Jenny Swift, previously known as Jonathan, was found dead at HMP Doncaster on December 30.
Suicide is suspected.
Swift, aged 49, was remanded into custody at HMP Doncaster on November 17 after being charged with stabbing 26-year-old Eric Flanagan at a property in Surrey Street, Balby, two days earlier.
Swift, of Seaforth, Liverpool was initially charged with attempted murder in connection with the incident on November 15, but following the death of Mr Flanagan on December 15 police passed the case to the Crown Prosecution Service to upgrade the charge to murder. The charge had not been changed by the time Swift was found dead.
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A spokesman for the Ministry of Justice confirmed Swift’s death and said the MoJ was aware that Swift was transgender when she was remanded into the Category B private men’s prison at Marshgate.
No explanation has been given on the decision to place Swift at HMP Doncaster, but a MoJ spokesman confirmed a Prisons and Probation Ombudsman investigation into the case is now underway.
They added: “We have announced a major shake-up of the prison system with 2,500 extra prisons officers and new security measures to help make prisons places of safety and reform.
"Self-inflicted deaths are a tragedy and mental health in custody is taken extremely seriously.
"We have a range of measures already in place to help support prisoners suffering from these issues.
"But we recognise more can be done.
"That is why we have allocated more funding for prison safety and have launched a suicide and self-harm reduction project to address the increase in self-inflicted deaths and self-harm in our prisons.”
Detective Chief Inspector Vicky Short, the Senior Investigating officer, said: “On December 30 we were made aware that the person charged in this investigation had died. However, the inquiry into Mr Flanagan’s death remains ongoing at this time.”
A friend of Swift's who wishes to remain anonymous claims Swift asked to be put into a women's prison when she was charged with attempted murder at Doncaster Magistrates' Court but this request was denied.
She says Swift had being taking female hormones for three years as part of her transitioning process when she was remanded into custody, but says she was not provided with the same medication in prison.
She said: "She kept asking for the hormones and they said she would get them but she never did. I phoned up and explained that she needed them too.
"Jenny said that not having them was making her legs shake, making her feel sad and ill - she said it was like coming off drugs. It made her miserable."
A spokesman for the Prisons and Probation Ombudsman said: "We are sorry to be informed of the death of Ms Swift at HMP Doncaster, and can confirm that an independent investigation has begun.
"We will be in contact with Ms Swift’s family and will try to address any questions they may have.
"Our independent investigation will aim to identify the full circumstances of the death and whether there were any failings in Ms Swift’s care.
"Where possible we will identify lessons to be learned and make recommendations to help prevent similar deaths in future.
"We also share any findings with the Coroner to assist with their enquiries."
A spokesman for Doncaster Coroners' Court confirmed they have received Swift's file, and an inquest into her death is expected to be opened shortly.