report with International Stem Cell Corp - YouTube2.flv - Video [Last Updated On: October 30th, 2011] [Originally Added On: October 30th, 2011]
- 069 Dr Lyras Plastic Surgery - Skin Needling 3 - Tv 2011 - Video [Last Updated On: November 5th, 2011] [Originally Added On: November 5th, 2011]
- 070 Donna Queen-Lifeline Skin Care at the CACS - Video [Last Updated On: November 8th, 2011] [Originally Added On: November 8th, 2011]
- 071 Turning Science Into Action with Heather Livingston - Part 1 www.miraclecell.info - Video [Last Updated On: November 12th, 2011] [Originally Added On: November 12th, 2011]
- 072 US scientists unveil new cloning method for embryonic stem cells - Video [Last Updated On: November 12th, 2011] [Originally Added On: November 12th, 2011]
- 073 A Stem Cell Story - Video [Last Updated On: November 12th, 2011] [Originally Added On: November 12th, 2011]
- 074 Perspectives of a Stem Cell Donor Family - Video [Last Updated On: November 13th, 2011] [Originally Added On: November 13th, 2011]
- 075 Adult Stem Cell Success Stories - Amy Daniels - Video [Last Updated On: November 15th, 2011] [Originally Added On: November 15th, 2011]
- 076 StemCellTV - From National Geographic - The Skin Gun - Healing Burns with Stem Cells - Video [Last Updated On: November 16th, 2011] [Originally Added On: November 16th, 2011]
- 077 Stem Cell Skin Care Jeunesse- Dr Newman FAQ - Video [Last Updated On: November 18th, 2011] [Originally Added On: November 18th, 2011]
- 078 Dr Nathan Newman and Jeunesse Stem Cell Skin Care - Video [Last Updated On: November 26th, 2011] [Originally Added On: November 26th, 2011]
- 079 Apple Stem Cell-Skin aging solution - Video [Last Updated On: November 29th, 2011] [Originally Added On: November 29th, 2011]
- 080 Luminesce rejuvenation serum cellular rejuvenation stem cell skin Products - Video [Last Updated On: November 29th, 2011] [Originally Added On: November 29th, 2011]
